Biology subjects

Wagner, A.

Publications and source records attributed to Wagner, A..

99 records · Page 6Linked to original sources

bioRxiv2019

The positive role of noise for information acquisition in biological signaling pathways

All living systems acquire information about their environment. At the cellular level, they do so through signaling pathways, which rely on interactions between molecules that detect and transmit the presence of an extracellular cue or signal to the cells interior. Such interactions are inherently stochastic and thus noisy. In classical information theory, a noisy communication channel degrades the amount of transmissible information relative to a noise-free channel. For this reason, one would expect that the kinetic parameters that determine a pathways operation minimize noise. We show that this is not the case under a wide range of biologically sensible parameter values. Specifically, we perform computational simulations of simple signaling systems, which show that a noisy molecular interaction dynamics is a necessary condition for information acquisition. Moreover, we show that optimal information acquisition, where a system reacts most sensitively to changes in the environment, can be obtained close to the maximal attainable level of noise in the system. Our work highlights the positive role that noise can have in biological information processing.\n\nAuthor summaryThe acquisition of information is fundamental for living systems, because the decisions they take based on such information directly affect survival and reproduction. The molecular mechanisms used by cells to acquire information are signaling pathways. The molecular interactions of signaling pathways, such as the binding of a signal to a receptor, are by nature noisy. This is important, because noise disrupts information. Hence, to maximize the acquisition of information, signaling pathways should minimize the noise of their molecular interactions. Here we show that a noisy dynamic of the molecular interactions can improve the acquisition of information, and that the maximal capacity to acquire information can be obtained with a close-to-maximal level of noise in a signaling pathway. Thus, contrary to expectations, noise can improve the acquisition of information in living systems.

systems biology↗

bioRxiv2019

Interaction of pH stress and demography leads to convergent evolution in the protist Tetrahymena thermophila

Abiotic stress is a major force of selection that organisms are constantly facing. While the evolutionary effects of various stressors have been broadly studied, it is only more recently that the relevance of interactions between evolution and underlying ecological conditions, that is, eco-evolutionary feedbacks, have been highlighted. Here, we experimentally investigated how populations adapt to pH-stress under high population densities. Using the protist species Tetrahymena thermophila, we studied how four different genotypes evolved in response to stressfully low pH conditions and high population densities. We found that genotypes underwent evolutionary changes, some shifting up and others shifting down their intrinsic rates of increase (r0). Overall, evolution at low pH led to the convergence of r0 and intraspecific competitive ability () across the four genotypes. Given the strong correlation between r0 and , we argue that this convergence was a consequence of selection for increased density-dependent fitness at low pH under the experienced high density conditions. Increased density-dependent fitness was either attained through increase in r0, or decrease of , depending on the genetic background. In conclusion, we show that demography can influence the direction of evolution under abiotic stress.

evolutionary biology↗

bioRxiv2019

CX3CL1 and CX3CR1 Expressing Tendon Cells - A novel Immune Cell Population in the Tendon Core

Tendon disorders frequently occur and recent evidence has clearly implicated the presence of immune cells and inflammatory events during early tendinopathy. However, the origin and properties of these cells remain poorly defined. Therefore, the aim of this study was to determine the presence of myleoid cells in healthy rodent and human tendon tissue and to characterize them. Using various transgenic reporter mouse models, we demonstrate the presence of tendon cells in the dense matrix of the tendon core expressing the fractalkine (Fkn) receptor CX3CR1 and its cognate ligand CX3CL1/Fkn. Pro-inflammatory stimulation of 3D tendon-like constructs in vitro resulted in a significant increase in the expression of IL-1{beta}, IL-6, Mmp3, Mmp9, Cx3cl1, and epiregulin which has been reported to contribute to inflammation, wound healing, and tissue repair. Furthermore, we demonstrate that inhibition of the fractalkine receptor blocked tendon cell migration in vitro and show the presence of CX3CR1/CX3CL1/EREG expressing cells in healthy human tendons. Taken together, we demonstrate the presence of CX3CL1+/CX3CR1+ \"tenophages\" within the healthy tendon proper potentially fulfilling surveillance functions in tendons.\n\nSummary StatementHere, we demonstrate the presence of a macrophage-like, CX3CL1/CX3CR1-expressing cell population within the healthy tendon proper potentially fulfilling a surveillance function.

cell biology↗

bioRxiv2019

Species-specific recognition of Sulfolobales mediated by UV inducible pili and S-layer glycosylation patterns

The UV-inducible pili system of Sulfolobales (Ups) mediates the formation of species-specific cellular aggregates. Within these aggregates, cells exchange DNA in order to repair DNA double strand breaks via homologous recombination. Substitution of the S. acidocaldarius pilin subunits UpsA and UpsB with their homologs from Sulfolobus tokodaii showed that these subunits facilitate species-specific aggregation. A region of low conservation within the UpsA homologs is primarily important for this specificity. Aggregation assays in the presence of different sugars showed the importance of N-glycosylation in the recognition process. In addition, the N-glycan decorating the S-layer of S. tokodaii is different from the one of S. acidocaldarius. Therefore, each Sulfolobus species seems to have developed a unique UpsA binding pocket and unique N-glycan composition to ensure aggregation and consequently also DNA exchange with cells from only the same species, which is essential for DNA repair by homologous recombination.\n\nImportanceType IV pili can be found on the cell surface of many archaea and bacteria where they play important roles in different processes. The Ups-pili from the crenarchaeal Sulfolobales species are essential in establishing species-specific mating partners, ensuring genome stability. With this work, we show that different Sulfolobus species have species-specific regions in their Ups-pilin subunits, which allow them to interact only with cells from the same species. Additionally, different Sulfolobus species all have unique S-layer N-glycosylation patterns. We propose that the unique features of each species allow the recognition of specific mating partners. This knowledge for the first time gives insights into the molecular basis of archaeal self-recognition.

microbiology↗

bioRxiv2019

Identifying dynamic, partially occupied residues using anomalous scattering

X-ray crystallography is generally used to take single snapshots of a proteins conformation. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes Residual Anomalous and Electron Density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data collection and analysis strategy for partially occupied iodine anomalous signals. Using the long wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with as low as ~12% occupancy is demonstrated. The number and position of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly dynamic sections of crystal structures.\n\nSynopsisStructural studies on partially occupied, dynamic protein systems by crystallography are difficult. We present methods here for detecting these states in crystals.

biophysics↗

bioRxiv2018

Hydra Bcl-2 and TMBIMP family proteins display anti-apoptotic functions

BackgroundMechanisms of programmed cell death differ considerably between animals, plants and fungi. In animals they depend on caspases and Bcl-2 family proteins and this kind of cell death is called apoptosis. Most gene families encoding proteins involved in apoptosis are found in multicellular animals already in the eldest phyla but their functional conservation is still being studied. Much older protein families have cytoprotective functions across all kingdoms of life. This includes the TMBIMP-family, the presence and function of which in early metazoans has not been investigated yet.\n\nMethodsWe quantified apoptosis in transgenic Hydra overexpressing HyBcl-2-like 4. Moreover, we investigated putative TMBIMP-family members in Hydra by sequence comparison. By overexpression of TMBIMP-family members in Hydra and human HEK cells we analysed their subcellular localisation and in one case their capacity to protect cells from camptothecin induced apoptosis.\n\nResultsHyBcl-2-like 4, as previously shown in a heterologous system, was localised to mitochondria and able to protect Hydra epithelial cells from apoptosis. The TMBIMP-family in Hydra includes HyBax-Inhibitor-1, HyLifeguard-1a and -1b and HyLifeguard 4 proteins. HyBax-inhibitor-1 protein was found localised to ER-membranes, HyLifeguard-family members were found at the plasma membrane and in Golgi-vesicles. Moreover, HyBax-inhibitor-1 protected human cells from apoptosis.\n\nConclusionThis work provides the first functional study to support an anti-apoptotic function of Bcl-2 like proteins in pre-bilaterians within a physiological context. Furthermore it illustrates that genes that were \"inherited\" from non-animal ancestors, like the TMBIMP-family, were recruited to carry out cell protective anti-apoptotic functions already in early metazoans.

developmental biology↗

bioRxiv2018

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here we perform a genome-wide prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.

cancer biology↗

bioRxiv2017

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

Systematic measurement biases make data normalization an essential preprocessing step in single-cell RNA sequencing (scRNA-seq) analysis. There may be multiple, competing considerations behind the assessment of normalization performance, some of them study-specific. Because normalization can have a large impact on downstream results (e.g., clustering and differential expression), it is critically important that practitioners assess the performance of competing methods.\n\nWe have developed scone -- a flexible framework for assessing normalization performance based on a comprehensive panel of data-driven metrics. Through graphical summaries and quantitative reports, scone summarizes performance trade-offs and ranks large numbers of normalization methods by aggregate panel performance. The method is implemented in the open-source Bioconductor R software package scone. We demonstrate the effectiveness of scone on a collection of scRNA-seq datasets, generated with different protocols, including Fluidigm C1 and 10x platforms. We show that top-performing normalization methods lead to better agreement with independent validation data.

genomics↗

bioRxiv2017

Mechanistic causes of constrained phenotypic variation revealed by synthetic gene regulatory networks

Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such restrictions are still poorly understood. Gene regulatory networks have been proposed as one cause of constrained phenotypic variation. However, most of the evidence for this is theoretical rather than experimental. Here, we study evolutionary biases in two synthetic gene regulatory circuits expressed in E. coli that produce a gene expression stripe - a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. Consequently, seemingly equivalent networks can indeed be distinct in how they constrain the outcome of further evolution.

systems biology↗