Genomic Transformation of the Picoeukaryote Ostreococcus tauri

Common problems hindering rapid progress in Plant Sciences include cellular, tissue and whole organism complexity, and notably the high level of genomic redundancy affecting simple genetics in higher plants. The novel model organism Ostreococcus tauri is the smallest free-living eukaryote known to date, and possesses a greatly reduced genome size and cellular complexity(1,2), manifested by the presence of just one of most organelles (mitochondrion, chloroplast, golgi stack) per cell, and a genome containing only ~8000 genes. Furthermore, the combination of unicellularity and easy culture provides a platform amenable to chemical biology approaches. Recently, Ostreococcus has been successfully employed to study basic mechanisms underlying circadian timekeeping(3-6). Results from this model organism have impacted not only plant science, but also mammalian biology(7). This example highlights how rapid experimentation in a simple eukaryote from the green lineage can accelerate research in more complex organisms by generating testable hypotheses using methods technically feasible only in this background of reduced complexity. Knowledge of a genome and the possibility to modify genes are essential tools in any model species. Genomic(1), Transcriptomic(8), and Proteomic(9) information for this species is freely available, whereas the previously reported methods(6,10) to genetically transform Ostreococcus are known to few laboratories worldwide. In this article, the experimental methods to genetically transform this novel model organism with an overexpression construct by means of electroporation are outlined in detail, as well as the method of inclusion of transformed cells in low percentage agarose to allow selection of transformed lines originating from a single transformed cell. Following the successful application of Ostreococcus to circadian research, growing interest in Ostreococcus can be expected from diverse research areas within and outside plant sciences, including biotechnological areas. Researchers from a broad range of biological and medical sciences that work on conserved biochemical pathways may consider pursuing research in Ostreococcus, free from the genomic and organismal complexity of larger model species

Concurrent Segmentation and Localization for Tracking of Surgical Instruments

Real-time instrument tracking is a crucial requirement for various computer-assisted interventions. In order to overcome problems such as specular reflections and motion blur, we propose a novel method that takes advantage of the interdependency between localization and segmentation of the surgical tool. In particular, we reformulate the 2D instrument pose estimation as heatmap regression and thereby enable a concurrent, robust and near real-time regression of both tasks via deep learning. As demonstrated by our experimental results, this modeling leads to a significantly improved performance than directly regressing the tool position and allows our method to outperform the state of the art on a Retinal Microsurgery benchmark and the MICCAI EndoVis Challenge 2015.Comment: I. Laina and N. Rieke contributed equally to this work. Accepted to MICCAI 201

Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles

Background: Picoeukaryotes represent an important, yet poorly characterized component of marine phytoplankton. The recent genome availability for two species of Ostreococcus and Micromonas has led to the emergence of picophytoplankton comparative genomics. Sequencing has revealed many unexpected features about genome structure and led to several hypotheses on Ostreococcus biology and physiology. Despite the accumulation of genomic data, little is known about gene expression in eukaryotic picophytoplankton. Results: We have conducted a genome-wide analysis of gene expression in Ostreococcus tauri cells exposed to light/dark cycles (L/D). A Bayesian Fourier Clustering method was implemented to cluster rhythmic genes according to their expression waveform. In a single L/D condition nearly all expressed genes displayed rhythmic patterns of expression. Clusters of genes were associated with the main biological processes such as transcription in the nucleus and the organelles, photosynthesis, DNA replication and mitosis. Conclusions: Light/Dark time-dependent transcription of the genes involved in the main steps leading to protein synthesis (transcription basic machinery, ribosome biogenesis, translation and aminoacid synthesis) was observed, to an unprecedented extent in eukaryotes, suggesting a major input of transcriptional regulations in Ostreococcus. We propose that the diurnal co-regulation of genes involved in photoprotection, defence against oxidative stress and DNA repair might be an efficient mechanism, which protects cells against photo-damage thereby, contributing to the ability of O. tauri to grow under a wide range of light intensities

Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

<p>Abstract</p> <p>Background</p> <p>The storage of photosynthetic carbohydrate products such as starch is subject to complex regulation, effected at both transcriptional and post-translational levels. The relevant genes in plants show pronounced daily regulation. Their temporal RNA expression profiles, however, do not predict the dynamics of metabolite levels, due to the divergence of enzyme activity from the RNA profiles.</p> <p>Unicellular phytoplankton retains the complexity of plant carbohydrate metabolism, and recent transcriptomic profiling suggests a major input of transcriptional regulation.</p> <p>Results</p> <p>We used a quasi-steady-state, constraint-based modelling approach to infer the dynamics of starch content during the 12 h light/12 h dark cycle in the model alga <it>Ostreococcus tauri</it>. Measured RNA expression datasets from microarray analysis were integrated with a detailed stoichiometric reconstruction of starch metabolism in <it>O. tauri </it>in order to predict the optimal flux distribution and the dynamics of the starch content in the light/dark cycle. The predicted starch profile was validated by experimental data over the 24 h cycle. The main genetic regulatory targets within the pathway were predicted by <it>in silico </it>analysis.</p> <p>Conclusions</p> <p>A single-reaction description of starch production is not able to account for the observed variability of diurnal activity profiles of starch-related enzymes. We developed a detailed reaction model of starch metabolism, which, to our knowledge, is the first attempt to describe this polysaccharide polymerization while preserving the mass balance relationships. Our model and method demonstrate the utility of a quasi-steady-state approach for inferring dynamic metabolic information in <it>O. tauri </it>directly from time-series gene expression data.</p

Body Wall Force Sensor for Simulated Minimally Invasive Surgery: Application to Fetal Surgery

Surgical interventions are increasingly executed minimal invasively. Surgeons insert instruments through tiny incisions in the body and pivot slender instruments to treat organs or tissue below the surface. While a blessing for patients, surgeons need to pay extra attention to overcome the fulcrum effect, reduced haptic feedback and deal with lost hand-eye coordination. The mental load makes it difficult to pay sufficient attention to the forces that are exerted on the body wall. In delicate procedures such as fetal surgery, this might be problematic as irreparable damage could cause premature delivery. As a first attempt to quantify the interaction forces applied on the patient's body wall, a novel 6 degrees of freedom force sensor was developed for an ex-vivo set up. The performance of the sensor was characterised. User experiments were conducted by 3 clinicians on a set up simulating a fetal surgical intervention. During these simulated interventions, the interaction forces were recorded and analysed when a normal instrument was employed. These results were compared with a session where a flexible instrument under haptic guidance was used. The conducted experiments resulted in interesting insights in the interaction forces and stresses that develop during such difficult surgical intervention. The results also implicated that haptic guidance schemes and the use of flexible instruments rather than rigid ones could have a significant impact on the stresses that occur at the body wall

Robustness of circadian clocks to daylight fluctuations: hints from the picoeucaryote Ostreococcus tauri

The development of systemic approaches in biology has put emphasis on identifying genetic modules whose behavior can be modeled accurately so as to gain insight into their structure and function. However most gene circuits in a cell are under control of external signals and thus quantitative agreement between experimental data and a mathematical model is difficult. Circadian biology has been one notable exception: quantitative models of the internal clock that orchestrates biological processes over the 24-hour diurnal cycle have been constructed for a few organisms, from cyanobacteria to plants and mammals. In most cases, a complex architecture with interlocked feedback loops has been evidenced. Here we present first modeling results for the circadian clock of the green unicellular alga Ostreococcus tauri. Two plant-like clock genes have been shown to play a central role in Ostreococcus clock. We find that their expression time profiles can be accurately reproduced by a minimal model of a two-gene transcriptional feedback loop. Remarkably, best adjustment of data recorded under light/dark alternation is obtained when assuming that the oscillator is not coupled to the diurnal cycle. This suggests that coupling to light is confined to specific time intervals and has no dynamical effect when the oscillator is entrained by the diurnal cycle. This intringuing property may reflect a strategy to minimize the impact of fluctuations in daylight intensity on the core circadian oscillator, a type of perturbation that has been rarely considered when assessing the robustness of circadian clocks

SLO-ML:A Language for Service Level Objective Modelling in Multi-cloud applications

Cloud modelling languages (CMLs) are designed to assist customers in tackling the diversity of services in the current cloud market. While many CMLs have been proposed in the literature, they lack practical support for automating the selection of services based on the specific service level objectives of a customer's application. We put forward SLO-ML, a novel and generative CML to capture service level requirements. Subsequently, SLO-ML selects the services to honour the customer's requirements and generates the deployment code appropriate to these services. We present the architectural design of SLO-ML and the associated broker that realises the deployment operations. We evaluate SLO-ML using an experimental case study with a group of researchers and developers using a real-world cloud application. We also assess SLO-ML's overheads through empirical scalability tests. We express the promises of SLO-ML in terms of gained productivity and experienced usability, and we highlight its limitations by analysing it as application requirements grow

Discovery pipelines for marine resources : an ocean of opportunity for biotechnology?

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant agreement No 645884. CABI is an international intergovernmental organisation, and we gratefully acknowledge the core financial support from our member countries (and lead agencies) including the United Kingdom (Department for International Development), China (Chinese Ministry of Agriculture), Australia (Australian Centre for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate-General for International Cooperation),and Switzerland (Swiss Agency for Development and Cooperation). See https://www.cabi.org/about-cabi/who-we-work-with/key-donors/ for full details.Marine microbial diversity offers enormous potential for discovery of compounds of crucial importance in healthcare, food security and bioindustry. However, access to it has been hampered by the difficulty of accessing and growing the organisms for study. The discovery and exploitation of marine bioproducts for research and commercial development requires state-of-the-art technologies and innovative approaches. Technologies and approaches are advancing rapidly and keeping pace is expensive and time consuming. There is a pressing need for clear guidance that will allow researchers to operate in a way that enables the optimal return on their efforts whilst being fully compliant with the current regulatory framework. One major initiative launched to achieve this, has been the advent of European Research Infrastructures. Research Infrastructures (RI) and associated centres of excellence currently build harmonized multidisciplinary workflows that support academic and private sector users. The European Marine Biological Research Infrastructure Cluster (EMBRIC) has brought together six such RIs in a European project to promote the blue bio-economy. The overarching objective is to develop coherent chains of high-quality services for access to biological, analytical and data resources providing improvements in the throughput and efficiency of workflows for discovery of novel marine products. In order to test the efficiency of this prototype pipeline for discovery, 248 rarely-grown organisms were isolated and analysed, some extracts demonstrated interesting biochemical properties and are currently undergoing further analysis. EMBRIC has established an overarching and operational structure to facilitate the integration of the multidisciplinary value chains of services to access such resources whilst enabling critical mass to focus on problem resolution.Publisher PDFPeer reviewe

Glioblastoma surgery imaging—reporting and data system: Standardized reporting of tumor volume, location, and resectability based on automated segmentations

Treatment decisions for patients with presumed glioblastoma are based on tumor characteristics available from a preoperative MR scan. Tumor characteristics, including volume, location, and resectability, are often estimated or manually delineated. This process is time consuming and subjective. Hence, comparison across cohorts, trials, or registries are subject to assessment bias. In this study, we propose a standardized Glioblastoma Surgery Imaging Reporting and Data System (GSI-RADS) based on an automated method of tumor segmentation that provides standard reports on tumor features that are potentially relevant for glioblastoma surgery. As clinical validation, we determine the agreement in extracted tumor features between the automated method and the current standard of manual segmentations from routine clinical MR scans before treatment. In an observational consecutive cohort of 1596 adult patients with a first time surgery of a glioblastoma from 13 institutions, we segmented gadolinium-enhanced tumor parts both by a human rater and by an automated algorithm. Tumor features were extracted from segmentations of both methods and compared to assess differences, concordance, and equivalence. The laterality, contralateral infiltration, and the laterality indices were in excellent agreement. The native and normalized tumor volumes had excellent agreement, consistency, and equivalence. Multifocality, but not the number of foci, had good agreement and equivalence. The location profiles of cortical and subcortical structures were in excellent agreement. The expected residual tumor volumes and resectability indices had excellent agreement, consistency, and equivalence. Tumor probability maps were in good agreement. In conclusion, automated segmentations are in excellent agreement with manual segmentations and practically equivalent regarding tumor features that are potentially relevant for neurosurgical purposes. Standard GSI-RADS reports can be generated by open access software