Determining growth rates from bright-field images of budding cells through identifying overlaps.

Much of biochemical regulation ultimately controls growth rate, particularly in microbes. Although time-lapse microscopy visualises cells, determining their growth rates is challenging, particularly for those that divide asymmetrically, like Saccharomyces cerevisiae, because cells often overlap in images. Here, we present the Birth Annotator for Budding Yeast (BABY), an algorithm to determine single-cell growth rates from label-free images. Using a convolutional neural network, BABY resolves overlaps through separating cells by size and assigns buds to mothers by identifying bud necks. BABY uses machine learning to track cells and determine lineages and estimates growth rates as the rates of change of volumes. Using BABY and a microfluidic device, we show that bud growth is likely first sizer- then timer-controlled, that the nuclear concentration of Sfp1, a regulator of ribosome biogenesis, varies before the growth rate does, and that growth rate can be used for real-time control. By estimating single-cell growth rates and so fitness, BABY should generate much biological insight.

Potential margin reduction in prostate cancer proton therapy with prompt gamma imaging for online treatment verification.

The potential of proton therapy is currently limited due to large safety margins. We estimated the potential reduction of clinical margins when using prompt gamma imaging (PGI) for online treatment verification of prostate cancer. For two adaptive scenarios a potential reduction relative to clinical practice was evaluated. The use of a trolley-mounted PGI system for online treatment verification to trigger an adaptation reduced the current range margins from 7 mm to 3 mm. In a case example, the dose reduction due to reduced range margins was substantially larger compared to reduced setup margins when using pre-treatment volumetric imaging.

Detectability of Anatomical Changes With Prompt-Gamma Imaging: First Systematic Evaluation of Clinical Application During Prostate-Cancer Proton Therapy.

PURPOSE: The development of online-adaptive proton therapy (PT) is essential to overcome limitations encountered by day-to-day variations of the patient's anatomy. Range verification could play an essential role in an online feedback loop for the detection of treatment deviations such as anatomical changes. Here, we present the results of the first systematic patient study regarding the detectability of anatomical changes by a prompt-gamma imaging (PGI) slit-camera system. METHODS AND MATERIALS: For 15 patients with prostate cancer, PGI measurements were performed during 105 fractions (201 fields) with in-room control computed tomography (CT)acquisitions. Field-wise doses on control CT scans were manually classified as whether showing relevant or non-relevant anatomical changes. This manual classification of the treatment fields was then used to establish an automatic field-wise ground truth based on spot-wise dosimetric range shifts, which were retrieved from integrated depth-dose (IDD) profiles. To determine the detection capability of anatomical changes with PGI, spot-wise PGI-based range shifts were initially compared with corresponding dosimetric IDD range shifts. As final endpoint, the agreement of a developed field-wise PGI classification model with the field-wise ground truth was determined. Therefore, the PGI model was optimized and tested for a subcohort of 131 and 70 treatment fields, respectively. RESULTS: The correlation between PGI and IDD range shifts was high, ρpearson = 0.67 (p < 0.01). Field-wise binary PGI classification resulted in an area under the curve of 0.72 and 0.80 for training and test cohorts, respectively. The model detected relevant anatomical changes in the independent test cohort, with a sensitivity and specificity of 74% and 79%, respectively. CONCLUSIONS: For the first time, evidence of the detection capability of anatomical changes in prostate-cancer PT from clinically acquired PGI data is shown. This emphasizes the benefit of PGI-based range verification and demonstrates its potential for online-adaptive PT.

Regulation by cyclic di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli.

Curli amyloid fibers are a major constituent of the extracellular biofilm matrix formed by bacteria of the Enterobacteriaceae family. Within Escherichia coli biofilms, curli gene expression is limited to a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Here we show that bimodal activation of curli gene expression also occurs in well-mixed planktonic cultures of E. coli, resulting in all-or-none stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Stochastic curli activation in individual E. coli cells could further be observed during continuous growth in a conditioned medium in a microfluidic device, which further revealed that the curli-positive state is only metastable. In agreement with previous reports, regulation of curli gene expression by the second messenger c-di-GMP via two pairs of diguanylate cyclase and phosphodiesterase enzymes, DgcE/PdeH and DgcM/PdeR, modulates the fraction of curli-positive cells. Unexpectedly, removal of this regulatory network does not abolish the bimodality of curli gene expression, although it affects dynamics of activation and increases heterogeneity of expression levels among individual cells. Moreover, the fraction of curli-positive cells within an E. coli population shows stronger dependence on growth conditions in the absence of regulation by DgcE/PdeH and DgcM/PdeR pairs. We thus conclude that, while not required for the emergence of bimodal curli gene expression in E. coli, this c-di-GMP regulatory network attenuates the frequency and dynamics of gene activation and increases its robustness to cellular heterogeneity and environmental variation.

Automatic detection and classification of treatment deviations in proton therapy from realistically simulated prompt gamma imaging data.

BACKGROUND: A clinical study regarding the potential of range verification in proton therapy (PT) by prompt gamma imaging (PGI) is carried out at our institution. Manual interpretation of the detected spot-wise range shift information is time-consuming, highly complex, and therefore not feasible in a broad routine application. PURPOSE: Here, we present an approach to automatically detect and classify treatment deviations in realistically simulated PGI data for head-and-neck cancer (HNC) treatments using convolutional neural networks (CNNs) and conventional machine learning (ML) approaches. METHODS: For 12 HNC patients and 1 anthropomorphic head phantom (n = 13), pencil beam scanning (PBS) treatment plans were generated, and 1 field per plan was assumed to be monitored with a PGI slit camera system. In total, 386 scenarios resembling different relevant or non-relevant treatment deviations were simulated on planning and control CTs and manually classified into 7 classes: non-relevant changes (NR) and relevant changes (RE) triggering treatment intervention due to range prediction errors (±RP), setup errors in beam direction (±SE), anatomical changes (AC), or a combination of such errors (CB). PBS spots with reliable PGI information were considered with their nominal Bragg peak position for the generation of two 3D spatial maps of 16 × 16 × 16 voxels containing PGI-determined range shift and proton number information. Three complexity levels of simulated PGI data were investigated: (I) optimal PGI data, (II) realistic PGI data with simulated Poisson noise based on the locally delivered proton number, and (III) realistic PGI data with an additional positioning uncertainty of the slit camera following an experimentally determined distribution. For each complexity level, 3D-CNNs were trained on a data subset (n = 9) using patient-wise leave-one-out cross-validation and tested on an independent test cohort (n = 4). Both the binary task of detecting RE and the multi-class task of classifying the underlying error source were investigated. Similarly, four different conventional ML classifiers (logistic regression, multilayer perceptron, random forest, and support vector machine) were trained using five previously established handcrafted features extracted from the PGI data and used for performance comparison. RESULTS: On the test data, the CNN ensemble achieved a binary accuracy of 0.95, 0.96, and 0.93 and a multi-class accuracy of 0.83, 0.81, and 0.76 for the complexity levels (I), (II), and (III), respectively. In the case of binary classification, the CNN ensemble detected treatment deviations in the most realistic scenario with a sensitivity of 0.95 and a specificity of 0.88. The best performing ML classifiers showed a similar test performance. CONCLUSIONS: This study demonstrates that CNNs can reliably detect relevant changes in realistically simulated PGI data and classify most of the underlying sources of treatment deviations. The CNNs extracted meaningful features from the PGI data with a performance comparable to ML classifiers trained on previously established handcrafted features. These results highlight the potential of a reliable, automatic interpretation of PGI data for treatment verification, which is highly desired for a broad clinical application and a prerequisite for the inclusion of PGI in an automated feedback loop for online adaptive PT.

Roadmap on biology in time varying environments.

Biological organisms experience constantly changing environments, from sudden changes in physiology brought about by feeding, to the regular rising and setting of the Sun, to ecological changes over evolutionary timescales. Living organisms have evolved to thrive in this changing world but the general principles by which organisms shape and are shaped by time varying environments remain elusive. Our understanding is particularly poor in the intermediate regime with no separation of timescales, where the environment changes on the same timescale as the physiological or evolutionary response. Experiments to systematically characterize the response to dynamic environments are challenging since such environments are inherently high dimensional. This roadmap deals with the unique role played by time varying environments in biological phenomena across scales, from physiology to evolution, seeking to emphasize the commonalities and the challenges faced in this emerging area of research.

Instability of CII is needed for efficient switching between lytic and lysogenic development in bacteriophage 186.

The CII protein of temperate coliphage 186, like the unrelated CII protein of phage λ, is a transcriptional activator that primes expression of the CI immunity repressor and is critical for efficient establishment of lysogeny. 186-CII is also highly unstable, and we show that in vivo degradation is mediated by both FtsH and RseP. We investigated the role of CII instability by constructing a 186 phage encoding a protease resistant CII. The stabilised-CII phage was defective in the lysis-lysogeny decision: choosing lysogeny with close to 100% frequency after infection, and forming prophages that were defective in entering lytic development after UV treatment. While lysogenic CI concentration was unaffected by CII stabilisation, lysogenic transcription and CI expression was elevated after UV. A stochastic model of the 186 network after infection indicated that an unstable CII allowed a rapid increase in CI expression without a large overshoot of the lysogenic level, suggesting that instability enables a decisive commitment to lysogeny with a rapid attainment of sensitivity to prophage induction.

PyOmeroUpload: A Python toolkit for uploading images and metadata to OMERO.

Tools and software that automate repetitive tasks, such as metadata extraction and deposition to data repositories, are essential for researchers to share Open Data, routinely. For research that generates microscopy image data, OMERO is an ideal platform for storage, annotation and publication according to open research principles. We present PyOmeroUpload, a Python toolkit for automatically extracting metadata from experiment logs and text files, processing images and uploading these payloads to OMERO servers to create fully annotated, multidimensional datasets. The toolkit comes packaged in portable, platform-independent Docker images that enable users to deploy and run the utilities easily, regardless of Operating System constraints. A selection of use cases is provided, illustrating the primary capabilities and flexibility offered with the toolkit, along with a discussion of limitations and potential future extensions. PyOmeroUpload is available from: https://github.com/SynthSys/pyOmeroUpload.

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources.

Cells constantly adapt to environmental fluctuations. These physiological changes require time and therefore cause a lag phase during which the cells do not function optimally. Interestingly, past exposure to an environmental condition can shorten the time needed to adapt when the condition re-occurs, even in daughter cells that never directly encountered the initial condition. Here, we use the molecular toolbox of Saccharomyces cerevisiae to systematically unravel the molecular mechanism underlying such history-dependent behavior in transitions between glucose and maltose. In contrast to previous hypotheses, the behavior does not depend on persistence of proteins involved in metabolism of a specific sugar. Instead, presence of glucose induces a gradual decline in the cells' ability to activate respiration, which is needed to metabolize alternative carbon sources. These results reveal how trans-generational transitions in central carbon metabolism generate history-dependent behavior in yeast, and provide a mechanistic framework for similar phenomena in other cell types.

Distributed and dynamic intracellular organization of extracellular information.

Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.