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Biology subjects

Schroeder, J.

Publications and source records attributed to Schroeder, J..

At least 37 records · Page 2Linked to original sources

Age-specific survival in an English Twite population.

Like many bird species associated with agricultural habitats in the UK, the Twite Linaria flavirostris has undergone severe declines over recent decades due to habitat degradation, with populations in England, Wales and Ireland now restricted to a few small pockets. However, the demographic drivers of these declines are still largely unresolved. We estimated the survival of Twite from a small population at the southernmost edge of the English range in Derbyshire using capture-mark-recapture data from 2016-2019. Annual apparent survival for juveniles (0.14-0.34) was lower than for adults (0.29-0.56) and less than that of other Cardueline finches. Our results suggest that low juvenile survival may be one demographic driver underpinning the recent decline of the Derbyshire Twite population, although we also cannot rule out the possibility that differences in emigration of juveniles and adults from the population also contribute to the observed age-specific apparent survival rates.

ecology↗

What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value

Fitness is at the core of evolutionary theory, but it is difficult to measure accurately. One way to measure long-term fitness is by calculating the individuals reproductive value, which represents the expected number of allele copies an individual passes on to distant future generations. However, this metric of fitness is scarcely used because the estimation of individuals reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. Wild study systems therefore use short-term fitness metrics as proxies, such as the number of offspring produced. This study obtained three frequently used short-term proxies for fitness obtained at different offspring life stages (eggs, hatchlings, fledglings and recruits), and compared their ability to predict reproductive values derived from the genetic pedigree of a wild passerine bird population. We used twenty years of precise field observations and a near-complete genetic pedigree to calculate reproductive success, individual growth rate and de-lifed fitness as lifetime fitness measures, and as annual de-lifed fitness. We compared the power of these metrics to predict reproductive values and lineage survival to the end of the study period. The three short-term fitness proxies predict the reproductive values and lineage survival only when measured at the recruit stage. There were no significant differences between the different fitness proxies at the same offspring stages in predicting the reproductive values and lineage survival. Annual fitness at one year old predicted reproductive values equally well as lifetime de-lifed fitness. However, none of the short-term fitness proxies was strongly associated with the reproductive values. In summary, the commonly short-term fitness proxies capture long-term fitness with intermediate accuracy at best, if measured at recruitment stage. As lifetime fitness measured at recruit stage and annual fitness in the first year of life were the best proxies of long-term fitness, we encourage their future use.

evolutionary biology↗

The local anaesthetic procaine prodrugs ProcCluster(R) and Procaine-hydrochloride impair SARS-CoV-2 replication in vitro

The SARS-CoV-2 pandemic has had the world in suspense for more than a year. Even if more and more vaccines are approved there is still an urgent need for efficient antiviral treatment strategies. Here, we present data on the inhibitory effect of the local anaesthetic procaine, especially the prodrugs ProcCluster(R) and Procaine-hydrochloride on SARS-CoV-2 infection in vitro. Remarkably, similar effects could be shown on the replication of influenza A viruses in cell culture systems. Since the active ingredient procaine is well-tolerated and already used in the clinics for anaesthetic purposes, the further investigation of this substance could enable its reuse in antiviral therapy, including SARS-CoV-2.

microbiology↗

BoolSim, a Graphical Interface for Open Access Boolean Network Simulations and Use in Guard Cell CO2 Signaling

Signaling networks are at the heart of almost all biological processes. Most of these networks contain a large number of components and often the connections between these components are either not known, or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to more detailed mathematical models but can be difficult to implement. Therefore, open source format of such models for community use is desirable. Here we present BoolSim, a freely available graphical user interface (GUI) that allows users to easily construct and analyze Boolean networks. BoolSim can be applied to any Boolean network. We demonstrate BoolSims application using a previously published network for abscisic acid-driven stomatal closure in Arabidopsis. We also show how BoolSim can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested and the model was iteratively modified based on experiments showing that ABA closes stomata even at near zero CO2 concentrations (1.5 ppm CO2). One Sentence SummaryThis study presents an open-source, graphical interface for the simulation of Boolean networks and applies it to an abscisic acid signaling network in guard cells, extended to include input from CO2.

plant biology↗

The SLIM1 transcription factor regulates arsenic sensitivity in Arabidopsis thaliana

The transcriptional regulators of arsenic-induced gene expression remain largely unknown. Sulfur assimilation is tightly linked with arsenic detoxification. Here we report that mutant alleles in the SLIM1 transcription factor are substantially more sensitive to arsenic than cadmium. Arsenic treatment caused high levels of oxidative stress in the slim1 mutants, and slim1 alleles were impaired in both thiol and sulfate accumulation. We further found enhanced arsenic accumulation in roots of slim1 mutants. Transcriptome analyses indicate an important role for SLIM1 in arsenic-induced tolerance mechanisms. The present study identifies the SLIM1 transcription factor as an essential component in arsenic tolerance and arsenic-induced gene expression. Our results suggest that the severe arsenic sensitivity of the slim1 mutants is caused by altered redox status.

plant biology↗

The comprehensive roadmaps of reprogramming and transformation unveiled antagonistic roles for bHLH transcription factors in the control of cellular plasticity

Coordinated changes of cellular identity and plasticity are critical for pluripotent reprogramming (PR) and malignant transformation (MT). However, the molecular circuitries orchestrating these modifications, as well as their degree of analogy during reprogramming and transformation, remain unknown. To address this question, we generated "repro-transformable" mice models and dissected comparatively the early events underpinning PR - mediated by Oct4, Sox2, Klf4, c-Myc - and MT - triggered by oncogenic Ras and c-Myc. Transcriptomic analyses allowed the identification of a unique set of markers - the cell surface glycoprotein Thy1 and the transcription factor (TF) Bcl11b - that are commonly downregulated during PR and MT and delineate cellular intermediates (CI) highly amenable to generate pluripotent or malignant derivatives. Comprehensive transcriptomic, epigenomic and functional analyses of different CI, prone or refractory to PR/MT, unveiled that cellular plasticity acquisition precedes the broad extinction of cellular identity. It also demonstrated the existence of specific and shared molecular features of PR and MT while ensuring the identification of broad-range regulators of cellular plasticity. As a proof-of-concept, we revealed that the basic helix-loop-helix (bHLH) class A TF Atoh8 constrains rodent and human iPS cells generation as well as MT and direct neuron conversion. Mechanistically, this TF hampers the reactivation of the pluripotent network during PR and limits the acquisition of phenotypic plasticity during MT. Furthermore, an integrated analysis of Atoh8 genome-wide binding, alongside the other bHLH TFs c-Myc, Ascl1 and MyoD promoting reprogramming/transdifferentiation, unveiled how Atoh8 constrains cellular plasticity by occupying a specific subset of MEF enhancers and by finetuning WNT signalling activity. Collectively, by deconvoluting the early steps of the reprogramming and transformation roadmaps, this integrated study uncoupled changes of cellular plasticity and identity to shed light on novel insights into reprogramming and cancer biology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/424606v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1718383org.highwire.dtl.DTLVardef@1714ab8org.highwire.dtl.DTLVardef@e0958borg.highwire.dtl.DTLVardef@7a0643_HPS_FORMAT_FIGEXP M_FIG C_FIG One-sentence summaryComparative roadmaps of cellular plasticity acquisition during pluripotent reprogramming and malignant transformation.

cell biology↗

Polyandry and senescence shape egg size variation in a precocial bird.

Gamete size variation between the sexes is central to the concept of sex roles, however, to what extent gamete size variation within the sexes relates to sex role variation remains unclear. Comparative and theoretical studies suggest that, when clutch size is invariable, polyandry is linked to a reduction of egg size, while increased female-female competition for mates favors early breeding when females cannot monopolize multiple males. To understand whether and how breeding phenology, egg size, and mating behavior are related at the individual level, we studied the reproductive histories of 424 snowy plover females observed in the wild over a 15-year period. Egg size, but not polyandry, were highly repeatable for individual females. Consistent with theoretical predictions, we found that polyandrous females were the earliest breeders and that early clutches contained smaller eggs than clutches initiated later. Neither egg size nor mating behavior showed clear signs of an age-related deterioration, on the contrary, prior experience acquired either through age or local recruitment enabled females to nest early. Taken together, these results suggest that gamete size variation is not linked to mating behavior at the individual level, and, consequently, the adaptive potential of such variation appears to be limited. Teaser TextComparative avian analyses have linked female polyandry and sex-role reversal to the production of smaller eggs: the notion being that smaller eggs allow polyandrous females to lay multiple sequential clutches quickly. Our research, however, has found that the notion is more complex at the individual level. We found that females who started breeding early in the season were more likely to be polyandrous and produce smaller eggs. Experience was also found to give older and locally-raised females a competitive advantage over younger and inexperienced females vying for early breeding opportunities. Despite this, we found limited evidence that egg size reduction gives a competitive advantage in the scramble for mates. Instead, seasonal variations in egg size can likely be attributed to other factors, such as the survival of early-hatching chicks, resource limitations during egg production, and individual differences. We found that senescence had little impact on egg size or mating behavior. Future research should also examine how seasonality, age, and mating behavior impact the reproductive fitness of males, who provide more parental care than females in many sex role reversed systems. By studying these effects in concert, we can gain a deeper understanding of sex roles in natural populations.

evolutionary biology↗

TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novel Nanog regulators in mouse embryonic stem cells

Cellular identity is ultimately controlled by transcription factors (TFs), which bind to specific regulatory elements (REs) within the genome to regulate gene expression and cell fate changes. While recent advances in genome-wide epigenetic profiling techniques have significantly increased our understanding of which REs are utilized in which cell type, it remains largely unknown which TFs and cofactors interact with these REs to modulate gene expression. A major hurdle in dissecting the whole composition of a multi-protein complex formed at a specific RE is the shortage of appropriate techniques. We have developed a novel method termed TALE-mediated Isolation of Nuclear Chromatin (TINC). TINC utilizes epitope-tagged TALEs to isolate a specific genomic region from the mammalian genome and includes a nuclei isolation and chromatin enrichment step for increased specificity. Upon cross-linking of the cells and isolation of the chromatin, the target region is purified based on affinity purification of the TALE and associated nucleic acid and protein molecules can be subjected to further analyses. A key TF in the pluripotency network and therefore in embryonic stem cells (ESCs) is NANOG. It is currently not fully understood how Nanog expression is regulated and consequently it remains unclear how the ESC state is maintained. Using TINC we dissected the protein complex formed at the Nanog promoter in mouse ESCs and identified many known and numerous novel factors.

genomics↗

The Hox transcription factor Ubx ensures somatic myogenesis by suppressing the mesodermal master regulator Twist

Early determination factors and lineage-specific master regulators are essential for the specification of cell and tissue types. However, once a cell has committed to a specific fate, it is equally critical to restrict the activity of such factors to enable proper differentiation. In many studies the functional network for master regulators are under constant investigations. Yet, how these factors are silenced remains unclear. Using the Drosophila mesoderm as a model and a comparative genomic approach, we identified the Hox transcription factor (TF) Ultrabithorax (Ubx) to be critical for the repression of the mesodermal master regulator Twist (Twi). Mesoderm-specific Ubx loss-of-function experiments using CRISPR/Cas9 as well as overexpression experiments demonstrated that Ubx majorly impacts twi transcription. A detailed mechanistic analysis revealed that Ubx requires the function of the NK-homeodomain protein Tinman (Tin) but not the muscle differentiation factor Myocyte enhancer factor 2 (Mef2) to bind to the twi promoter. Furthermore, we found these TF interactions to be critical for silencing of the twi promoter region by recruiting the Polycomb DNA binding protein Pleiohomeotic (Pho). In sum, our study demonstrates that the Hox TF Ubx is a critical player in mediating the silencing of the mesodermal master regulator Twi, which is crucial for coordinated muscle differentiation.

developmental biology↗

Dynamic regulation of immunity through post-translational control of defense transcript splicing

Survival of all living organisms requires the ability to detect attack and swiftly counter with protective immune responses. Despite considerable mechanistic advances, interconnectivity of signaling circuits often remains unclear. A newly-characterized protein, IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR), negatively regulates immune responses in both maize and Arabidopsis, with disrupted function resulting in enhanced disease resistance. IRR physically interacts with, and promotes canonical splicing of, transcripts encoding defense signaling proteins, including the key negative regulator of pattern recognition receptor signaling complexes, CALCIUM-DEPENDENT PROTEIN KINASE 28 (CPK28). Upon immune activation by Plant Elicitor Peptides (Peps), IRR is dephosphorylated, disrupting interaction with CPK28 transcripts and resulting in accumulation of an alternative splice variant encoding a truncated CPK28 protein with impaired kinase activity and diminished function as a negative regulator. We demonstrate a novel circuit linking Pep-induced post-translational modification of IRR with post-transcriptionally-mediated attenuation of CPK28 function to dynamically amplify Pep signaling and immune output.\n\nOne Sentence SummaryPlant innate immunity is promoted by post-translational modification of a novel RNA-binding protein that regulates alternative splicing of transcripts encoding defense signaling proteins to dynamically increase immune receptor signaling capacity through deactivation of a key signal-buffering circuit.

plant biology↗

Ageing in house sparrows is insensitive to environmental effects

Variation in individual life histories, and physiology, determines the rates at which new life is generated (reproduction) and lost (death) in a population. Studying the demography of deaths thus reveals fundamental aspects of the biology of individuals within a population. We studied mortality senescence - the increase in mortality rate with age - in wild and captive house sparrows (Passer domesticus), and demonstrate highly similar mortality senescence in both, but markedly lower vulnerability to death (frailty) in captivity. This suggests that house sparrows have a species-specific rate of ageing that is insensitive to environmental effects. Unexpectedly, juvenile and adult mortality co-varied positively across years in the wild, indicating that mortality is not strongly density-dependent. Mortality also varied widely among years, suggesting a strong environmental effect, and we explain the observed patterns using temperature data and predation by birds of prey. We discuss how stochastic environmental effects can affect the evolution of ageing.

evolutionary biology↗

No evidence for kin recognition in a passerine bird.

Theory predicts that individuals behave altruistically towards their relatives. Hence, some form of kin recognition is useful for individuals to optimize their behaviour. In species displaying bi-parental care and subject to extra-pair matings, kin recognition theoretically allows cuckolded fathers to reduce their parental investment, and thus optimize their fitness, but whether this is possible remains unclear in birds. This study investigates the ability of male sparrows to recognize their own chicks, using a large cross-foster experiment, parental care as an indicator and House Sparrows (Passer domesticus) as a model organism. We cross-fostered chicks after hatching, and then expected that fathers would show a decrease in their parental efforts when tending to a clutch of unrelated offspring. However, there was no significant effect of relatedness on provisioning rates. This suggests that sparrows may not be capable of kin recognition, or at least do not display kin discrimination despite its apparent evolutionary advantage.

animal behavior and cognition↗

Higher frequency of extra-pair offspring in urban than forest broods of great tits (Parus major)

Urbanization increasingly changes the ecological conditions for wild animal populations, influencing their demography, reproduction, and behaviour. While studies on the ecological consequences of urbanization frequently document a reduced number and poorer body condition of offspring in urban than in non-urban bird populations, consequences for other components of reproduction are rarely investigated. Mating with partners outside the social pair-bond is widespread in birds, and although theory predicts that the occurrence of extra-pair fertilizations (EPF) may be sensitive to the altered ecological conditions of cities, the effect of urbanization on EPF is poorly known. Here we used data from two urban and two forest populations collected over three years to test whether the frequency of extra-pair offspring (EPO) in great tit broods differed between the habitats. We found that significantly more broods contained EPO in urban habitats (48.9 %) than in forests (24.4 %). In broods with EPO, the number and proportion of EPO was similar in urban and forest broods. These results suggest that females that live in urban habitats are more likely to engage in EPF than those living in forests. Urban environments may either 1) provide more spatiotemporal opportunities to EPF because of higher breeding density and lower or more constant caterpillar supply in cities compared to natural habitats, or 2) enhance the benefits of EPF via increased fertility or due to disrupted quality signals caused by anthropogenic pollution. In addition, 3) females with higher propensity to engage in EPF may more likely settle in urban habitats.

ecology↗

Mature sperm small RNA profile in the sparrow: implications for transgenerational effects of age on fitness

Mammalian sperm RNA has recently received a lot of interest due to its involvement in epigenetic germline inheritance. Studies of epigenetic germline inheritance have shown that environmental exposures can induce effects in the offspring without altering the DNA sequence of germ cells. Most mechanistic studies were conducted in laboratory rodents and C.elegans while observational studies confirm the phenotypic phenomenon in wild populations of humans and other species including birds. Prominently, paternal age in house sparrows affects offspring fitness, yet the mechanism is unknown. This study provides a first reference of house sparrow sperm small RNA as an attempt to uncover their role in the transmission of the effects of paternal age on the offspring. In this small scale pilot, we found no statistically significant differences between miRNA and tRNA fragments in aged and prime sparrow sperm. These results indicate a role of other epigenetic information carriers, such as distinct RNA classes, RNA modifications, DNA methylation and retained histones, and a clear necessity of future studies in wild populations.

developmental biology↗

A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

The identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like (AIG2) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.\n\nHighlightThe generation of over 14,000 amiRNA-expressing plants is reported that are being made publicly available enabling screens of redundant genes in Arabidopsis. Identification of known and new genes is reported.

plant biology↗

Meta-analysis challenges a textbook example of status signalling: evidence for publication bias

The status signalling hypothesis aims to explain conspecific variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook example of this hypothesis, the black bib of house sparrows (Passer domesticus). We conducted a systematic review, and obtained raw data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, our meta-analysis did not support this prediction. Furthermore, we found several biases in the literature that further question the support available for the status signalling hypothesis. First, the overall effect size of unpublished studies was zero, compared to the medium effect size detected in published studies. Second, the effect sizes of published studies decreased over time, and recently published effects were, on average, no longer distinguishable from zero. We discuss several explanations including pleiotropic, population- and context-dependent effects. Our findings call for reconsidering this established textbook example in evolutionary and behavioural ecology, raise important concerns about the validity of the current scientific publishing culture, and should stimulate renewed interest in understanding within-species variation in ornamental traits.

evolutionary biology↗

Male age is associated with extra-pair paternity, but not with extra-pair mating behaviour

Extra-pair paternity is the result of copulation between a female and a male other than her social partner. In socially monogamous birds, old males are most likely to sire extra-pair offspring. The male manipulation and female choice hypotheses predict that age-specific male mating behaviour could explain this old-over-young male advantage. These hypotheses have been difficult to test because copulations and the individuals involved are hard to observe. Here, we studied the mating behaviour and pairing contexts of captive house sparrows, Passer domesticus. Our set-up mimicked the complex social environment experienced by wild house sparrows. We found that middle-aged males, that would be considered old in natural populations, gained most extra-pair paternity. However, both female solicitation behaviour and subsequent extra-pair matings were unrelated to male age. Further, copulations were more likely when solicited by females than those initiated by males (i.e. unsolicited copulations), and unsolicited within-pair copulations were more common than unsolicited extrapair copulations. To conclude, our results did not support either hypotheses regarding age-specific male mating behaviour. Instead, female choice, independent of male age, governed copulation success, especially in an extra-pair context and post-copulatory mechanisms might determine why older males sire more extra-pair offspring.

evolutionary biology↗