Biology subjects

Schneider, D.

Publications and source records attributed to Schneider, D..

61 records · Page 4Linked to original sources

bioRxiv2019

Dynamic light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM

BackgroundOver the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under fluctuating light despite being indistinguishable from wild-type plants under standard constant light. Moreover, many subtle plant phenotypes become intensified and thus can be studied in more detail. This observation has caused a paradigm shift within the photosynthesis research community and an increasing number of scientists are interested in using fluctuating light growth conditions. However, high installation costs for commercial controllable LED setups as well as costly phenotyping equipment can make it hard for small academic groups to compete in this emerging field. ResultsWe show a simple do-it-yourself approach to enable fluctuating light growth experiments. Our results using previously published fluctuating light sensitive mutants, stn7 and pgr5, confirm that our low-cost setup yields similar results as top-prized commercial growth regimes. Moreover, we show how we increased the throughput of our Walz IMAGING-PAM, also found in many other departments around the world. We have designed a Python and R-based open source toolkit that allows for semi-automated sample segmentation and data analysis thereby reducing the processing bottleneck of large experimental datasets. We provide detailed instructions on how to build and functionally test each setup. ConclusionsWith material costs well below USD$1000, it is possible to setup a fluctuating light rack including a constant light control shelf for comparison. This allows more scientists to perform experiments closer to natural light conditions and contribute to an emerging research field. A small addition to the IMAGING-PAM hardware not only increases sample throughput but also enables larger-scale plant phenotyping with automated data analysis.

plant biology↗

bioRxiv2019

Mechanical Feedback and Robustness of Apical Constrictions in Drosophila Embryo Ventral Furrow Formation

Formation of the ventral furrow in the Drosophila embryo relies on the apical constriction of cells in the ventral region to produce bending forces that drive tissue invagination. Recently [J Phys Condens Matter. 2016;28(41):414021], we observed that apical constrictions during the initial phase of ventral furrow formation produce elongated patterns of cellular constriction chains prior to invagination, and argued that these are indicative of tensile stress feedback. Here, we quantitatively analyze the constriction patterns preceding ventral furrow formation and find that they are consistent with the predictions of our active-granular-fluid model of a monolayer of mechanically coupled stress-sensitive constricting particles. Our model shows that tensile feedback causes constriction chains to develop along underlying precursor tensile stress chains that gradually strengthen with subsequent cellular constrictions. As seen in both our model and available optogenetic experiments, this mechanism allows constriction chains to penetrate or circumvent zones of reduced cell contractility, thus increasing the robustness of ventral furrow formation to spatial variation of cell contractility by rescuing cellular constrictions in the disrupted regions.

biophysics↗

bioRxiv2019

Excitatory and inhibitory attentional mechanisms involved in the control of distractor interference in working memory: A neural oscillations perspective

There is an ongoing debate on the contribution of target enhancement and distractor inhibition processes to selective attention. In a working memory task, we presented to-be-memorized information in a way that posterior hemispheric asymmetries in oscillatory power could be unambiguously linked to lateral target vs. distractor processing. Alpha power asymmetries (8-14 Hz) were insensitive to the number of cued or non-cued items, supporting their relation to spatial attention. Furthermore, we found an increase in alpha power contralateral to non-cued working memory content and an alpha power suppression contralateral to relevant information. These oscillatory patterns relative to the positions of cued and non-cued items were related to the participants ability to control for the impact of irrelevant information on working memory retrieval. Based on these results, we propose that spatially specific modulations of posterior alpha power are related to accessing vs. inhibiting the spatial context of information stored in working memory.

neuroscience↗

bioRxiv2019

Unraveling the relation between EEG-correlates of attentional orienting and sound localization performance: a diffusion model approach

Understanding the contribution of cognitive processes and their underlying neurophysiological signals to behavioral phenomena has been a key objective in recent neuroscience research. Using a diffusion-model framework, we investigated to what extent well-established correlates of spatial attention in the electro-encephalogram contribute to behavioral performance in an auditory free-field sound-localization task. Younger and older participants were instructed to indicate the horizontal position of a pre-defined target among three simultaneously presented distractors. The central question of interest was whether posterior alpha lateralization and amplitudes of the anterior contralateral N2 subcomponent (N2ac) predict sound localization performance (accuracy, mean reaction time) and/or diffusion model parameters (drift rate, boundary separation, non-decision time). Two age groups were compared to explore whether in older adults, who struggle with multi-speaker environments, the brain-behavior relationship would differ from younger adults. Regression analyses revealed that N2ac amplitudes predicted drift rate and accuracy, whereas alpha lateralization was not related to behavioral or diffusion modeling parameters. This was true irrespective of age. The results indicate that a more efficient attentional filtering and selection of information within an auditory scene, reflected by increased N2ac amplitudes, was associated with a higher speed of information uptake (drift rate) and better localization performance (accuracy), while the underlying response criteria (threshold separation), mean reaction times, and non-decisional processes remained unaffected. The lack of a behavioral correlate of post-stimulus alpha power lateralization constrast the well-established notion that pre-stimulus alpha power reflects a functionally relevant attentional mechanism. This highlights the importance of distinguishing anticipatory from post-stimulus alpha power modulations.

neuroscience↗

bioRxiv2019

Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.

microbiology↗

bioRxiv2017

Distractor inhibition contributes to retroactive attentional orienting within working memory: Evidence by lateralized event-related parameters of the EEG

Shifts of attention within mental representations based on retroactive cues (retro-cues) facilitate performance in working memory tasks. It was suggested that this retro-cue benefit is related to the concentration of working memory resources on a subset of representations, thereby improving storage and retrieval at the cost of non-cued items. However, the attentional mechanisms underlying this updating of working memory representations remain unknown. Here, we present EEG data for distinguishing between target enhancement and distractor suppression processes in the context of retroactive attentional orienting. Therefore, we used a working memory paradigm with retro-cues indicating a shift of attention to either a lateralized or non-lateralized item. There was an increase of posterior alpha power contralateral compared to ipsilateral to the irrelevant item when a non-lateralized mental representation was cued and a contralateral suppression of posterior alpha power when a lateralized item had to be selected. This suggests that both inhibition of the non-cued information and enhancement of the target representation are important features of attentional orienting within working memory. By further presenting cues to either remember or to forget a working memory representation, we give a first impression of these retroactive attentional sub-processes as two separable cognitive mechanisms.

neuroscience↗

bioRxiv2017

Timing of host feeding drives rhythms in parasite replication

Circadian rhythms enable organisms to synchronise the processes underpinning survival and reproduction to anticipate daily changes in the external environment. Recent work shows that daily (circadian) rhythms also enable parasites to maximise fitness in the context of ecological interactions with their hosts. Because parasite rhythms matter for their fitness, understanding how they are regulated could lead to innovative ways to reduce the severity and spread of diseases. Here, we examine how host circadian rhythms influence rhythms in the asexual replication of malaria parasites. Asexual replication is responsible for the severity of malaria and fuels transmission of the disease, yet, how parasite rhythms are driven remains a mystery. We perturbed feeding rhythms of hosts by 12 hours (i.e. diurnal feeding in nocturnal mice) to desynchronise the hosts peripheral oscillators from the central, light-entrained oscillator in the brain and their rhythmic outputs. We demonstrate that the rhythms of rodent malaria parasites in day-fed hosts become inverted relative to the rhythms of parasites in night-fed hosts. Our results reveal that the hosts peripheral rhythms (associated with the timing of feeding and metabolism), but not rhythms driven by the central, light-entrained circadian oscillator in the brain, determine the timing (phase) of parasite rhythms. Further investigation reveals that parasite rhythms correlate closely with blood glucose rhythms. In addition, we show that parasite rhythms resynchronise to the altered host feeding rhythms when food availability is shifted, which is not mediated through rhythms in the host immune system. Our observations suggest that parasites actively control their developmental rhythms. Finally, counter to expectation, the severity of disease symptoms expressed by hosts was not affected by desynchronisation of their central and peripheral rhythms. Our study at the intersection of disease ecology and chronobiology opens up a new arena for studying host-parasite-vector coevolution and has broad implications for applied bioscience.\n\nAuthor summaryHow cycles of asexual replication by malaria parasites are coordinated to occur in synchrony with the circadian rhythms of the host is a long-standing mystery. We reveal that rhythms associated with the time-of-day that hosts feed are responsible for the timing of rhythms in parasite development. Specifically, we altered host feeding time to phase-shift peripheral rhythms, whilst leaving rhythms driven by the central circadian oscillator in the brain unchanged. We found that parasite developmental rhythms remained synchronous but changed their phase, by 12 hours, to follow the timing of host feeding. Furthermore, our results suggest that parasites themselves schedule rhythms in their replication to coordinate with rhythms in glucose in the hosts blood, rather than have rhythms imposed upon them by, for example, host immune responses. Our findings reveal a novel relationship between hosts and parasites that if disrupted, could reduce both the severity and transmission of malaria infection.

microbiology↗