Robert Smith

Robert Smith
Wageningen University & Research | WUR · Laboratory of Systems & Synthetic Biology

PhD Systems Biology

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77
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Introduction
Skills and Expertise

Publications

Publications (77)
Chapter
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Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to cal...
Article
Full-text available
The immune system distinguishes between self and foreign antigens. The kinetic proofreading (KPR) model proposes that T cells discriminate self from foreign ligands by the different ligand binding half-lives to the T cell receptor (TCR). It is challenging to test KPR as the available experimental systems fall short of only altering the binding half...
Article
Full-text available
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. Whi...
Preprint
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. Whi...
Preprint
Full-text available
The pivotal task of the immune system is to distinguish between self and foreign antigens. The kinetic proofreading model (KPR) proposes that T cells discriminate self from foreign ligands by the different ligand binding half-lives to the T cell receptor (TCR). It is challenging to test KPR as the available experimental systems fall short of only a...
Article
Full-text available
Vegetation shade is characterised by marked decreases in the red/far-red ratio and photosynthetic irradiance. The activity of phytochrome in the field has typically been described by its photoequilibrium, defined by the photochemical properties of the pigment in combination with the spectral distribution of the light. This approach represents an ov...
Article
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Background: Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic systems, a number of conclusions have been drawn using mathematical methods with simplifying assumptions. For example, constraint-bas...
Article
Full-text available
Spatial relocalization of proteins is crucial for the correct functioning of living cells. An interesting example of spatial ordering is the light-induced clustering of plant photoreceptor proteins. Upon irradiation by white or red light, the red light-active phytochrome, phytochrome B, enters the nucleus and accumulates in large nuclear bodies. Th...
Article
Full-text available
Background: Evolution has led to the development of biological networks that are shaped by environmental signals. Elucidating, understanding and then reconstructing important network motifs is one of the principal aims of Systems & Synthetic Biology. Consequently, previous research has focused on finding optimal network structures and reaction rat...
Chapter
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Systems Biology has brought together researchers from biology, mathematics, physics and computer science to illuminate our understanding of biological mechanisms. In this chapter, we provide an overview of numerical techniques and considerations required to construct useful models describing natural phenomena. Initially, we show how the dynamics of...
Article
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The dynamic behaviour of the plant red/far-red light photoreceptor phytochrome B (phyB) has been elucidated in natural and synthetic systems. Red light switches phyB from the inactive Pr state to the active Pfr state, a process that is reversed by far-red light. Alongside light signals, phyB activity is constrained by thermal reversion (that is pro...
Article
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Background Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorith...
Data
Figure S2. Diagram illustrating selection of differentially expressed genes.
Data
Figure S3. Differential expression of transcription factor (TF) encoding genes in response to infection at subjective dawn or night under LL conditions.
Data
Figure S4. JAZ6 expression is transiently induced during B. cinerea infection.
Data
Table S1. Primers used in quantitative PCR experiments.
Data
Dataset S2. Arabidopsis genes whose expression changes significantly in response to B. cinerea and to the time of day at which inoculation occurred.
Data
Figure S5. Stomata are not a primary point of entry for B. cinerea hyphae during infection of Arabidopsis.
Data
Figure S6. Expression of JAZ6 in the jaz6 mutant line and Col‐0 18 hpi with B. cinerea or mock control.
Data
Dataset S4. Biological Process Gene Ontology terms significantly overrepresented in groups of genes differentially expressed in response to inoculation at different times of the day.
Data
Methods S1. Grouping of the differentially expressed genes for Gene Ontology and motif analysis.
Data
Dataset S3. Transcription factor genes that are differentially expressed in response to inoculation with B. cinerea at different times of the day.
Data
Dataset S5. Motifs significantly overrepresented in upstream regions of groups of genes differentially expressed in response to inoculation at different times of the day.
Data
Figure S1. Growth of Botrytis cinerea is restricted in plants inoculated at subjective dawn versus subjective night.
Data
Dataset S1. Expression data 18 and 22 hpi after subjective dawn and night inoculations with B. cinerea for genes with consistent expression patterns in previous studies.
Article
Full-text available
The circadian clock, an internal timekeeping mechanism, allows plants to anticipate regular changes in the environment, such as light and dark, and biotic challenges such as pathogens and herbivores. Here, we demonstrate that the plant circadian clock influences susceptibility to the necrotrophic fungal pathogen, Botrytis cinerea. Arabidopsis plant...
Article
Full-text available
Plants have evolved complex mechanisms to balance the efficient use of absorbed light energy in photosynthesis with the capacity to use that energy in assimilation, so avoiding potential damage from excess light. This is particularly important under natural light, which can vary according to weather, solar movement and canopy movement. Photosynthet...
Article
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Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR...
Article
Full-text available
Plants respond to changes in the environment by triggering a suite of regulatory networks that control and synchronize molecular signaling in different tissues, organs, and the whole plant. Molecular studies through genetic and environmental perturbations, particularly in the model plant Arabidopsis thaliana, have revealed many of the mechanisms by...
Article
Full-text available
Circadian clocks confer advantages by restricting biological processes to certain times of day through the control of specific phased outputs. Control of temperature signalling is an important function of the plant oscillator, but the architecture of the gene network controlling cold signalling by the clock is not well understood. Here we use a mod...
Data
Generalised method used for comparing models. Figure S2. Effect of τ2 Figure S3. Effect of d. Figure S4. Published CBF1 Real-time PCR primers appear to prime from CBF1 and CBF3. Figure S5. Alignment of published CBF1-specific primers with CBF1 and CBF3 cDNA sequences.
Data
Optimised new parameter values for each of the thirteen models. Table S2. AICcU analysis results. Table S3. Sensitivity heatmap for the expression of CBF3 at the indicated time after dawn. Table S4. Primer sequences for chromatin Immunoprecipitation.
Article
Full-text available
Plants use day-length information to coordinate flowering time with the appropriate season to maximize reproduction. In Arabidopsis, the long day–specific expression of CONSTANS (CO) protein is crucial for flowering induction. Although light signaling regulates CO protein stability, the mechanism by which CO is stabilized in the long-day afternoon...

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