Genetic Regulatory Circuit Dynamics: Analysis and Synthesis

Recent evidence indicates that branched actin might control cell progression through G1 in addition to lamellipodium protrusion.

Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels, but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels. The majority of genes whose expression varied between the species maintained a conserved dynamic pattern. Cases of diverged dynamic pattern correspond to genes that were induced under distinct subsets of conditions in the two species. Profiling the interspecific hybrid allowed us to distinguish between genes with predominantly cis- or trans-regulatory variation. We find that trans-varying alleles are dominantly inherited, and that cis-variations are often complemented by variations in trans. Based on these results, we suggest that gene expression diverges primarily through changes in expression levels, but does not alter the pattern by which these levels are dynamically regulated.

Introduction In our program, simulated patients (SPs) give feedback to medical students in the course of communication skills training. To ensure effective training, quality control of the SPs’ feedback should be implemented. At other institutions, medical students evaluate the SPs’ feedback for quality control (Bouter et al., 2012). Thinking about implementing quality control for SPs’ feedback in our program, we wondered whether the evaluation by students would result in the same scores as evaluation by experts. Methods Consultations simulated by 4th-year medical students with SPs were video taped including the SP’s feedback to the students (n=85). At the end of the training sessions students rated the SPs’ performance using a rating instrument called Bernese Assessment for Role-play and Feedback (BARF) containing 11 items concerning feedback quality. Additionally the videos were evaluated by 3 trained experts using the BARF. Results The experts showed a high interrater agreement when rating identical feedbacks (ICCunjust=0.953). Comparing the rating of students and experts, high agreement was found with regard to the following items: 1. The SP invited the student to reflect on the consultation first, Amin (= minimal agreement) 97% 2. The SP asked the student what he/she liked about the consultation, Amin = 88%. 3. The SP started with positive feedback, Amin = 91%. 4. The SP was comparing the student with other students, Amin = 92%. In contrast the following items showed differences between the rating of experts and students: 1. The SP used precise situations for feedback, Amax (=maximal agreement) 55%, Students rated 67 of SPs’ feedbacks to be perfect with regard to this item (highest rating on a 5 point Likert scale), while only 29 feedbacks were rated this way by the experts. 2. The SP gave precise suggestions for improvement, Amax 75%, 62 of SPs’ feedbacks obtained the highest rating from students, while only 44 of SPs’ feedbacks achieved the highest rating in the view of the experts. 3. The SP speaks about his/her role in the third person, Amax 60%. Students rated 77 feedbacks with the highest score, while experts judged only 43 feedbacks this way. Conclusion Although evaluation by the students was in agreement with that of experts concerning some items, students rated the SPs’ feedback more often with the optimal score than experts did. Moreover it seems difficult for students to notice when SPs talk about the role in the first instead of the third person. Since precision and talking about the role in the third person are important quality criteria of feedback, this result should be taken into account when thinking about students’ evaluation of SPs’ feedback for quality control. Bouter, S., E. van Weel-Baumgarten, and S. Bolhuis. 2012. Construction and Validation of the Nijmegen Evaluation of the Simulated Patient (NESP): Assessing Simulated Patients’ Ability to Role-Play and Provide Feedback to Students. Academic Medicine: Journal of the Association of American Medical Colleges

The genome in the cell nucleus is organized by a dynamic process influenced by structural memory from mitosis. In this study, we develop a model of human genome dynamics through cell cycles by extending the previously developed whole-genome model to cover the mitotic phase. With this extension, we focus on the role of mitotic and cell cycle memory in genome organization. The simulation progresses from mitosis to interphase and the subsequent mitosis, leading to successive cell cycles. During mitosis, our model describes microtubule dynamics, showing how forces orchestrate the assembly of chromosomes into a rosette ring structure at metaphase. The model explains how the positioning of chromosomes depends on their size in metaphase. The memory of the metaphase configuration persists through mitosis and into interphase in dimensions perpendicular to the cell division axis, effectively guiding the distribution of chromosome territories over multiple cell cycles. At the onset of each G1 phase, phase separation of active and inactive chromatin domains occurs, leading to A/B compartmentalization. Our cycling simulations show that the compartments are unaffected by structural memory from previous cycles and are consistently established in each cell cycle. The genome model developed in this study highlights the interplay between chromosome dynamics and structural memory across cell cycles, providing insights for the analyses of cellular processes.

Lack of self-esteem may play an important role in the development of eating disorders (ED). This study investigated the differential impact of positive and negative feedback on implicit and explicit self-esteem in women with an ED (N=25) as compared to women without an ED (N=29). False feedback (positive or negative) was given on participant's performance on a specifically developed intellectual test. Before and after the performance, explicit and implicit self-esteem was measured. On the explicit measure ED patients reacted congruently with the nature of the feedback. On the implicit measure only ED patients responded to the positive feedback with an improvement of self-esteem, with no effect for negative feedback. The control group was unaffected by either feedback. Furthermore, no correlation was observed between the explicit and implicit measures, a finding suggesting that these measurements tap different constructs. Positive feedback affects implicit self-esteem of female patients with eating disorders. The results underline the importance of positively approaching women with ED.

Bidirectional Human-Robot Learning: Imitation and Skill Improvement

Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide. Unexpectedly, this approach revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response. In contrast, a more complex picture involving both negative and positive feedback loops was observed on IFNγ treatment. IFNγ-induced repression of genes associated with regulation of gene expression, cellular development, apoptosis and cell growth resulted from cycloheximide-resistant primary IFNγ signalling. In silico promoter analysis revealed significant overrepresentation of SP1/SP3-binding sites and/or GC-rich stretches. Although signal transducer and activator of transcription 1 (STAT1)-binding sites were not overrepresented, repression was lost in absence of STAT1. Interestingly, basal expression of the majority of these IFNγ-repressed genes was dependent on STAT1 in IFN-naïve fibroblasts. Finally, IFNγ-mediated repression was also found to be evident in primary murine macrophages. IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu.

When the DNA damage is generated, the tumor suppressor gene p53 is activated and selects the cell fate such as the cell cycle arrest, the DNA repair and the induction of apoptosis. Recently, the p53 oscillation was observed in MCF7 cell line. However, the biological meaning of p53 oscillation was still unclear. Here, we constructed a novel mathematical model of cell cycle regulatory system with p53 signaling network to investigate the relationship between the p53 oscillation and the cell cycle progression. First, the simulated result without DNA damage agreed with the biological findings. Next, the simulations with DNA damage realized both the p53 oscillation and the cell cycle arrest, and indicated that the generation of multiple p53 pulses disrupted the cell cycle progression. Moreover, the simulated results showed that the cell cycle disruption was caused by the catastrophe of M phase in the cell cycle, which resulted from the decline in cyclin A/cyclin-dependent kinase 2. The results in this study suggested that the generation of multiple p53 pulses against DNA damage may be used as a marker of cell cycle disruption.

A new technique for vibration suppression in Large Space Structures is demonstrated in laboratory experiments on a thin cantilever beam, resulting in substantially reduced dynamic response. This technique, called Positive Position Feedback, makes use of generalized displacement measurements to accomplish vibration suppression. The concept of a piezoelectric active-member is developed in relation to controlling space-truss type structures. The active-member functions dually as a structural member and a control actuator. Piezoelectric ceramic material is adhered to a thin cantilever beam and simulates the use of an active-member. This space-realizable control scheme makes use of strain measurements, a preferred measurement quantity for vibration suppression, and internal control forces which completely decouple the rigid-body motion from the elastic motion. A simple necessary and sufficient condition for stability with Positive Position Feedback is presented. This condition is non-dynamic and is in general easily satisfied. As a result, Positive Position Feedback is demonstrated to have superior robust stability properties. It is also demonstrated that with Positive Position Feedback, all control and observation spillover is stabilizing. Five experiments are described in which the first six modes of vibration of the cantilever beam are controlled.

About 65% of all emissions of nitrous oxide, N2O, are from soils, and are caused by aerobic nitrification and anaerobic denitrification. Tropical forest soils are probably the most important single source, followed by cultivated soils. Emission rates in natural systems are related to the rate of N mineralization from organic matter, and N deposition; in agricultural systems they are related to the quantities of N used as fertilizers and, where relevant, to recent land use change. The global budget for N2O is not well balanced, and sources may still be underestimated. Direct evidence of a positive feedback of global warming on N2O emissions comes from studies of air in ice cores. One of the projected effects of future global warming is a lowering of water tables in northern peatlands; experiments suggest that this would lead to increased emissions, but that the effect on total emissions would be small. The results of many experiments with non‐peatland soils indicate that the effect of temperature on soil emissions is generally positive, and that the rate of increase may be very steep when denitrification is the principal process involved. Process‐level modelling suggests that the reason is increased soil respiration, which causes an increase in anaerobic volume in which denitrification can take place, in addition to the increased denitrification rate per unit anaerobic volume brought about directly by the rise in temperature. These results imply that generally a positive feedback on emissions from soils is likely. However, in some environments, a large proportion of total annual emissions can occur during freeze–thaw cycles; such cycles may become more or less frequent, depending on the climatic zone, and this may result in either a positive or negative feedback effect due to global warming. Models of global and regional trends give very conflicting predictions of the direction and the magnitude of climatic impacts on fluxes, but the prediction of a positive feedback seems to be the more soundly based.

Pulse-modulated RF atmospheric pressure glow discharges (APDGs) were investigated in recent years to reduce the thermal accumulation and extend the operation region of the stable alpha glow mode. Different pulse-modulated voltage and current waveforms were acquired in previous experiments, but no attention was paid to the interpretation. We investigated this issue and associated phenomenon via positive and negative feedback effects derived from varying the series capacitor in the inversely L-shaped matching network used in our pulse-modulated RF APGD source. The evolutions of pulse-modulated RF waveforms were found to be associated with the feedback region and the pulsed plasma absorbed RF power. In the positive feedback region, pulse-modulated RF APGDs are relatively stable. In the negative feedback region, wide spikes as well as undershoots occur in RF voltage and current waveforms and the plasma absorbed RF power. In case of a high RF power discharge with a low modulation frequency, the pulse-modulated RF APGD is extinguished and re-ignited due to the enhanced undershoot during the initial pulse phase. The pulse-modulated RF APGD can transit from positive to negative feedback region in a range of series capacitance. Experimental results are discussed by the aid of equivalent circuit, negative and positive feedback effects.

Knowing the complete genome of a given species is just a piece of the puzzle. To fully unveil the systems behavior of an organism, an organ, or even a single cell, we need to understand the underlying gene regulatory dynamics. Given the complexity of the whole system, the ultimate goal is unattainable for the moment. But perhaps, by analyzing the most simple genetic systems, we may be able to develop the mathematical techniques and procedures required to tackle more complex genetic networks in the near future.In the present work, the techniques for developing mathematical models of simple bacterial gene networks, like the tryptophan and lactose operons are introduced. Despite all of the underlying assumptions, such models can provide valuable information regarding gene regulation dynamics. Here, we pay special attention to robustness as an emergent property.These notes are organized as follows. In the first section, the long historical relation between mathematics, physics, and biology is briefly reviewed...

Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity

Early erythroid progenitors known as CFU-e undergo multiple self-renewal cell cycles. The CFU-e developmental stage ends with the onset of erythroid terminal differentiation (ETD). The transition from CFU-e to ETD is a critical cell fate decision that determines erythropoietic rate. Here we review recent insights into the regulation of this transition, garnered from flow cytometric and single-cell RNA sequencing studies. We find that the CFU-e/ETD transition is a rapid S phase-dependent transcriptional switch. It takes place during an S phase that is much shorter than in preceding or subsequent cycles, as a result of globally faster replication forks. Furthermore, it is preceded by cycles in which G1 becomes gradually shorter. These dramatic cell cycle and S phase remodeling events are directly linked to regulation of the CFU-e/ETD switch. Moreover, regulators of erythropoietic rate exert their effects by modulating cell cycle duration and S phase speed. Glucocorticoids increase erythropoietic rate by inducing the CDK inhibitor p57KIP2, which slows replication forks, inhibiting the CFU-e/ETD switch. Conversely, erythropoietin promotes induction of ETD by shortening the cycle. S phase shortening was reported during cell fate decisions in non-erythroid lineages, suggesting a fundamentally new developmental role for cell cycle speed.

I. INTRODUCTION A. Overview The fission yeast Schizosaccharomyces pombe has proved to be a good model system for analysis of the eukaryotic cell cycle. A number of the key cell cycle regulatory molecules now being extensively studied in higher eukaryotes were first identified and characterized in fission yeast, and it has become clear that many of the regulatory networks elucidated through genetic analysis in S. pombe are conserved in higher eukaryotes as well (Nurse 1990). In this chapter, we consider the regulatory mechanisms that control progression through the mitotic cycle of fission yeast with particular emphasis on those mechanisms that ensure the correct timing and temporal ordering of key cell cycle transitions. However, we do not deal with the control of cytokinesis, which is discussed elsewhere in this volume (Su and Yanagida, this volume). We also consider what is known of the enzymology of DNA replication in fission yeast, whereas the accompanying chapters focus on the processes of mitosis and cytokinesis (Su and Yanagida, this volume) and of conjugation, meiosis, and sporulation (Yamamoto et al., this volume). We begin with a brief introduction to S. pombe and its life cycle. B. Life Cycle and Genetics S. pombe is a unicellular ascomycete fungus only distantly related to the budding yeast Saccharomyces cerevisiae (for discussion of phylogenetic relationships, see Sipiczki 1995). Fission yeast cells are rod-shaped, grow by apical extension, and divide by medial fission. The cells are usually haploid, with a haploid genome size similar to that of budding yeast at...