Solid–liquid interfaces play an important role for functional devices. Hence, a detailed understanding of the interaction of soft matter objects with solid supports and of the often concomitant ...structural deformations is of great importance. We address this topic in a combined experimental and simulation approach. We investigated thermoresponsive poly(N-isopropylmethacrylamide) microgels (μGs) at different surfaces in an aqueous environment. As super-resolution fluorescence imaging method, three-dimensional direct stochastical optical reconstruction microscopy (dSTORM) allowed for visualizing μGs in their three-dimensional (3D) shape, for example, in a “fried-egg” conformation depending on the hydrophilicity of the surface (strength of adsorption). The 3D shape, as defined by point clouds obtained from single-molecule localizations, was analyzed. A new fitting algorithm yielded an isosurface of constant density which defines the deformation of μGs at the different surfaces. The presented methodology quantifies deformation of objects with fuzzy surfaces and allows for comparison of their structures, whereby it is completely independent from the data acquisition method. Finally, the experimental data are complemented with mesoscopic computer simulations in order to (i) rationalize the experimental results and (ii) to track the evolution of the shape with changing surface hydrophilicity; a good correlation of the shapes obtained experimentally and with computer simulations was found.
Spermatogenesis, the complex process of male germ cell proliferation, differentiation, and maturation, is the basis of male fertility. In the seminiferous tubules of the testes, spermatozoa are ...constantly generated from spermatogonial stem cells through a stereotyped sequence of mitotic and meiotic divisions. The basic physiological principles, however, that control both maturation and luminal transport of the still immotile spermatozoa within the seminiferous tubules remain poorly, if at all, defined. Here, we show that coordinated contractions of smooth muscle-like testicular peritubular cells provide the propulsive force for luminal sperm transport toward the rete testis. Using a mouse model for in vivo imaging, we describe and quantify spontaneous tubular contractions and show a causal relationship between peritubular Ca
waves and peristaltic transport. Moreover, we identify P2 receptor-dependent purinergic signaling pathways as physiological triggers of tubular contractions both in vitro and in vivo. When challenged with extracellular ATP, transport of luminal content inside the seminiferous tubules displays stage-dependent directionality. We thus suggest that paracrine purinergic signaling coordinates peristaltic recurrent contractions of the mouse seminiferous tubules to propel immotile spermatozoa to the rete testis.
The beet cyst nematode
Heterodera schachtii
is a plant pest responsible for crop loss on a global scale. Here, we introduce a high-throughput system based on computer vision that allows quantifying ...beet cyst nematode infestation and measuring phenotypic traits of cysts. After recording microscopic images of soil sample extracts in a standardized setting, an instance segmentation algorithm serves to detect nematode cysts in these images. In an evaluation using both ground truth samples with known cyst numbers and manually annotated images, the computer vision approach produced accurate nematode cyst counts, as well as accurate cyst segmentations. Based on such segmentations, cyst features could be computed that served to reveal phenotypical differences between nematode populations in different soils and in populations observed before and after the sugar beet planting period. The computer vision approach enables not only fast and precise cyst counting, but also phenotyping of cyst features under different conditions, providing the basis for high-throughput applications in agriculture and plant breeding research. Source code and annotated image data sets are freely available for scientific use.
Imaging in three dimensions is necessary for thick tissues and small organisms. This is possible with tomographic optical microscopy techniques such as confocal, multiphoton and light sheet ...microscopy. All these techniques suffer from anisotropic resolution and limited penetration depth. In the past, Multiview microscopy-imaging the sample from different angles followed by 3D image reconstruction-was developed to address this issue for light sheet microscopy based on fluorescence signal. In this study we applied this methodology to accomplish Multiview imaging with multiphoton microscopy based on fluorescence and additionally second harmonic signal from myosin and collagen. It was shown that isotropic resolution was achieved, the entirety of the sample was visualized, and interference artifacts were suppressed allowing clear visualization of collagen fibrils and myofibrils. This method can be applied to any scanning microscopy technique without microscope modifications. It can be used for imaging tissue and whole mount small organisms such as heart tissue, and zebrafish larva in 3D, label-free or stained, with at least threefold axial resolution improvement which can be significant for the accurate quantification of small 3D structures.
Neuronal plasticity allows an animal to respond to environmental changes by modulating its response to stimuli. In the honey bee (Apis mellifera), the biogenic amine octopamine plays a crucial role ...in appetitive odor learning, but little is known about how octopamine affects the brain. We investigated its effect in the antennal lobe, the first olfactory center in the brain, using calcium imaging to record background activity and odor responses before and after octopamine application. We show that octopamine increases background activity in olfactory output neurons, while reducing average calcium levels. Odor responses were modulated both upwards and downwards, with more odor response increases in glomeruli with negative or weak odor responses. Importantly, the octopamine effect was variable across glomeruli, odorants, odorant concentrations and animals, suggesting that the octopaminergic network is shaped by plasticity depending on an individual animal’s history and possibly other factors. Using RNA interference, we show that the octopamine receptor AmOA1 (homolog of the Drosophila OAMB receptor) is involved in the octopamine effect. We propose a network model in which octopamine receptors are plastic in their density and located on a subpopulation of inhibitory neurons in a disinhibitory pathway. This would improve odor-coding of behaviorally relevant, previously experienced odors.
Cells dynamically adapt their gene expression patterns in response to various stimuli. This response is orchestrated into a number of gene expression modules consisting of co-regulated genes. A ...growing pool of publicly available microarray datasets allows the identification of modules by monitoring expression changes over time. These time-series datasets can be searched for gene expression modules by one of the many clustering methods published to date. For an integrative analysis, several time-series datasets can be joined into a three-dimensional gene-condition-time dataset, to which standard clustering or biclustering methods are, however, not applicable. We thus devise a probabilistic clustering algorithm for gene-condition-time datasets.
In this work, we present the EDISA (Extended Dimension Iterative Signature Algorithm), a novel probabilistic clustering approach for 3D gene-condition-time datasets. Based on mathematical definitions of gene expression modules, the EDISA samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality. We applied the algorithm to a synthetic dataset and were able to successfully recover the implanted modules over a range of background noise intensities. Analysis of microarray datasets has lead us to define three biologically relevant module types: 1) We found modules with independent response profiles to be the most prevalent ones. These modules comprise genes which are co-regulated under several conditions, yet with a different response pattern under each condition. 2) Coherent modules with similar responses under all conditions occurred frequently, too, and were often contained within these modules. 3) A third module type, which covers a response specific to a single condition was also detected, but rarely. All of these modules are essentially different types of biclusters.
We successfully applied the EDISA to different 3D datasets. While previous studies were mostly aimed at detecting coherent modules only, our results show that coherent responses are often part of a more general module type with independent response profiles under different conditions. Our approach thus allows for a more comprehensive view of the gene expression response. After subsequent analysis of the resulting modules, the EDISA helped to shed light on the global organization of transcriptional control. An implementation of the algorithm is available at http://www-ra.informatik.uni-tuebingen.de/software/IAGEN/.
The calcium-imaging technique allows us to record movies of brain activity in the antennal lobe of the fruitfly Drosophila melanogaster, a brain compartment dedicated to information about odors. ...Signal processing, e.g. with source separation techniques, can be slow on the large movie datasets.
We have developed an approximate Principal Component Analysis (PCA) for fast dimensionality reduction. The method samples relevant pixels from the movies, such that PCA can be performed on a smaller matrix. Utilising a priori knowledge about the nature of the data, we minimise the risk of missing important pixels.
Our method allows for fast approximate computation of PCA with adaptive resolution and running time. Utilising a priori knowledge about the data enables us to concentrate more biological signals in a small pixel sample than a general sampling method based on vector norms.
Fast dimensionality reduction with approximate PCA removes a computational bottleneck and leads to running time improvements for subsequent algorithms. Once in PCA space, we can efficiently perform source separation, e.g to detect biological signals in the movies or to remove artifacts.
A globally invasive form of the mosquito Aedes aegypti specializes in biting humans, making it an efficient disease vector
. Host-seeking female mosquitoes strongly prefer human odour over the odour ...of animals
, but exactly how they distinguish between the two is not known. Vertebrate odours are complex blends of volatile chemicals with many shared components
, making discrimination an interesting sensory coding challenge. Here we show that human and animal odours evoke activity in distinct combinations of olfactory glomeruli within the Ae. aegypti antennal lobe. One glomerulus in particular is strongly activated by human odour but responds weakly, or not at all, to animal odour. This human-sensitive glomerulus is selectively tuned to the long-chain aldehydes decanal and undecanal, which we show are consistently enriched in human odour and which probably originate from unique human skin lipids. Using synthetic blends, we further demonstrate that signalling in the human-sensitive glomerulus significantly enhances long-range host-seeking behaviour in a wind tunnel, recapitulating preference for human over animal odours. Our research suggests that animal brains may distil complex odour stimuli of innate biological relevance into simple neural codes and reveals targets for the design of next-generation mosquito-control strategies.
Modern microscopy techniques can be used to investigate soft nano-objects at the nanometer scale. However, time-consuming microscopy measurements combined with low numbers of observable polydisperse ...objects often limit the statistics. We propose a method for identifying the most representative objects from their respective point clouds. These point cloud data are obtained, for example, through the localization of single emitters in super-resolution fluorescence microscopy. External stimuli, such as temperature, can cause changes in the shape and properties of adaptive objects. Due to the demanding and time-consuming nature of super-resolution microscopy experiments, only a limited number of temperature steps can be performed. Therefore, we propose a deep generative model that learns the underlying point distribution of temperature-dependent microgels, enabling the reliable generation of unlimited samples with an arbitrary number of localizations. Our method greatly cuts down the data collection effort across diverse experimental conditions, proving invaluable for soft condensed matter studies.
This experimental study focused on the intra- and inter-rater reproducibility of vertical bone level (VBL) measurements at strategic mini-implants (MI) using digital panoramic radiographs (PR).
VBLs ...of 152 MIs for removable partial denture stabilization at 50 randomly chosen PRs from a clinical trial were digitally evaluated by three ratters. Rater deviations exceeding 0.5 mm were re-examined. The intra-class correlation coefficient (ICC) was applied to estimate reliability. The smallest detectable change (SDC) was interrelated to the minimal clinically important change of 0.2 mm.
The first measurement round revealed intra- and inter-rater ICCs of > 0.8. However, 28 sites (9 %) were unreadable, and 97 sites (32 %) revealed differences between observers of ≥ 0.5 mm. Following a consensus session and re-training, an additional 8 sites were excluded and all remaining VBL differences were ≤ 0.5 mm. Thus, the SDCs with 95 % credibility were improved from 0.73 to 0.31 mm in the intra-rater and from 1.52 to 0.34 mm in the inter-rater statistics. Given a 50 % credibility for this special setting, both the intra- and inter-rater SDCs were 0.11 mm.
Digital PR can be reliably utilized to determine VBLs around MIs under conditions of at least two trained observers, mutual calibration sessions, and exclusion of unquantifiable radiographs.
DRKS00007589, www.germanctr.de.
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