A FAIR approach to genomics

The aim of this thesis was to increase our understanding on how genome information leads to function and phenotype. To address these questions, I developed a semantic systems biology framework capable of extracting knowledge, biological concepts and emergent system properties, from a vast array of publicly available genome information. In chapter 2, Empusa is described as an infrastructure that bridges the gap between the intended and actual content of a database. This infrastructure was used in chapters 3 and 4 to develop the framework. Chapter 3 describes the development of the Genome Biology Ontology Language and the GBOL stack of supporting tools enforcing consistency within and between the GBOL definitions in the ontology (OWL) and the Shape Expressions (ShEx) language describing the graph structure. A practical implementation of a semantic systems biology framework for FAIR (de novo) genome annotation is provided in chapter 4. The semantic framework and genome annotation tool described in this chapter has been used throughout this thesis to consistently, structurally and functionally annotate and mine microbial genomes used in chapter 5-10. In chapter 5, we introduced how the concept of protein domains and corresponding architectures can be used in comparative functional genomics to provide for a fast, efficient and scalable alternative to sequence-based methods. This allowed us to effectively compare and identify functional variations between hundreds to thousands of genomes. In chapter 6, we used 432 available complete Pseudomonas genomes to study the relationship between domain essentiality and persistence. In this chapter the focus was mainly on domains involved in metabolic functions. The metabolic domain space was explored for domain essentiality and persistence through the integration of heterogeneous data sources including six published metabolic models, a vast gene expression repository and transposon data. In chapter 7, the correlation between the expected and observed genotypes was explored using 16S-rRNA phylogeny and protein domain class content as input. In this chapter it was shown that domain class content yields a higher resolution in comparison to 16S-rRNA when analysing evolutionary distances. Using protein domain classes, we also were able to identify signifying domains, which may have important roles in shaping a species. To demonstrate the use of semantic systems biology workflows in a biotechnological setting we expanded the resource with more than 80.000 bacterial genomes. The genomic information of this resource was mined using a top down approach to identify strains having the trait for 1,3-propanediol production. This resulted in the molecular identification of 49 new species. In addition, we also experimentally verified that 4 species were capable of producing 1,3-propanediol. As discussed in chapter 10, the here developed semantic systems biology workflows were successfully applied in the discovery of key elements in symbiotic relationships, to improve functional genome annotation and in comparative genomics studies. Wet/dry-lab collaboration was often at the basis of the obtained results. The success of the collaboration between the wet and dry field, prompted me to develop an undergraduate course in which the concept of the “Moist” workflow was introduced (Chapter 9).</p

Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell

The frequency-domain open photoacoustic cell (OPC) approach was used to determine room temperature thermal diffusivity of skins (pericarps) from the raw tomatoes (Lycopersicon esculetum Mill.) characterized by the three different stages of ripeness (from immature-green to a mature-red). Periodically interrupted 532 nm laser radiation was used to heat the dry tomato skins, typically 10 mm in diameter and up to 68 µm thick; the modulating frequency f varied from 8 to 150 Hz. Initially, a combined OPC-model that takes into account both, the thermoelastic bending and the effect of thermal diffusion (TD), has been applied. Preliminary results showed that until at least 40 Hz, the effect of TD dominates; above this value the combined model fits the experimental data only poorly. For this reason a less complex OPC-TD approach was applied to all investigated skins instead, which predicts an exponential decrease for the amplitude of measured photoacoustic signal S with increasing f. For a specimen that is simultaneously opaque and thermally thick, S depends on f as S~exp(-b f1/2) where b is a fitting parameter. The S versus f plot enables one to deduce the numerical value for b which, on its turn allows for the assessment of skin’s thermal diffusivity a. Thermal diffusivities obtained for the immature green, orange, and red skins (periderms) are 9.9×10-8 m2¿s-1, 7.2×10-8 m2¿s-1, and 4.6×10-8 m2¿s-1, respectively; the uncertainty was typically 5% of the measured value

Assess Applicability of the Functional Programming Paradigms in Embedded Hardware

Programming in embedded lighting domain is commonly done using the C language with the Object Oriented programming paradigm at Philips Lighting. However applying that paradigm in combination with the low-level language like C creates a conceptual gap between the requirements and design and actual implementation. This results in reduced source code readability and maintainability. Functional programming paradigm was expected to alleviate this problem by reducing the gap and enhancing readability. A proof of concept was built on an advanced, IP-connected, digital LED driver (Power over Ethernet) device. The actual code was inspired by the rule-based decision engine concept developed by EnLight.Based on the hardware specifications of the device, the existing code to communicate with, and adherence to the functional paradigm, Lua was chosen to build the proof with. The implementation of the decision engine was altered to exploit characteristics of functional programming, such as representing actions as functions rather than as an enumeration value, using the common filter function to replace loops, and many more.The proof of concept was able to run in the device. It was also relatively more readable and maintainable. However, it was slightly slower, less memory efficient, and less capable in dealing with low-level problems such as garbage compared to the engine in C language

Design, Implementation and Evaluation of PsyWeb, a Learning Environment in a Problem Based Learning Curriculum.

In this article we describe the design and implementation of PsyWeb, a rich learning environment for the new problem based study in Psychology at Erasmus University Rotterdam Experiences are reported for the first five (of eight) courses of the first year of the new study. Students opinions have been collected as part of a survey at the end of each course. Results indicate that students are positive about PsyWeb. The overall appreciation shows a slight increase over time. Starting with the second course, usage of PsyWeb has been logged. Usage has been quantified in terms of the number of unique IP-addresses per day. Using this measure we assume that PsyWeb has a student reach between 25% and 100% per day. Usage shows a slight increase over the courses. The implementation of a series of additions to PsyWeb has been planned for the next year

Milk protein oxidation in healthy subjects:A preliminary study

The role of protein oxidation in the regulation of whole body protein metabolism is unknown. Previously, it was observed that vigorous exercise led to increased protein oxidation. To further characterise 13C-milk protein oxidation in healthy subjects, the oxidation of ingested 13C-protein after an overnight fast was measured using a non-invasive 13C-protein breath test. This approach enables the analysis of 13C-protein oxidation kinetics and the effect of interfering factors. It was found that the estimated maximal 13C-milk protein oxidation was 0.07 g min−1, corresponding to a theoretical maximal oxidation capacity of ≈1.4 g kg body weight−1 d−1. No indications were found for preferential oxidation of non-essential amino acids. Combined ingestion of 30 g 13C-whey protein with 30 g glucose resulted in a 19% decrease of 13C-whey protein oxidation. It was concluded that exogenous 13C-whey protein oxidation can be affected by other co-ingested nutrients like glucose

Effects of Argonaute on gene expression in Thermus thermophilus.

This is the final version of the article. Available from the publisher via the DOI in this record.BACKGROUND: Eukaryotic Argonaute proteins mediate RNA-guided RNA interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. Recently, it has become evident that prokaryotic Argonaute homologs mediate DNA-guided DNA interference, and play a role in host defense. Argonaute of the bacterium Thermus thermophilus (TtAgo) targets invading plasmid DNA during and after transformation. Using small interfering DNA guides, TtAgo can cleave single and double stranded DNAs. Although TtAgo additionally has been demonstrated to cleave RNA targets complementary to its DNA guide in vitro, RNA targeting by TtAgo has not been demonstrated in vivo. METHODS: To investigate if TtAgo also has the potential to control RNA levels, we analyzed RNA-seq data derived from cultures of four T. thermophilus strain HB27 variants: wild type, TtAgo knockout (Δago), and either strain transformed with a plasmid. Additionally we determined the effect of TtAgo on expression of plasmid-encoded RNA and plasmid DNA levels. RESULTS: In the absence of exogenous DNA (plasmid), TtAgo presence or absence had no effect on gene expression levels. When plasmid DNA is present, TtAgo reduces plasmid DNA levels 4-fold, and a corresponding reduction of plasmid gene transcript levels was observed. We therefore conclude that TtAgo interferes with plasmid DNA, but not with plasmid-encoded RNA. Interestingly, TtAgo presence stimulates expression of specific endogenous genes, but only when exogenous plasmid DNA was present. Specifically, the presence of TtAgo directly or indirectly stimulates expression of CRISPR loci and associated genes, some of which are involved in CRISPR adaptation. This suggests that TtAgo-mediated interference with plasmid DNA stimulates CRISPR adaptation.Funding: This study was financially supported by a TOP grant from the Netherlands Organisation for Scientific Research (NWO) to John van der Oost (NWO-TOP 854.10.003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The Biomarker Potential of miRNAs in Myotonic Dystrophy Type I

MicroRNAs (miRNAs) are mostly known for their gene regulation properties, but they also play an important role in intercellular signaling. This means that they can be found in bodily fluids, giving them excellent biomarker potential. Myotonic Dystrophy type I (DM1) is the most frequent autosomal dominant muscle dystrophy in adults, with an estimated prevalence of 1:8000. DM1 symptoms include muscle weakness, myotonia, respiratory failure, cardiac conduction defects, cataracts, and endocrine disturbances. Patients display heterogeneity in both age of onset and disease manifestation. No treatment or cure currently exists for DM1, which shows the necessity for a biomarker that can predict disease progression, providing the opportunity to implement preventative measures before symptoms arise. In the past two decades, extensive research has been conducted in the miRNA expression profiles of DM1 patients and their biomarker potential. Here we review the current state of the field with a tissue-specific focus, given the multi-systemic nature of DM1 and the intracellular signaling role of miRNAs

Diagnostic accuracy of patient interview items and clinical tests for cervical radiculopathy.

ObjectiveTo determine the diagnostic accuracy of patient interview items and clinical tests to diagnose cervical radiculopathy.DesignA prospective diagnostic accuracy study.ParticipantsConsecutive patients (N=134) with a suspicion of cervical radiculopathy were included. A medical specialist made the diagnosis of cervical radiculopathy based on the patient's clinical presentation and corresponding Magnetic Resonance Imaging findings. Participants completed a list of patient interview items and the clinical tests were performed by a physiotherapist.Main outcome measuresDiagnostic accuracy was determined in terms of sensitivity, specificity, and positive (+LR) and negative likelihood ratios (-LR). Sensitivity and specificity values ≥0.80 were considered high. We considered +LR≥5 and -LR≤0.20 moderate, and +LR≥10 and -LR≤0.10 high.ResultsThe history items 'arm pain worse than neck pain', 'provocation of symptoms when ironing', 'reduction of symptoms by walking with your hand in your pocket', the Spurling test and the presence of reduced reflexes showed high specificity and are therefore useful to increase the probability of cervical radiculopathy when positive. The presence of 'paraesthesia' and 'paraesthesia and/or numbness' showed high sensitivity, indicating that the absence of these patient interview items decreases the probability of cervical radiculopathy. Although most of these items had potentially relevant likelihood ratios, none showed moderate or high likelihood ratios.ConclusionsSeveral patient interview items, the Spurling test and reduced reflexes are useful to assist in the diagnosis of cervical radiculopathy. Because there is no gold standard for cervical radiculopathy, caution is required to not over-interpret diagnostic accuracy values