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1.  Conjunctival FOXP3 Expression in Trachoma: Do Regulatory T Cells Have a Role in Human Ocular Chlamydia trachomatis Infection? 
PLoS Medicine  2006;3(8):e266.
Background
Trachoma, caused by ocular infection with Chlamydia trachomatis, remains the leading infectious cause of blindness and in 2002 was responsible for 3.6% of total global blindness. Although transmission can be successfully interrupted using antibiotics and improvements in public and personal hygiene, the long-term success of the control programmes advocated by the World Health Organization are still uncertain. For the complete control and prevention of trachoma, a vaccine would be highly desirable. Currently there are no licensed vaccines for trachoma, and no human vaccine trials have been conducted since the 1960s. A barrier to new attempts to design and introduce a vaccine is the identification of immunologic correlates of protective immunity or immunopathology. We studied important correlates of the immune response in a trachoma-endemic population in order to improve our knowledge of this disease. This is essential for the successful development of a vaccine against both ocular and genital C. trachomatis infection.
Methods and Findings
We used quantitative real-time PCR for C. trachomatis 16S rRNA to identify conjunctival infection. The expression of IFN-γ, IDO, IL-10, and FOXP3 mRNA transcripts was measured. We evaluated the role of immune effector and regulatory responses in the control of chlamydial infection and in the resolution of clinical signs of trachoma in endemic communities in Gambia. All host transcripts examined were detectable even in normal conjunctiva. The levels of these transcripts were increased, compared to normal uninfected conjunctiva, when infection was detected, with or without clinical disease signs. Interestingly, when clinical disease signs were present in the absence of infection, the expression of a regulatory T cell transcription factor, FOXP3, remained elevated.
Conclusions
There is evidence of an increase in the magnitude of the local anti-chlamydial cytokine immune responses with age. This increase is coupled to a decline in the prevalence of infection and active trachoma, suggesting that effective adaptive immunity is acquired over a number of years. The anti-chlamydial and inflammatory immune response at the conjunctival surface, which may control chlamydial replication, is closely matched by counter inflammatory or regulatory IL-10 expression. Differences in the level of FOXP3 expression in the conjunctiva may indicate a role for regulatory T cells in the resolution of the conjunctival immune response, which is important in protection from immunopathology. However, the expression of cytokines that control chlamydial replication and those that regulate the conjunctival immune response is not simply juxtaposed; the interaction between the infection and the clinical disease process is therefore more complex.
The immune response in a trachoma-endemic population showed an increase in local anti-chlamydial cytokine responses with age, associated with a decline in the prevalence of infection and active trachoma.
Editors' Summary
Background.
Trachoma is the leading infectious cause of blindness worldwide. Six million people—most of whom live in crowded, unhygienic conditions with limited water supplies—are blind because of repeated eye infections with Chlamydia trachomatis. This bacterium passes easily from person to person on hands or clothing and is also spread by flies. Successive infections starting in childhood cause progressive scarring of the inside of the eyelid. Eventually, the eyelashes turn inwards and rub painfully over the front of the eye (the cornea). This causes corneal scarring, loss of corneal transparency, and, finally, irreversible loss of sight, usually in adulthood. C. trachomatis infections can be prevented by improving personal hygiene and by reducing fly breeding sites, and they can be treated with antibiotics. In addition, early scarring of the eyelid and turned-in eyelashes can be treated surgically.
Why Was This Study Done?
Through the above interventions, the World Health Organization hopes to eliminate trachoma by 2020, but a vaccine might also be necessary. To develop a vaccine, the human immune response to C. trachomatis needs to be better understood. As with other diseases, the immune response to C. trachomatis includes a pro-inflammatory side, which activates immune cells to attack the bacteria, and a regulatory side, which keeps the pro-inflammatory responses in check. The balance between these two sides is not perfect, however. Although the immune response deals with C. trachomatis infections efficiently, it also causes some of the tissue damage that leads to scarring and loss of sight. In this study, the researchers have investigated the human immune response to C. trachomatis to provide immunological information that might help vaccine development.
What Did the Researchers Do and Find?
The researchers examined school children living in Gambia, where trachoma is very common, for clinical signs of active trachoma (for example, red or swollen eyelids). To find out which children were infected with C. trachomatis, the researchers collected a few cells from the surface of their eyes and looked for a ribonucleic acid (RNA) molecule that is only made by C. trachomatis. The researchers also looked in these samples for human messenger RNA (mRNA) molecules that are made during pro-inflammatory and regulatory immune responses.
The children formed four groups based on infection with C. trachomatis and clinical signs. Some children—particularly the older ones—were uninfected and had no clinical signs. Others were infected but showed no clinical signs—these children were incubating the bacteria. Some were infected and had clinical disease; these children had the highest bacterial loads. Finally, children recovering from an infection carried no bacteria but still had some clinical signs.
The researchers detected different types of immune response in each of these groups. Children incubating the bacteria had a strong pro-inflammatory response—their immune systems were trying to fight off infection. The pro-inflammatory response was even stronger in the infected children with clinical signs, but now the regulatory response had also increased, presumably to limit inflammation. In children in the recovery phase, only regulatory immune cells, which were making an mRNA from a gene called FOXP3, remained active.
What Do These Findings Mean?
The relative rarity of infections and active disease in older children together with indications of a more active immune response to infection indicates that protective immunity to C. trachomatis is acquired through repeated exposure to it. This bodes well for the development of a vaccine, which would speed up the acquisition of this natural immunity. Furthermore, the new information about immune responses at different stages of infection with C. trachomatis should help in vaccine design. The findings need to be confirmed by tracking immune responses in individual children during episodes of infection, but could then be used to help design vaccines that produce good protective immunity against C. trachomatis without causing too much collateral tissue damage. The current results suggest, for example, that regulatory immune cells are important in limiting the inflammatory response, so vaccine developers may need to ensure that their vaccines stimulate the production of this sort of cell as well as of the pro-inflammatory cells needed to clear the infection.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0030266.
• NHS Direct Online patient information on trachoma
• World Health Organization information on trachoma and its elimination
• US Centers for Disease Control and Prevention general information on trachoma
• MedlinePlus encyclopedia entry on trachoma
doi:10.1371/journal.pmed.0030266
PMCID: PMC1526769  PMID: 16881731
2.  Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli 
We have designed an experimental/computational framework for studying complex phenotypes in bacteria.Our framework relies on whole-genome fitness profiling coupled with a module-level analysis to discover pathways that directly affect fitness.As a proof-of-principle, we studied ethanol tolerance in Escherichia coli and we identified key pathways that contribute to this phenotype.We then validated our findings through genetic manipulations, gene-expression profiling, metabolite-level measurements, and stable-isotope labeling.
Elucidating the genetic basis of complex phenotypes remains a fundamental challenge in biology. We have developed a systematic framework for comprehensive genetic analysis of microbial phenotypes. Our approach combines the power of fitness profiling (Girgis et al, 2007; Amini et al, 2009) with the sensitivity of module-level analysis (Goodarzi et al, 2009a) to identify key genetic modules that directly affect a phenotype under study. We applied our technology to ethanol tolerance, a complex phenotype with broad industrial relevance. Ethanol affects a variety of cellular components and pathways, including but not limited to membrane integrity (Dombek and Ingram, 1984), enzyme activities (Millar et al, 1982), and proton flux (D'Amore et al, 1990). Given the diversity of targets, the emergence of ethanol tolerance requires modifications to multiple pathway (D'Amore and Stewart, 1987).
To reveal the genetic basis of ethanol tolerance in Escherichia coli, we used two high-coverage mutant libraries (a transposon library and an overexpression library) to assess the fitness consequences of single-locus perturbations. Each cell in our transposon library contains a random transposon insertion in its genome (Girgis et al, 2007); whereas the cells in the overexpression library carry 1–3 kb genomic fragments cloned into a cloning vector (Amini et al, 2009). We grew these libraries under mild (4% v/v) and harsh (5.5% v/v) ethanol concentrations. On growth, the abundance of each transposon insertion or overexpression mutant changes as a function of its fitness, a process that can be monitored through parallel genetic footprinting and microarray hybridization (Figure 1A). This results in a global fitness profile, where the contribution of each genetic locus to ethanol tolerance can be quantified in parallel. However, in the context of ethanol tolerance and other complex phenotypes, single-locus perturbations typically result in modest changes in fitness. Although these small differences can be amplified through multiple rounds of selection, the number of generations is limited as spontaneous beneficial mutations emerge in the population and cause strong biases in the resulting fitness profiles. To boost our analytical power without introducing these biases in the data, we used a module-level computational method to discover the pathways and components that are strongly associated with the data as opposed to focusing on the genes individually (Goodarzi et al, 2009a). Genes function in the context of pathways and modules and module-level analyses increase statistical power through combining information from multiple genes functioning as part of a given pathway (Subramanian et al, 2005).
The module-level analysis of the fitness scores from both libraries revealed a diverse set of pathways that have a direct function in ethanol tolerance. Some of these pathways, including heat-shock stress response and osmoregulation, are known modifiers of ethanol tolerance; whereas others such as acid-stress response and fimbrial structures are novel pathways. Among our findings was the important function of three regulatory proteins: FNR, ArcA, and CafA. Knocking out FNR/ArcA that upregulates aerobic respiration proteins and TCA cycle components results in a marked increase in ethanol tolerance. Similarly, knocking out CafA, a post-transcriptional regulator of alcohol dehydrogenase, is beneficial for tolerance. Given these observations, we hypothesized that selection for ethanol tolerance can result in higher ethanol degradation.
As a large fraction of discovered pathways belonged to central metabolism, we used metabolomics to evaluate our findings. To directly assess the metabolic consequences of adaptation to ethanol, we evolved ethanol-tolerant strains in minimal media plus glucose for ∼30 and 160 generations. We then compared the steady-state level of metabolites in these strains to that of the wild type (Figure 1B). In agreement with our fitness profiling results, we observed a significant increase in TCA cycle metabolites in one of our ethanol-tolerant strains. Higher concentrations of TCA cycle components along with a high free coenzyme A (CoA) to acetyl-coenzyme A (acetyl-CoA) ratio hinted at the capacity of this strain to metabolize ethanol. To test this hypothesis, we performed stable-isotope labeling on our ethanol-tolerant strain versus wild type. After growth on labeled ethanol, we measured the fraction of metabolites that were labeled at each timepoint (Figure 1B). Our results confirmed that the ethanol-tolerant strain has the capacity to consume ethanol through its conversion into acetyl-CoA and further assimilation in the TCA cycle.
By using a variety of systems-level approaches, we have been able to genetically dissect ethanol tolerance in E. coli. We have shown that fitness profiling, in combination with module-level analysis tools, can serve as a powerful approach for revealing the genetic basis of complex phenotypes. The fact that laboratory evolution ended up using the very modules that we discovered, highlights the biological and adaptive relevance of the proposed framework.
Understanding the genetic basis of adaptation is a central problem in biology. However, revealing the underlying molecular mechanisms has been challenging as changes in fitness may result from perturbations to many pathways, any of which may contribute relatively little. We have developed a combined experimental/computational framework to address this problem and used it to understand the genetic basis of ethanol tolerance in Escherichia coli. We used fitness profiling to measure the consequences of single-locus perturbations in the context of ethanol exposure. A module-level computational analysis was then used to reveal the organization of the contributing loci into cellular processes and regulatory pathways (e.g. osmoregulation and cell-wall biogenesis) whose modifications significantly affect ethanol tolerance. Strikingly, we discovered that a dominant component of adaptation involves metabolic rewiring that boosts intracellular ethanol degradation and assimilation. Through phenotypic and metabolomic analysis of laboratory-evolved ethanol-tolerant strains, we investigated naturally accessible pathways of ethanol tolerance. Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape.
doi:10.1038/msb.2010.33
PMCID: PMC2913397  PMID: 20531407
adaptation; ethanol tolerance; evolution; fitness profiling
3.  Molecular characterization of the evolution of phagosomes 
First large-scale comparative proteomics/phosphoproteomics study characterizing some of the key steps that contributed to the remodeling of phagosomes that occurred during evolution. Comparison of profiling analyses of isolated phagosomes from three distant organisms (Dictyostelium, Drosophila, and mouse) revealed a protein core that defines a potential ‘ancient' phagosome and a set of 50 proteins that emerged while adaptive immunity was already well established.Gene duplication events of mouse phagosome paralogs occurred mostly in Bilateria and Euteleostomi, coinciding with the emergence of innate and adaptive immunity, and thus, provided the functional innovations needed for the establishment of these two crucial evolutionary steps of the immune system.Phosphoproteomics of isolated phagosomes from the same three distant species indicate that the phagosome phosphoproteome has been extensively modified during evolution. Still, some phosphosites have been maintained for >1.2 billion years, and thus, highlight their particular significance in the regulation of key phagosomal functions.
Phagocytosis is the process by which multiple cell types internalize large particulate material from the external milieu. The functional properties of phagosomes are acquired through a complex maturation process, referred to as phagolysosome biogenesis. This pathway involves a series of rapid interactions with organelles of the endocytic apparatus, enabling the gradual transformation of newly formed phagosomes into phagolysosomes in which proteolytic degradation occurs. The degradative environment encountered in the phagosome lumen has enabled the use of phagocytosis as a predation mechanism for feeding (phagotrophy) in amoeba, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in jawed vertebrates (fish), initiate a sustained immune response.
High-throughput proteomics profiling of isolated phagosomes has been tremendously helpful for the molecular comprehension of this organelle. This approach is achieved by feeding low buoyancy latex beads to phagocytic cells, enabling the subsequent isolation of latex bead-containing phagosomes, away from all the other cell organelles, by a single-isopicnic centrifugation in sucrose gradient. In order to characterize some of the key steps that contributed to the remodeling of phagosomes during evolution, we isolated this organelle from three distant organisms: the amoeba Dictyostelium discoideum, the fruit fly Drosophila melanogaster, and mouse (Mus musculus) that use phagocytosis for different purposes, and performed detailed proteomics and phosphoproteomics analyses with unparallel protein coverage for this organelle (two- to four-fold enhancements in identified proteins).
In order to establish the origin of the mouse phagosome proteome, we performed comparative analyses among 39 taxa including plants/algea, unicellular organisms, fungi, and more complex animal multicellular organisms. These genomic comparisons indicated that a large proportion of the mouse phagosome proteome is of ancient origin (73.1% of the proteome is conserved in eukaryotic organisms) (Figure 2A). This stresses the fact that phagocytosis is a very ancient process, as shown by its possible involvement in the emergence of eukaryotic cells (eukaryogenesis). Indeed, we identified close to 300 phagosome mouse proteins also present on Drosophila and Dictyostelium phagosomes, defining a potential ‘ancient' core of proteins from which the immune functions of phagosomes likely evolved. Around 16.7% of the mouse phagosome proteins appeared in organisms that use phagocytosis for innate immunity (Bilateria to Chordata), whereas 10.2% appeared in Euteleostomi or Tetrapoda where phagosomes have an important function in linking the killing of microorganisms with the development of a specific sustained immune response following antigen recognition. The phagosome is made of molecules taken from a variety of sources within the cell, including the cytoplasm, the cytoskeleton and membrane organelles. Despite the evolution and diversification of these various cellular systems, the mammalian phagosome proteome is made preferentially of ancient proteins (Figure 2B). Comparison of functional annotation during evolution highlighted the emergence of specific phagosomal functions at various steps during evolution (Figure 2C). Some of these proteins and their point of origin during evolution are highlighted in Figure 2D. Strikingly, we identified in Tetrapods a set of 50 proteins that arose while adaptive immunity was already well established in teleosts (fish), indicating that the phagocytic system is still evolving.
Our study highlights the fact that the functional properties of phagosomes emerged by the remodeling of ancient molecules, the addition of novel components, and the duplication of existing proteins (paralogs) leading to the formation of molecular machines of mixed origin. Gene duplication is a process that contributed continuously to the complexification of the mouse proteome during evolution. In sharp contrast, paralog analysis indicated that the phagosome proteome was mainly reorganized through two periods of gene duplication, in Bilateria and Euteleostomi, coinciding with the emergence of adaptive immunity (in jawed fish), and innate immunity (at the split between Metazoa and Bilateria). These results strongly suggest that selective constraints may have favored the maintenance of phagosome paralogs to ensure the establishment of novel functions associated with this organelle at these two crucial evolutionary steps of the immune system.
The emergence of genes associated to the MHC locus in mammals that appeared originally in the genome of jawed fishes, contributed to the development of complex molecular mechanisms linking innate (our immune system that defends the host from infection in a non-specific manner) and adaptive immunity (the part of the immune system triggered specifically after antigen recognition). Several of the genes of this locus encode proteins known to have important functions in antigen presentation, such as subunits of the immunoproteasome (LMP2 and LMP7), MHC class I and class II molecules, as well as tapasin and the transporter associated with antigen processing (TAP1 and TAP2), involved in the transport and loading of peptides on MHC class I molecules (Figure 6). In addition to their ability to present peptides on MHC class II molecules, phagosomes of vertebrates have been shown to be competent for the presentation of exogenous peptides on MHC class I molecules, a process referred to as cross-presentation. From a functional point of view, the involvement of phagosomes in antigen cross-presentation is the outcome of the successful integration of a wide range of multimolecular components that emerged throughout evolution (Figure 6). The trimming of exogenous proteins into small peptides that can be loaded on MHC class I molecules is inherited from the phagotrophic properties of unicellular organisms, where internalized bacteria are degraded into basic molecules and used as a source of nutrients. Ancient processes have therefore been co-opted (the use of an existing biological structure or feature for a new function) for new functionalities. A summarizing model of the various steps that enabled phagosome antigen presentation is presented in Figure 6. This model highlights the fact that although antigen presentation is unique to evolutionary recent phagosomes (starting in jawed fishes about 450 million years ago), it uses and integrates molecular machines composed of proteins that emerged throughout evolution.
In summary, we present here the first large-scale comparative proteomics/phosphoproteomics study characterizing some of the key evolutionary steps that contributed to the remodeling of phagosomes during evolution. Functional properties of this organelle emerged by the remodeling of ancient molecules, the addition of novel components, the extensive adaption of protein phosphorylation sites and the duplication of existing proteins leading to the formation of molecular machines of mixed origin.
Amoeba use phagocytosis to internalize bacteria as a source of nutrients, whereas multicellular organisms utilize this process as a defense mechanism to kill microbes and, in vertebrates, initiate a sustained immune response. By using a large-scale approach to identify and compare the proteome and phosphoproteome of phagosomes isolated from distant organisms, and by comparative analysis over 39 taxa, we identified an ‘ancient' core of phagosomal proteins around which the immune functions of this organelle have likely organized. Our data indicate that a larger proportion of the phagosome proteome, compared with the whole cell proteome, has been acquired through gene duplication at a period coinciding with the emergence of innate and adaptive immunity. Our study also characterizes in detail the acquisition of novel proteins and the significant remodeling of the phagosome phosphoproteome that contributed to modify the core constituents of this organelle in evolution. Our work thus provides the first thorough analysis of the changes that enabled the transformation of the phagosome from a phagotrophic compartment into an organelle fully competent for antigen presentation.
doi:10.1038/msb.2010.80
PMCID: PMC2990642  PMID: 20959821
evolution; immunity; phosphoproteomics; phylogeny; proteomics
4.  Robustness and Fragility in Immunosenescence 
PLoS Computational Biology  2006;2(11):e160.
We construct a model to study tradeoffs associated with aging in the adaptive immune system, focusing on cumulative effects of replacing naive cells with memory cells. Binding affinities are characterized by a stochastic shape space model. System loss arising from an individual infection is associated with disease severity, as measured by the total antigen population over the course of an infection. We monitor evolution of cell populations on the shape space over a string of infections, and find that the distribution of losses becomes increasingly heavy-tailed with time. Initially this lowers the average loss: the memory cell population becomes tuned to the history of past exposures, reducing the loss of the system when subjected to a second, similar infection. This is accompanied by a corresponding increase in vulnerability to novel infections, which ultimately causes the expected loss to increase due to overspecialization, leading to increasing fragility with age (i.e., immunosenescence). In our model, immunosenescence is not the result of a performance degradation of some specific lymphocyte, but rather a natural consequence of the built-in mechanisms for system adaptation. This “robust, yet fragile” behavior is a key signature of Highly Optimized Tolerance.
Synopsis
The immune system can be viewed as a complex system, which adapts, over time, to reflect the history of infections experienced by the organism. This paper describes a model that captures this adaptation and corresponding robust, yet fragile behavior. To model immunological processes that rely on binding specificity, researchers typically utilize abstract shape space models. These models describe the binding characteristics of a receptor or antigen as points in a high dimensional vector space. Stromberg and Carlson have incorporated the concept of shape space into a dynamical model of immune response. They use this model to examine the development of the system over a series of infections and monitor the severity of disease for each infection. The diseases are drawn at random from a distribution having a few frequently reoccurring and many rare. The system is observed to adapt over a series of infections, becoming robust to the frequent diseases while developing fragility to the rare diseases. This age-correlated weakness arises from the underlying dynamics of system adaptation rather than from an accumulation of defects. This robust, yet fragile behavior is a signature of Highly Optimized Tolerance, a mechanism for complexity based on robustness tradeoffs.
doi:10.1371/journal.pcbi.0020160
PMCID: PMC1664698  PMID: 17121459
5.  Nonlinear vibration behavior of graphene resonators and their applications in sensitive mass detection 
Nanoscale Research Letters  2012;7(1):499.
Graphene has received significant attention due to its excellent mechanical properties, which has resulted in the emergence of graphene-based nano-electro-mechanical system such as nanoresonators. The nonlinear vibration of a graphene resonator and its application to mass sensing (based on nonlinear oscillation) have been poorly studied, although a graphene resonator is able to easily reach the nonlinear vibration. In this work, we have studied the nonlinear vibration of a graphene resonator driven by a geometric nonlinear effect due to an edge-clamped boundary condition using a continuum elastic model such as a plate model. We have shown that an in-plane tension can play a role in modulating the nonlinearity of a resonance for a graphene. It has been found that the detection sensitivity of a graphene resonator can be improved by using nonlinear vibration induced by an actuation force-driven geometric nonlinear effect. It is also shown that an in-plane tension can control the detection sensitivity of a graphene resonator that operates both harmonic and nonlinear oscillation regimes. Our study suggests the design principles of a graphene resonator as a mass sensor for developing a novel detection scheme using graphene-based nonlinear oscillators.
doi:10.1186/1556-276X-7-499
PMCID: PMC3462111  PMID: 22947221
Graphene resonator; Mass sensing; Nonlinear oscillation; NEMS
6.  The Basic Immune Simulator: An agent-based model to study the interactions between innate and adaptive immunity 
Background
We introduce the Basic Immune Simulator (BIS), an agent-based model created to study the interactions between the cells of the innate and adaptive immune system. Innate immunity, the initial host response to a pathogen, generally precedes adaptive immunity, which generates immune memory for an antigen. The BIS simulates basic cell types, mediators and antibodies, and consists of three virtual spaces representing parenchymal tissue, secondary lymphoid tissue and the lymphatic/humoral circulation. The BIS includes a Graphical User Interface (GUI) to facilitate its use as an educational and research tool.
Results
The BIS was used to qualitatively examine the innate and adaptive interactions of the immune response to a viral infection. Calibration was accomplished via a parameter sweep of initial agent population size, and comparison of simulation patterns to those reported in the basic science literature. The BIS demonstrated that the degree of the initial innate response was a crucial determinant for an appropriate adaptive response. Deficiency or excess in innate immunity resulted in excessive proliferation of adaptive immune cells. Deficiency in any of the immune system components increased the probability of failure to clear the simulated viral infection.
Conclusion
The behavior of the BIS matches both normal and pathological behavior patterns in a generic viral infection scenario. Thus, the BIS effectively translates mechanistic cellular and molecular knowledge regarding the innate and adaptive immune response and reproduces the immune system's complex behavioral patterns. The BIS can be used both as an educational tool to demonstrate the emergence of these patterns and as a research tool to systematically identify potential targets for more effective treatment strategies for diseases processes including hypersensitivity reactions (allergies, asthma), autoimmunity and cancer. We believe that the BIS can be a useful addition to the growing suite of in-silico platforms used as an adjunct to traditional research efforts.
doi:10.1186/1742-4682-4-39
PMCID: PMC2186321  PMID: 17900357
7.  A Canonical Model of Multistability and Scale-Invariance in Biological Systems 
PLoS Computational Biology  2012;8(8):e1002634.
Multistability and scale-invariant fluctuations occur in a wide variety of biological organisms from bacteria to humans as well as financial, chemical and complex physical systems. Multistability refers to noise driven switches between multiple weakly stable states. Scale-invariant fluctuations arise when there is an approximately constant ratio between the mean and standard deviation of a system's fluctuations. Both are an important property of human perception, movement, decision making and computation and they occur together in the human alpha rhythm, imparting it with complex dynamical behavior. Here, we elucidate their fundamental dynamical mechanisms in a canonical model of nonlinear bifurcations under stochastic fluctuations. We find that the co-occurrence of multistability and scale-invariant fluctuations mandates two important dynamical properties: Multistability arises in the presence of a subcritical Hopf bifurcation, which generates co-existing attractors, whilst the introduction of multiplicative (state-dependent) noise ensures that as the system jumps between these attractors, fluctuations remain in constant proportion to their mean and their temporal statistics become long-tailed. The simple algebraic construction of this model affords a systematic analysis of the contribution of stochastic and nonlinear processes to cortical rhythms, complementing a recently proposed biophysical model. Similar dynamics also occur in a kinetic model of gene regulation, suggesting universality across a broad class of biological phenomena.
Author Summary
Biological systems are able to adapt to rapidly and widely changing environments. Many biological organisms employ two distinct mechanisms that improve their survival in these circumstances: Firstly they exhibit rapid, qualitative changes in their internal dynamics; secondly they possess the ability to respond to change that is not absolute, but scales in proportion to the underlying intensity of the environment. In this paper, we study a simple class of noisy, dynamical systems that mathematically represent a very broad range of more complex models. We hence show how a combination of nonlinear instabilities and state-dependent noise in this model is able to unify these two apparently distinct biological phenomena. To illustrate its unifying potential, this simple model is applied to two very distinct biological processes – the spontaneous activity of the human cortex (i.e. when subjects are at rest), and genetic regulation in a bacteriophage. We also provide proof of principle that our model can be inverted from empirical data, allowing estimation of the parameters that express the nonlinear and stochastic influences at play in the underlying system.
doi:10.1371/journal.pcbi.1002634
PMCID: PMC3415415  PMID: 22912567
8.  Quantitative analysis of regulatory flexibility under changing environmental conditions 
Day length changes with the seasons in temperate latitudes, affecting the many biological rhythms that entrain to the day/night cycle: we measure these effects on the expression of Arabidopsis clock genes, using RNA and reporter gene readouts, with a new method of phase analysis.Dusk sensitivity is proposed as a simple, natural and general mathematical measure to analyse and manipulate the changing phase of a clock output relative to the change in the day/night cycle.Dusk sensitivity shows how increasing the numbers of feedback loops in the Arabidopsis clock models allows more flexible regulation, consistent with a previously-proposed, general operating principle of biological networks.The Arabidopsis clock genes show flexibility of regulation that is characteristic of a three-loop clock model, validating aspects of the model and the operating principle, but some clock output genes show greater flexibility arising from direct light regulation.
The analysis of dynamic, non-linear regulation with the aid of mechanistic models is central to Systems Biology. This study compares the predictions of mechanistic, mathematical models of the circadian clock with molecular time-series data on rhythmic gene expression in the higher plant Arabidopsis thaliana. Analysis of the models helps us to understand (explain and predict) how the clock gene circuit balances regulation by external and endogenous factors to achieve particular behaviours. Such multi-factorial regulation is ubiquitous in, and characteristic of, living systems.
The Earth's rotation causes predictable changes in the environment, notably in the availability of sunlight for photosynthesis. Many biological processes are driven by the environmental input via sensory pathways, for example, from photoreceptors. Circadian clocks provide an alternative strategy. These endogenous, 24-h rhythms can drive biological processes that anticipate the regular environmental changes, rather than merely responding. Many rhythmic processes have both light and clock control. Indeed, the clock components themselves must balance internal timing with external inputs, because circadian clocks are reset daily through light regulation of one or more clock components. This process of entrainment is complicated by the change in day length. When the times of dawn and dusk move apart in summer, and closer together in winter, does the clock track dawn, track dusk or interpolate between them?
In plants, the clock controls leaf and petal movements, the opening and closing of stomatal pores, the discharge of floral fragrances, and many metabolic activities, especially those associated with photosynthesis. Centuries of physiological studies have shown that these rhythms can behave differently. Flowering in Ipomoea nil (Pharbitis nil, Japanese morning glory) is controlled by a rhythm that tracks the time of dusk, to give a classic example. We showed that two other rhythms associated with vegetative growth track dawn in this species (Figure 5A), so the clock system allows flexible regulation.
The relatively small number of components involved in the circadian clockwork makes it an ideal candidate for mathematical modelling. Molecular genetic studies in a variety of model eukaryotes have shown that the circadian rhythm is generated by a network of 6–20 genes. These genes form feedback loops generating a rhythm in mRNA production. A single negative feedback loop in which a gene encodes a protein that, after several hours, turns off transcription is capable of generating a circadian rhythm, in principle. A single light input can entrain the clock to ‘local time', synchronised with a light–dark cycle. However, real circadian clocks have proven to be more complicated than this, with multiple light inputs and interlocked feedback loops.
We have previously argued from mathematical analysis that multi-loop networks increase the flexibility of regulation (Rand et al, 2004) and have shown that appropriately deployed flexibility can confer functional robustness (Akman et al, 2010). Here we test whether that flexibility can be demonstrated in vivo, in the model plant, A. thaliana. The Arabidopsis clock mechanism comprises a feedback loop in which two partially redundant, myb transcription factors, LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), repress the expression of their activator, TIMING OF CAB EXPRESSION 1 (TOC1). We previously modelled this single-loop circuit and showed that it was not capable of recreating important data (Locke et al, 2005a). An extended, two-loop model was developed to match observed behaviours, incorporating a hypothetical gene Y, for which the best identified candidate was the GIGANTEA gene (GI) (Locke et al, 2005b). Two further models incorporated the TOC1 homologues PSEUDO-RESPONSE REGULATOR (PRR) 9 and PRR7 (Locke et al, 2006; Zeilinger et al, 2006). In these circuits, a morning oscillator (LHY/CCA1–PRR9/7) is coupled to an evening oscillator (Y/GI–TOC1) via the original LHY/CCA1–TOC1 loop.
These clock models, like those for all other organisms, were developed using data from simple conditions of constant light, darkness or 12-h light–12-h dark cycles. We therefore tested how the clock genes in Arabidopsis responded to light–dark cycles with different photoperiods, from 3 h light to 18 h light per 24-h cycle (Edinburgh, 56° North latitude, has 17.5 h light in midsummer). The time-series assays of mRNA and in vivo reporter gene images showed a range of peak times for different genes, depending on the photoperiod (Figure 5C). A new data analysis method, mFourfit, was introduced to measure the peak times, in the Biological Rhythms Analysis Software Suite (BRASS v3.0). None of the genes showed the dusk-tracking behaviour characteristic of the Ipomoea flowering rhythm. The one-, two- and three-loop models were analysed to understand the observed patterns. A new mathematical measure, dusk sensitivity, was introduced to measure the change in timing of a model component versus a change in the time of dusk. The one- and two-loop models tracked dawn and dusk, respectively, under all conditions. Only the three-loop model (Figure 5B) had the flexibility required to match the photoperiod-dependent changes that we found in vivo, and in particular the unexpected, V-shaped pattern in the peak time of TOC1 expression. This pattern of regulation depends on the structure and light inputs to the model's evening oscillator, so the in vivo data supported this aspect of the model. LHY and CCA1 gene expression under short photoperiods showed greater dusk sensitivity, in the interval 2–6 h before dawn, than the three-loop model predicted, so these data will help to constrain future models.
The approach described here could act as a template for experimental biologists seeking to understand biological regulation using dynamic, experimental perturbations and time-series data. Simulation of mathematical models (despite known imperfections) can provide contrasting hypotheses that guide understanding. The system's detailed behaviour is complex, so a natural and general measure such as dusk sensitivity is helpful to focus on one property of the system. We used the measure to compare models, and to predict how this property could be manipulated. To enable additional analysis of this system, we provide the time-series data and experimental metadata online.
The circadian clock controls 24-h rhythms in many biological processes, allowing appropriate timing of biological rhythms relative to dawn and dusk. Known clock circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation, which was analysed by comparison with three contrasting models. A simple, quantitative measure, Dusk Sensitivity, was introduced to compare the behaviour of clock models with varying loop complexity. Evening-expressed clock genes showed photoperiod-dependent dusk sensitivity, as predicted by the three-loop model, whereas the one- and two-loop models tracked dawn and dusk, respectively. Output genes for starch degradation achieved dusk-tracking expression through light regulation, rather than a dusk-tracking rhythm. Model analysis predicted which biochemical processes could be manipulated to extend dusk tracking. Our results reveal how an operating principle of biological regulators applies specifically to the plant circadian clock.
doi:10.1038/msb.2010.81
PMCID: PMC3010117  PMID: 21045818
Arabidopsis thaliana; biological clocks; dynamical systems; gene regulatory networks; mathematical models; photoperiodism
9.  Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge 
By recruiting the essential HIS3 gene to the GAL regulatory system and switching to a repressing glucose medium, we confronted yeast cells with a novel challenge they had not encountered before along their history in evolution.Adaptation to this challenge involved a global transcriptional response of a sizeable fraction of the genome, which relaxed on the time scale of the population adaptation, of order of 10 generations.For a large fraction of the responding genes there is no simple biological interpretation, connecting them to the specific cellular demands imposed by the novel challenge.Strikingly, repeating the experiment did not reproduce similar transcription patterns neither in the transient phase nor in the adapted state in glucose.These results suggest that physiological selection operates on the new metabolic configurations generated by the non-specific large scale transcriptional response to eventually stabilize an adaptive state.
Cells adjust their transcriptional state to accommodate environmental and genetic perturbations. Some common perturbations, such as changes in nutrient composition, elicit well-characterized transcriptional responses that can be understood by simple engineering-like design principles as satisfying specific demands imposed by the perturbation. However, cells also have the ability to adapt to novel and unforeseen challenges. This ability is central in realizing the evolvability potential of cells as they respond to dramatic genetic or environmental changes along evolution. Little is known about the mechanisms underlying such adaptations to novel challenges; in particular, the role of the transcriptional regulatory network in such adaptations has not been characterized. Genome-wide measurements have revealed that, in many cases, perturbations lead to a global transcriptional response involving a sizeable fraction of the genome (Gasch et al, 2000; Jelinsky et al, 2000; Causton et al, 2001; Ideker et al, 2001; Lai et al, 2005). Such global behavior suggests that general collective properties of the genetic network, rather than specific pre-designed pathways, determine an important part of the transcriptional response. It is not known however what fraction of genes within such massive transcriptional responses is essential to the specific cellular demands. It is also unknown whether the non-pre-designed part of the response can have a functional role in adaptation to novel challenges.
To study these questions, we confronted yeast cells with a novel challenge they had not encountered before along their history in evolution. A strain of the yeast Saccharomyces cerevisiae was engineered to recruit the gene HIS3, an essential enzyme from the histidine biosynthesis pathway (Hinnebusch, 1992), to the GAL regulatory system, responsible for galactose utilization (Stolovicki et al, 2006). The GAL system is known to be strongly repressed when the cells are exposed to glucose. Therefore, upon switching to a medium containing glucose and lacking histidine, the GAL system and with it HIS3 are highly repressed immediately following the switch and the cells encounter a severe challenge. We have recently shown that a cell population carrying this rewired genome can adapt to grow competitively in a chemostat in a medium containing pure glucose (Stolovicki et al, 2006). This adaptation occurred on a timescale of ∼10 generations; applying a stronger environmental pressure in the form of a competitive inhibitor to HIS3 (3AT) resulted in a similar adaptation albeit with a longer timescale. Figure 1 shows the dynamics of the population's cell density (blue lines, measured by OD) following a medium switch from galactose to glucose in the chemostat without (A) and with (B) 3AT. The experiments revealed that adaptation occurs on physiological timescales (much shorter than required by spontaneous random mutations), but the mechanisms underlying this adaptation have remained unclear (Stolovicki et al, 2006).
Yeast cells had not encountered recruitment of HIS3 to the GAL system along their evolutionary history, and their genome could not possibly have been selected to specifically address glucose repression of HIS3. This experiment, therefore, provides a unique opportunity to characterize the spontaneous transcriptional response during adaptation to a novel challenge and to assess the functional role of the regulatory system in this adaptation. We used DNA microarrays to measure the genome-wide expression levels at time points along the adaptation process, with and without 3AT. These measurements revealed that a sizeable fraction of the genome responded by induction or repression to the switch into glucose. Superimposed on the OD traces, Figure 1 shows the results of a clustering analysis of the expression of genes as measured by the arrays along time in the experiments. This analysis revealed two dominant clusters, each containing hundreds of genes in each experiment, which responded to the medium switch to glucose by a strong transient induction or repression followed by relaxation to steady state on the timescale of the adaptation process, ∼ 10 generations. The two clusters in each experiment show similar but opposite dynamics.
A detailed analysis of the gene content in the two clusters revealed that only a small portion of the response was induced by a change in carbon source (15% overlap between the corresponding clusters in the two experiments, with and without 3AT). Moreover, it revealed a very low overlap with the universal stress response observed for a wide range of environmental stresses (Gasch et al, 2000; Causton et al, 2001) and with the typical response to amino-acid starvation (Natarajan et al, 2001). Additionally, all known specific responses to stress in the literature are characterized by transient induction or repression with relaxation to steady state within a generation time (Gasch et al, 2000; Koerkamp et al, 2002; Wu et al, 2004), whereas in our experiments relaxation of the transcriptional response occurs over many generations. Taken together, these results show that the transcriptional response observed here is neither a metabolic response to the change in carbon source nor is it a standard response to stress or amino-acid starvation. This raises the possibility that it is a spontaneous collective response that is largely composed of genes that do not have a specific function. This possibility was tested directly by repeating the experiment with different populations and comparing their responses. This procedure revealed reproducible adaptation dynamics and steady states in terms of population density, but showed significantly different transcriptional transient responses and steady states for the two repeated experiments. Thus, a significant portion of the genes that changed their expression during the adaptation process do not have a well-defined and reproducible function in the challenging environment.
The application of a stronger environmental pressure in the form of 3AT had a dramatic effect on the global characteristics of the transcriptional response: it induced a markedly higher correlation among the hundreds of responding genes. Figure 3A compares the array data in color code for the two experiments. It is seen that the emergent pattern of transcription exhibits a higher degree of order by the introduction of high external pressure. Observation of the transcriptional patterns for specific metabolic pathways illustrates the different contributions to the correlated dynamics (Figure 3B–D). A general energetic module such as glycolysis exhibited similar patterns of induction and relaxation in experiments with and without 3AT (Figure 3B). However, in general, we found that more than one-third of the known metabolic modules (30 out of 88 modules described in KEGG) exhibited high expression correlation among their genes when the environmental pressure was high but not when it was low. As an example, Figure 3C shows the histidine biosynthesis pathway and Figure 3D the purine pathway. Note the highly ordered trajectories in the lower panels (with 3AT) compared to the disordered ones in the upper panels (no 3AT). This order extends also between genes belonging to different and even distant metabolic modules. It indicates that a global transcriptional regulatory mechanism is in operation, rather than a local specific one. Surprisingly, genes belonging to the same metabolic pathway exhibited simultaneous positively and negatively correlated dynamics. Thus, an important conclusion of this work is that the global transcriptional response to a novel challenge cannot be explained by a simple cellular or metabolic logic. This is to be expected if the response had not been specifically selected in evolution and was not pre-designed for the challenge.
Our data clearly reveal that the massive transcriptional response underlies the adaptation process to a novel challenge. The novelty of the challenge presented to the cells excludes the possibility that this response has been specifically selected toward this challenge. Thus, transcriptional regulation has dynamic properties resulting in a general massive nonspecific response to a novel perturbation. Such a response in turn allows for metabolic rearrangements, which by feeding back on transcription lead to adaptation of the cells to the unforeseen situation. The drastic change in the expression state of the cell opens multiple new metabolic pathways. Physiological selection works then on these multiple metabolic pathways to stabilize an adaptive state that causes relaxation of the perturbed expression pattern. This scenario, involving the creation of a library of possibilities and physiological selection over this library, is compatible with our understanding of a broad class of biological systems, placing the cellular metabolic/regulatory networks on the same footing as the neural or the immune systems (Gerhart and Kirschner, 1997).
Cells adjust their transcriptional state to accommodate environmental and genetic perturbations. An open question is to what extent transcriptional response to perturbations has been specifically selected along evolution. To test the possibility that transcriptional reprogramming does not need to be ‘pre-designed' to lead to an adaptive metabolic state on physiological timescales, we confronted yeast cells with a novel challenge they had not previously encountered. We rewired the genome by recruiting an essential gene, HIS3, from the histidine biosynthesis pathway to a foreign regulatory system, the GAL network responsible for galactose utilization. Switching medium to glucose in a chemostat caused repression of the essential gene and presented the cells with a severe challenge to which they adapted over approximately 10 generations. Using genome-wide expression arrays, we show here that a global transcriptional reprogramming (>1200 genes) underlies the adaptation. A large fraction of the responding genes is nonreproducible in repeated experiments. These results show that a nonspecific transcriptional response reflecting the natural plasticity of the regulatory network supports adaptation of cells to novel challenges.
doi:10.1038/msb4100147
PMCID: PMC1865588  PMID: 17453047
adaptation; cellular metabolism; expression arrays; plasticity; transcriptional response
10.  The Effect of Universal Influenza Immunization on Mortality and Health Care Use 
PLoS Medicine  2008;5(10):e211.
Background
In 2000, Ontario, Canada, initiated a universal influenza immunization program (UIIP) to provide free influenza vaccines for the entire population aged 6 mo or older. Influenza immunization increased more rapidly in younger age groups in Ontario compared to other Canadian provinces, which all maintained targeted immunization programs. We evaluated the effect of Ontario's UIIP on influenza-associated mortality, hospitalizations, emergency department (ED) use, and visits to doctors' offices.
Methods and Findings
Mortality and hospitalization data from 1997 to 2004 for all ten Canadian provinces were obtained from national datasets. Physician billing claims for visits to EDs and doctors' offices were obtained from provincial administrative datasets for four provinces with comprehensive data. Since outcomes coded as influenza are known to underestimate the true burden of influenza, we studied more broadly defined conditions. Hospitalizations, ED use, doctors' office visits for pneumonia and influenza, and all-cause mortality from 1997 to 2004 were modelled using Poisson regression, controlling for age, sex, province, influenza surveillance data, and temporal trends, and used to estimate the expected baseline outcome rates in the absence of influenza activity. The primary outcome was then defined as influenza-associated events, or the difference between the observed events and the expected baseline events. Changes in influenza-associated outcome rates before and after UIIP introduction in Ontario were compared to the corresponding changes in other provinces. After UIIP introduction, influenza-associated mortality decreased more in Ontario (relative rate [RR] = 0.26) than in other provinces (RR = 0.43) (ratio of RRs = 0.61, p = 0.002). Similar differences between Ontario and other provinces were observed for influenza-associated hospitalizations (RR = 0.25 versus 0.44, ratio of RRs = 0.58, p < 0.001), ED use (RR = 0.31 versus 0.69, ratio of RRs = 0.45, p < 0.001), and doctors' office visits (RR = 0.21 versus 0.52, ratio of RRs = 0.41, p < 0.001). Sensitivity analyses were carried out to assess consistency, specificity, and the presence of a dose-response relationship. Limitations of this study include the ecological study design, the nonspecific outcomes, difficulty in modeling baseline events, data quality and availability, and the inability to control for potentially important confounders.
Conclusions
Compared to targeted programs in other provinces, introduction of universal vaccination in Ontario in 2000 was associated with relative reductions in influenza-associated mortality and health care use. The results of this large-scale natural experiment suggest that universal vaccination may be an effective public health measure for reducing the annual burden of influenza.
Comparing influenza-related mortality and health care use between Ontario and other Canadian provinces, Jeffrey Kwong and colleagues find evidence that Ontario's universal vaccination program has reduced the burden of influenza.
Editors' Summary
Background.
Seasonal outbreaks (epidemics) of influenza—a viral disease of the nose, throat, and airways—affect millions of people and kill about 500,000 individuals every year. These epidemics occur because of “antigenic drift”: small but frequent changes in the viral proteins to which the human immune system responds mean that an immune response produced one year by exposure to an influenza virus provides only partial protection against influenza the next year. Immunization can boost this natural immunity and reduce a person's chances of catching influenza. That is, an injection of killed influenza viruses can be used to prime the immune system so that it responds quickly and efficiently when exposed to live virus. However, because of antigenic drift, for influenza immunization to be effective, it has to be repeated annually with a vaccine that contains the major circulating strains of the influenza virus.
Why Was This Study Done?
Public-health organizations recommend targeted vaccination programs, so that elderly people, infants, and chronically ill individuals—the people most likely to die from pneumonia and other complications of influenza—receive annual influenza vaccination. Some experts argue, however, that universal vaccination might provide populations with better protection from influenza, both directly by increasing the number of vaccinated people and indirectly through “herd immunity,” which occurs when a high proportion of the population is immune to an infectious disease, so that even unvaccinated people are unlikely to become infected (because infected people rarely come into contact with susceptible people). In this study, the researchers compare the effects of the world's first free universal influenza immunization program (UIIP), which started in 2000 in the Canadian province of Ontario, on influenza-associated deaths and health care use with the effects of targeted vaccine programs on the same outcomes elsewhere in Canada.
What Did the Researchers Do and Find?
Using national records, the researchers collected data on influenza vaccination, on all deaths, and on hospitalizations for pneumonia and influenza in all Canadian provinces between 1997 and 2004. They also collected data on emergency department and doctors' office visits for pneumonia and influenza for Ontario, Quebec, Alberta, and Manitoba. They then used a mathematical model to estimate the baseline rates for these outcomes in the absence of influenza activity, and from these calculated weekly rates for deaths and health care use specifically resulting from influenza. In 1996–1997, 18% of the population was vaccinated against influenza in Ontario whereas in the other provinces combined the vaccination rate was 13%. On average, since 2000—the year in which UIIP was introduced in Ontario—vaccination rates have risen to 38% and 24% in Ontario and the other provinces, respectively. Since the introduction of UIIP, the researchers report, influenza-associated deaths have decreased by 74% in Ontario but by only 57% in the other provinces combined. Influenza-associated use of health care facilities has also decreased more in Ontario than in the other provinces over the same period.
What Do These Findings Mean?
These findings are limited by some aspects of the study design. For example, they depend on the accuracy of the assumptions made when calculating events due specifically to influenza, and on the availability and accuracy of vaccination and clinical outcome data. In addition, it is possible that influenza-associated deaths and health care use may have decreased more in Ontario than in the other Canadian provinces because of some unrecognized health care changes specific to Ontario but unrelated to the introduction of universal influenza vaccination. Nevertheless, these findings indicate that, compared to the targeted vaccination programs in the other Canadian provinces, the Ontarian UIIP is associated with reductions in influenza-associated deaths and health care use, particularly in people younger than 65 years old. This effect is seen at a level of vaccination unlikely to produce herd immunity so might be more marked if the uptake of vaccination could be further increased. Thus, although it is possible that Canada is a special case, these findings suggest that universal influenza vaccination might be an effective way to reduce the global burden of influenza.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050211.
Read the related PLoSMedicine Perspective by Cécile Viboud and Mark Miller
A related PLoSMedicine Research Article by Carline van den Dool and colleagues is also available
The Ontario Ministry of Health provides information on its universal influenza immunization program (in English and French)
The World Health Organization provides information on influenza and on influenza vaccines (in several languages)
The US Centers for Disease Control and Prevention provide information for patients and professionals on all aspects of influenza (in English and Spanish)
MedlinePlus provides a list of links to other information about influenza (in English and Spanish)
The UK National Health Service provides information about the science of immunization, including a simple explanatory animation of immunity
doi:10.1371/journal.pmed.0050211
PMCID: PMC2573914  PMID: 18959473
11.  In Search of Integrated Specificity: Comment on Denson, Spanovic, and Miller (2009) 
Psychological bulletin  2009;135(6):854-856.
Psychologists have long been interested in the integrated specificity hypothesis, which maintains that stressors elicit fairly distinct behavioral, emotional, and biological responses, molded by selective pressures to meet specific demands from the environment. This issue of Psychological Bulletin features a meta-analytic review of the evidence for this proposition by Denson, Spanovic, and Miller (2009). It concludes that the meta-analytic findings support the “core concept behind the integrated specificity model (p. XX)” and reveal that “within the context of a stressful event, organisms produce an integrated and coordinated response at multiple levels (i.e., cognitive, emotional, physiological; p. XX).” In this commentary I argue that conclusions like this are unwarranted given the data. Aside from some effects for cortisol, in fact, there was little evidence of specificity, and most of the significant findings reported would be expected by chance alone. I also contend that Denson et al. fail to consider some important sources of evidence bearing on the specificity hypothesis, particularly how appraisals and emotions couple with autonomic nervous system endpoints and functional indices of immune response. If selective pressures did give rise to an integrated stress response, such pathways almost certainly would have been involved. By omitting such outcomes from the meta-analysis, the authors have overlooked what are probably the most definitive tests of the specificity hypothesis. As a result, the field is back where it started: with a lot of affection for the concept of integrated specificity, but little in the way of definitive evidence to refute or accept it.
doi:10.1037/a0017440
PMCID: PMC2774222  PMID: 19883138
12.  Global Entrainment of Transcriptional Systems to Periodic Inputs 
PLoS Computational Biology  2010;6(4):e1000739.
This paper addresses the problem of providing mathematical conditions that allow one to ensure that biological networks, such as transcriptional systems, can be globally entrained to external periodic inputs. Despite appearing obvious at first, this is by no means a generic property of nonlinear dynamical systems. Through the use of contraction theory, a powerful tool from dynamical systems theory, it is shown that certain systems driven by external periodic signals have the property that all their solutions converge to a fixed limit cycle. General results are proved, and the properties are verified in the specific cases of models of transcriptional systems as well as constructs of interest in synthetic biology. A self-contained exposition of all needed results is given in the paper.
Author Summary
The activities of living organisms are governed by complex sets of biochemical reactions. Often, entrainment to certain external signals helps control the timing and sequencing of reactions. An important open problem is to understand the onset of entrainment and under what conditions it can be ensured in the presence of uncertainties, noise, and environmental variations. In this paper, we focus mainly on transcriptional systems, modeled by Ordinary Differential Equations. These are basic building blocks for more complex biochemical systems. However, the results that we obtain are of more generality. To illustrate this generality, and to emphasize the use of our techniques in synthetic biology, we discuss the entrainment of a Repressilator circuit and the synchronization of a network of Repressilators. We answer the following two questions: 1) What are the dynamical mechanisms that ensure the entrainment to periodic inputs in transcriptional modules? 2) Starting from natural systems, what properties can be used to design novel synthetic biological circuits that can be entrained? For some biological systems which are always “in contact” with a continuously changing environment, entrainment may be a “desired” property. Thus, answering the above two questions is of fundamental importance. While entrainment may appear obvious at first thought, it is not a generic property of nonlinear dynamical systems. The main result of our paper shows that, even if the transcriptional modules are modeled by nonlinear ODEs, they can be entrained by any (positive) periodic signal. Surprisingly, such a property is preserved if the system parameters are varied: entrainment is obtained independently of the particular biochemical conditions. We prove that combinations of the above transcriptional module also show the same property. Finally, we show how the developed tools can be applied to design synthetic biochemical systems guaranteed to exhibit entrainment.
doi:10.1371/journal.pcbi.1000739
PMCID: PMC2855316  PMID: 20418962
13.  Governance of Health Systems Comment on “A Network Based Theory of Health Systems and Cycles of Well-Being”  
Health systems research aims to understand the governance of health systems (i.e. how health systems function and perform and how their actors interact with each other). This can be achieved by applying innovative methodologies and concepts that are going to capture the complexity and dynamics of health systems when they are affected by shocks. The capacity of health systems to adapt to shocks (i.e. the resilience of health systems) is a new area of investigation. Social network analysis is a great avenue that can help measure the properties of systems and analyse the relationships between its actors and between the structure of a health system and the performance of a health system. A new conceptual framework is presented to define the governance of health systems using a resilience perspective.
doi:10.15171/ijhpm.2013.31
PMCID: PMC3937924  PMID: 24596859
Health Systems; Social Network Analysis; Governance; Resilience
14.  Can Prenatal Malaria Exposure Produce an Immune Tolerant Phenotype?: A Prospective Birth Cohort Study in Kenya 
PLoS Medicine  2009;6(7):e1000116.
In a prospective cohort study of newborns residing in a malaria holoendemic area of Kenya, Christopher King and colleagues find a subset of children born to malaria-infected women who acquire a tolerant phenotype, which persists into childhood and is associated with increased susceptibility to malarial infection and anemia.
Background
Malaria in pregnancy can expose the fetus to malaria-infected erythrocytes or their soluble products, thereby stimulating T and B cell immune responses to malaria blood stage antigens. We hypothesized that fetal immune priming, or malaria exposure in the absence of priming (putative tolerance), affects the child's susceptibility to subsequent malaria infections.
Methods and Findings
We conducted a prospective birth cohort study of 586 newborns residing in a malaria-holoendemic area of Kenya who were examined biannually to age 3 years for malaria infection, and whose malaria-specific cellular and humoral immune responses were assessed. Newborns were classified as (i) sensitized (and thus exposed), as demonstrated by IFNγ, IL-2, IL-13, and/or IL-5 production by cord blood mononuclear cells (CBMCs) to malaria blood stage antigens, indicative of in utero priming (n = 246), (ii) exposed not sensitized (mother Plasmodium falciparum [Pf]+ and no CBMC production of IFNγ, IL-2, IL-13, and/or IL-5, n = 120), or (iii) not exposed (mother Pf−, no CBMC reactivity, n = 220). Exposed not sensitized children had evidence for prenatal immune experience demonstrated by increased IL-10 production and partial reversal of malaria antigen-specific hyporesponsiveness with IL-2+IL-15, indicative of immune tolerance. Relative risk data showed that the putatively tolerant children had a 1.61 (95% confidence interval [CI] 1.10–2.43; p = 0.024) and 1.34 (95% CI 0.95–1.87; p = 0.097) greater risk for malaria infection based on light microscopy (LM) or PCR diagnosis, respectively, compared to the not-exposed group, and a 1.41 (95%CI 0.97–2.07, p = 0.074) and 1.39 (95%CI 0.99–2.07, p = 0.053) greater risk of infection based on LM or PCR diagnosis, respectively, compared to the sensitized group. Putatively tolerant children had an average of 0.5 g/dl lower hemoglobin levels (p = 0.01) compared to the other two groups. Exposed not sensitized children also had 2- to 3-fold lower frequency of malaria antigen-driven IFNγ and/or IL-2 production (p<0.001) and higher IL-10 release (p<0.001) at 6-month follow-ups, when compared to sensitized and not-exposed children. Malaria blood stage–specific IgG antibody levels were similar among the three groups.
Conclusions
These results show that a subset of children exposed to malaria in utero acquire a tolerant phenotype to blood-stage antigens that persists into childhood and is associated with an increased susceptibility to malaria infection and anemia. This finding could have important implications for malaria vaccination of children residing in endemic areas.
Please see later in the article for Editors' Summary
Editors' Summary
Background
Each year, Plasmodium falciparum, a mosquito-borne parasite, causes about 500 million cases of malaria and about one million people die as a result. Most of these deaths occur in young children in sub-Saharan Africa. Indeed, malaria accounts for a fifth of all childhood deaths in Africa, which makes it one of the most important childhood infectious diseases in this region. Very young children—those up to 6 months old—are relatively resistant to high-density parasitaemia and to clinical malaria, but children between 6 and 36 months old have an increased susceptibility to parasitaemia and to clinical malaria. Parasitaemia is the presence of P. falciparum parasites in the blood; a high density of blood-stage parasites causes the symptoms of clinical malaria (including high fever) and life-threatening organ damage and anemia (a lack of red blood cells).
Why Was This Study Done?
The age-dependent pattern of susceptibility to malaria suggests that young babies are protected by antibodies provided by their mothers, but that by 6 months old, when these antibodies have largely disappeared, babies have not yet fully developed their own anti-malaria immunity. However, little is known about the acquisition of anti-malaria immunity in infants, a process that needs to be understood in order to design effective vaccines for this age group. In particular, it is unclear how maternal malaria infection affects the acquisition of anti-malaria immunity. Malaria in pregnancy may expose the unborn child to malaria-infected red blood cells and to soluble malaria antigens (molecules that the immune system recognizes as foreign). This exposure could increase or decrease the child's immune responses to blood-stage malaria antigens and thus affect his/her ability to fight off malaria. In this study, the researchers investigated how prenatal malaria exposure affects anti-malaria immunity in young children and their susceptibility to subsequent malaria infections.
What Did the Researchers Do and Find?
The researchers determined which of 586 newborn babies enrolled into their study in an area of Kenya where malaria is very common had been exposed to P. falciparum before birth by looking for parasites in their mother's blood at delivery. They looked for malaria-specific immune responses in T cells (a type of immune system cell) in the newborn babies' cord blood by measuring the production of cytokines (molecules that either activate or inhibit the immune system) by these cells after exposure to malaria antigens. Finally, they examined the infants twice yearly for 3 years for malaria infection, malaria-specific immune responses, and anemia. The researchers classified the babies into three groups; cord blood cells of “sensitized” babies made activating cytokines in response to malaria antigens; cord blood cells of “exposed, not-sensitized” babies did not make activating cytokines but made an inhibitory cytokine (IL-10); and “not-exposed” babies were born to mothers with no P. falciparum infection at delivery. In their first 3 years of life, the exposed, not-sensitized group had a 60% greater risk of malaria infection (measured by counting parasites in their blood) than the unexposed group and a slightly higher risk of malaria infection than the sensitized group. They also had lower hemoglobulin levels (a sign of anemia) than the other babies. At age 6 months, the T cells of exposed, not-sensitized children were less likely to make activating cytokines in response to malaria antigens but made more IL-10 than the T cells of the other children; malaria-specific antibody levels were similar in the three groups.
What Do These Findings Mean?
These findings suggest that some children who are exposed to malaria before birth become “tolerant” to blood-stage malaria antigens. Exposure to malaria antigens before birth “tricks” their T cells into recognizing these antigens as self antigens. This immune tolerance, which persists into childhood, reduces the ability of the immune system to attack and destroy parasites and increases the susceptibility of these tolerant children to malaria infection. Why some children who are exposed to malaria before birth become tolerant while exposure to malaria antigens “primes” the immune system of other children to respond efficiently to these antigens is not clear. However, these findings could have important implications for the design of malaria vaccines for use in areas where children are often exposed to malaria before birth and for the design of strategies for the prevention of malaria during pregnancy.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1000116.
This study is further discussed in a PLoS Medicine Perspective by Lars Hviid
Information is available from the World Health Organization on malaria (in several languages)
The US Centers for Disease Control and Prevention provides information on malaria (in English and Spanish)
Information is available from the Roll Back Malaria Partnership on all aspects of global malaria control, including information on malaria in pregnancy and on children and malaria
MedlinePlus provides links to additional information on malaria (in English and Spanish)
doi:10.1371/journal.pmed.1000116
PMCID: PMC2707618  PMID: 19636353
15.  Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion 
PLoS Computational Biology  2012;8(3):e1002449.
Several models of flocking have been promoted based on simulations with qualitatively naturalistic behavior. In this paper we provide the first direct application of computational modeling methods to infer flocking behavior from experimental field data. We show that this approach is able to infer general rules for interaction, or lack of interaction, among members of a flock or, more generally, any community. Using experimental field measurements of homing pigeons in flight we demonstrate the existence of a basic distance dependent attraction/repulsion relationship and show that this rule is sufficient to explain collective behavior observed in nature. Positional data of individuals over time are used as input data to a computational algorithm capable of building complex nonlinear functions that can represent the system behavior. Topological nearest neighbor interactions are considered to characterize the components within this model. The efficacy of this method is demonstrated with simulated noisy data generated from the classical (two dimensional) Vicsek model. When applied to experimental data from homing pigeon flights we show that the more complex three dimensional models are capable of simulating trajectories, as well as exhibiting realistic collective dynamics. The simulations of the reconstructed models are used to extract properties of the collective behavior in pigeons, and how it is affected by changing the initial conditions of the system. Our results demonstrate that this approach may be applied to construct models capable of simulating trajectories and collective dynamics using experimental field measurements of herd movement. From these models, the behavior of the individual agents (animals) may be inferred.
Author Summary
The construction of mathematical models from experimental time-series data has been considered with some success in many areas of science and engineering, using the power of computer algorithms to build model structures and suitably tuning their parameters. When considering complex systems with nonlinear or collective behavior, computational models built from real data are the alternative to emulating the system as best as possible, since classic modeling approaches based on observation could prove difficult for complex dynamics. In this study, we provide a method to build models of collective dynamics from homing pigeon flight data. We show that our models follow the source dynamics well, and from them we are able to infer that significant collective behavior occurs in pigeon flights. Our results are consistent with the basic principles of previous hypotheses and models that have been proposed. Our approach serves as an initial outline towards the usage of experimental data to construct computational models to understand many complex phenomena with hypothesized collective behavior.
doi:10.1371/journal.pcbi.1002449
PMCID: PMC3315451  PMID: 22479176
16.  Biomedical Engineering Strategies in System Design Space 
Annals of biomedical engineering  2011;39(4):1278-1295.
Modern systems biology and synthetic bioengineering face two major challenges in relating properties of the genetic components of a natural or engineered system to its integrated behavior. The first is the fundamental unsolved problem of relating the digital representation of the genotype to the analog representation of the parameters for the molecular components. For example, knowing the DNA sequence does not allow one to determine the kinetic parameters of an enzyme. The second is the fundamental unsolved problem of relating the parameters of the components and the environment to the phenotype of the global system. For example, knowing the parameters does not tell one how many qualitatively distinct phenotypes are in the organism's repertoire or the relative fitness of the phenotypes in different environments. These also are challenges for biomedical engineers as they attempt to develop therapeutic strategies to treat pathology or to redirect normal cellular functions for biotechnological purposes. In this article, the second of these fundamental challenges will be addressed, and the notion of a “system design space” for relating the parameter space of components to the phenotype space of bioengineering systems will be focused upon. First, the concept of a system design space will be motivated by introducing one of its key components from an intuitive perspective. Second, a simple linear example will be used to illustrate a generic method for constructing the design space in which qualitatively distinct phenotypes can be identified and counted, their fitness analyzed and compared, and their tolerance to change measured. Third, two examples of nonlinear systems from different areas of biomedical engineering will be presented. Finally, after giving reference to a few other applications that have made use of the system design space approach to reveal important design principles, some concluding remarks concerning challenges and opportunities for further development will be made.
doi:10.1007/s10439-010-0220-2
PMCID: PMC3074507  PMID: 21203848
Power-law formalism; Biochemical systems theory; Global tolerance; Pharmacokinetics; Targeted molecular imaging; Cellular biomechanics
17.  Lack of Mucosal Immune Reconstitution during Prolonged Treatment of Acute and Early HIV-1 Infection 
PLoS Medicine  2006;3(12):e484.
Background
During acute and early HIV-1 infection (AEI), up to 60% of CD4+ T cells in the lamina propria of the lower gastrointestinal (GI) tract are lost as early as 2–4 wk after infection. Reconstitution in the peripheral blood during therapy with highly active antiretroviral therapy (HAART) is well established. However, the extent of immune reconstitution in the GI tract is unknown.
Methods and Findings
Fifty-four AEI patients and 18 uninfected control participants underwent colonic biopsy. Forty of the 54 AEI patients were followed after initiation of antiretroviral therapy (18 were studied longitudinally with sequential biopsies over a 3-y period after beginning HAART, and 22 were studied cross sectionally after 1–7 y of uninterrupted therapy). Lymphocyte subsets, markers of immune activation and memory in the peripheral blood and GI tract were determined by flow cytometry and immunohistochemistry. In situ hybridization was performed in order to identify persistent HIV-1 RNA expression. Of the patients studied, 70% maintained, on average, a 50%–60% depletion of lamina propria lymphocytes despite 1–7 y of HAART. Lymphocytes expressing CCR5 and both CCR5 and CXCR4 were persistently and preferentially depleted. Levels of immune activation in the memory cell population, CD45RO+ HLA-DR+, returned to levels seen in the uninfected control participants in the peripheral blood, but were elevated in the GI tract of patients with persistent CD4+ T cell depletion despite therapy. Rare HIV-1 RNA–expressing cells were detected by in situ hybridization.
Conclusions
Apparently suppressive treatment with HAART during acute and early infection does not lead to complete immune reconstitution in the GI mucosa in the majority of patients studied, despite immune reconstitution in the peripheral blood. Though the mechanism remains obscure, the data suggest that there is either viral or immune-mediated accelerated T cell destruction or, possibly, alterations in T cell homing to the GI tract. Although clinically silent over the short term, the long-term consequences of the persistence of this lesion may emerge as the HIV-1–infected population survives longer owing to the benefits of HAART.
Despite early initiation of anti-HIV therapy, loss of T cells in the gastrointestinal mucosa persisted for years in most members of a clinical cohort identified early after HIV-1 infection.
Editors' Summary
Background.
AIDS causes disease by inactivating the body's immune response against infection. The AIDS virus (HIV) is most active against the white blood cells called T lymphocytes, particularly the CD4 T lymphocytes, which recognize infection and activate other cells of the immune system to fight it. In what was formerly believed to be a gradual process, HIV infection is now known to deplete a subset of the body's CD4 lymphocytes, called memory cells, quite rapidly—over only a few days—within a few weeks after a person becomes infected with the AIDS virus. This was not known until recently because researchers were counting CD4 cells only in blood, while a majority of the memory lymphocytes are located in and around the digestive system. It is these intestinal memory lymphocytes that are rapidly wiped out, while those in the blood fall much more gradually, usually over several years. Few studies of mucosal lymphocytes have been done in humans because such studies require biopsies of the intestinal lining (mucosa).
Why Was This Study Done?
Although CD4 cells in the blood can return and remain at normal levels when HIV infection is treated with antiviral drugs, it has been unclear as to whether the mucosal CD4 cells return as well. People who begin treatment as soon as possible after becoming infected with HIV might seem to have the best chance of regaining their mucosal immunity, compared to those who wait until the CD4 cells in their blood have fallen, which is a generally accepted reason to start medication for HIV. Therefore, the researchers wanted to see whether people who start treatment early after becoming infected with HIV might experience restoration of their mucosal immunity over time and, if so, what kinds of lymphocytes would return.
What Did the Researchers Do and Find?
The researchers studied people who started treatment for HIV within a few weeks to months of becoming infected and who then remained on treatment. Some volunteers underwent biopsies of the intestinal mucosa before starting treatment and then at various points from 1 y until as long as 3 y after infection. Others volunteered for biopsy only one time, anywhere from less than 1 y to 7 y following treatment. The biopsy specimens were examined under the microscope and with a technique called flow cytometry using specific staining methods to assess their structure and functional characteristics. Results were compared to biopsies from a group of HIV-uninfected volunteers.
The researchers found that the percentage of CD4 lymphocytes dropped much lower in the intestinal mucosa than in blood during early infection and then, unlike in blood, remained low even after several years of treatment for HIV. In the microscope images, they found that mucosal CD4 cells were lost mostly from regions of active battle against invading germs, rather than from “training sites” for new CD4 cells. Over time, only 30% of the volunteers showed return of CD4 cells to normal levels in these active sites.
Unlike T lymphocytes in the blood, which tend to return to a resting state after HIV is treated, the T lymphocytes in the intestinal mucosa tended to persist in an activated state despite HIV treatment, even though only a tiny fraction of these cells were found to be infected with HIV. A high level of activation of mucosal lymphocytes soon after infection was found to predict poor restoration of mucosal CD4 cells over time.
What Do These Findings Mean?
These experiments confirm that studying easily obtained blood lymphocytes provides only a limited view of how HIV affects the immune system as a whole. The finding that immune cells of the intestinal mucosa remain depleted and over-activated for years despite antiretroviral treatment raises the concern that over time this will result in clinical problems. Fortunately, this does not appear to be the case in most people currently being treated for HIV, some for as long as 10 y, but the results of this study suggest that we should remain vigilant for gastrointestinal problems resulting from impaired immunity over time. The finding that mucosal lymphocytes do appear to return to normal levels in a minority of volunteers is of interest, and suggests that early interventions to reduce activation of intestinal T cells (such as antimicrobial or immunomodulatory treatment) might be worth investigating in those recently infected with HIV. Finally, these results suggest that a vaccine to prevent HIV may need to stimulate immune responses that can act very quickly following infection, before the bulk of lymphocytes capable of countering the infection are lost, perhaps irreversibly.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0030484.
UCSF HIV InSite includes resources on HIV immunology and vaccine development
AIDS fact sheets and brochures from the US National Institute of Allergy and Infectious Diseases
Medline Plus article on acute HIV infection from the US National Library of Medicine
doi:10.1371/journal.pmed.0030484
PMCID: PMC1762085  PMID: 17147468
18.  Basic research in HIV vaccinology is hampered by reductionist thinking 
This review describes the structure-based reverse vaccinology approach aimed at developing vaccine immunogens capable of inducing antibodies that broadly neutralize HIV-1. Some basic principles of protein immunochemistry are reviewed and the implications of the extensive polyspecificity of antibodies for vaccine development are underlined. Although it is natural for investigators to want to know the cause of an effective immunological intervention, the classic notion of causality is shown to have little explanatory value for a system as complex as the immune system, where any observed effect always results from many interactions between a large number of components. Causal explanations are reductive because a single factor is singled out for attention and given undue explanatory weight on its own. Other examples of the negative impact of reductionist thinking on HIV vaccine development are discussed. These include (1) the failure to distinguish between the chemical nature of antigenicity and the biological nature of immunogenicity, (2) the belief that when an HIV-1 epitope is reconstructed by rational design to better fit a neutralizing monoclonal antibody (nMab), this will produce an immunogen able to elicit Abs with the same neutralizing capacity as the Ab used as template for designing the antigen, and (3) the belief that protection against infection can be analyzed at the level of individual molecular interactions although it has meaning only at the level of an entire organism. The numerous unsuccessful strategies that have been used to design HIV-1 vaccine immunogens are described and it is suggested that the convergence of so many negative experimental results justifies the conclusion that reverse vaccinology is unlikely to lead to the development of a preventive HIV-1 vaccine. Immune correlates of protection in vaccines have not yet been identified because this will become feasible only retrospectively once an effective vaccine exists. The finding that extensive antibody affinity maturation is needed to obtain mature anti-HIV-1 Abs endowed with a broad neutralizing capacity explains why antigens designed to fit matured Mabs are not effective vaccine immunogens since these are administered to naive recipients who possess only B-cell receptors corresponding to the germline version of the matured Abs.
doi:10.3389/fimmu.2012.00194
PMCID: PMC3391733  PMID: 22787464
antibody affinity maturation; antibody polyspecificity; discontinuous protein epitopes; HIV vaccines; rational vaccine design; reductionism; reverse vaccinology; systems biology
19.  Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells 
PLoS Computational Biology  2012;8(5):e1002526.
The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are classic examples of the complex adaptation of innate immune cells. Upon repetitive exposures to different doses of bacterial endotoxin (lipopolysaccharide) or other stimulants, macrophages show either suppressed or augmented inflammatory responses compared to a single exposure to the stimulant. Endotoxin tolerance and priming are critically involved in both immune homeostasis and the pathogenesis of diverse inflammatory diseases. However, the underlying molecular mechanisms are not well understood. By means of a computational search through the parameter space of a coarse-grained three-node network with a two-stage Metropolis sampling approach, we enumerated all the network topologies that can generate priming or tolerance. We discovered three major mechanisms for priming (pathway synergy, suppressor deactivation, activator induction) and one for tolerance (inhibitor persistence). These results not only explain existing experimental observations, but also reveal intriguing test scenarios for future experimental studies to clarify mechanisms of endotoxin priming and tolerance.
Author Summary
Inflammation is a fundamental response of animals to pathogen invasion. Among the first responders are macrophage cells, which identify and respond to multiple challenges. Their responses must be carefully regulated to kill invading pathogens without causing too much damage to host cells. Excessive activity of macrophages is associated with serious diseases like sclerosis and cancer. Macrophage responses are governed by a complex signaling network that receives cues, integrates information, implements appropriate responses and communicates with neighboring cells. This network must maintain a short-term memory of pathogen exposure. Endotoxin priming is an example. If macrophages are exposed to a small dose of bacterial toxins, they are primed to respond strongly to a second exposure to a large dose of toxin. Endotoxin tolerance, on the other hand, refers to the fact that macrophages are resistant to endotoxin challenges after a large dose pretreatment. The precise molecular mechanisms of both priming and tolerance are still poorly understood. Through computational systems biology, we have identified basic regulatory motifs for priming and for tolerance. Using information from databases and the literature, we have identified molecules that may contribute to priming and tolerance effects. Our methods are generally applicable to other types of cellular responses.
doi:10.1371/journal.pcbi.1002526
PMCID: PMC3355072  PMID: 22615556
20.  Toward an Understanding of Disengagement from HIV Treatment and Care in Sub-Saharan Africa: A Qualitative Study 
PLoS Medicine  2013;10(1):e1001369.
Norma Ware and colleagues conducted a large qualitative study among patients in HIV treatment programs in sub-Saharan Africa to investigate reasons for missed visits and provide an explanation for disengagement from care.
Background
The rollout of antiretroviral therapy in sub-Saharan Africa has brought lifesaving treatment to millions of HIV-infected individuals. Treatment is lifelong, however, and to continue to benefit, patients must remain in care. Despite this, systematic investigations of retention have repeatedly documented high rates of loss to follow-up from HIV treatment programs. This paper introduces an explanation for missed clinic visits and subsequent disengagement among patients enrolled in HIV treatment and care programs in Africa.
Methods and Findings
Eight-hundred-ninety patients enrolled in HIV treatment programs in Jos, Nigeria; Dar es Salaam, Tanzania; and Mbarara, Uganda who had extended absences from care were tracked for qualitative research interviews. Two-hundred-eighty-seven were located, and 91 took part in the study. Interview data were inductively analyzed to identify reasons for missed visits and to assemble them into a broader explanation of how missed visits may develop into disengagement. Findings reveal unintentional and intentional reasons for missing, along with reluctance to return to care following an absence. Disengagement is interpreted as a process through which missed visits and ensuing reluctance to return over time erode patients' subjective sense of connectedness to care.
Conclusions
Missed visits are inevitable over a lifelong course of HIV care. Efforts to prevent missed clinic visits combined with moves to minimize barriers to re-entry into care are more likely than either approach alone to keep missed visits from turning into long-term disengagement.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
The human immunodeficiency virus (HIV) infects cells of the immune system, destroying or impairing their function. As the infection progresses, the immune system becomes weaker, and the affected person becomes more susceptible to life-threatening infections. Over the past three decades, 25 million people have died from HIV, and according to the World Health Organization, in 2011, there were roughly 34.2 million people living with HIV, over 60% of whom lived in sub-Saharan Africa. Although HIV cannot be cured, the virus can be suppressed by combination antiretroviral therapy (ART) consisting of three or more antiretroviral drugs. ART controls viral replication and strengthens the immune system, allowing the affected person to fight off infections. With ART, HIV can be managed as a chronic disease: people living with HIV can live healthy lives as long as they take antiretroviral drugs regularly for the rest of their lives.
Why Was This Study Done?
Unfortunately, poor retention in HIV programs is a huge problem: a large proportion—30%–60% in some settings in sub-Saharan Africa—of people starting ART, are lost to follow-up and stop taking treatment. Few studies have looked in depth at the reasons why people with HIV in sub-Saharan Africa miss clinic appointments or even stop coming altogether. So in this study in Tanzania, Uganda, and Nigeria, the researchers did a qualitative analysis from the patients' perspective on the reasons for missing clinic visits. Qualitative research can use information-gathering techniques, such as open-ended interviews, to develop an in-depth understanding of human behavior and the reasons behind such behavior.
What Did the Researchers Do and Find?
The researchers indentified people to interview by using “tracking lists” from HIV/AIDS care clinics in the three countries—patient tracking by clinical trackers is increasingly used as a way to contact patients who have missed clinic appointments. The researchers included people in the study who had been tracked and contacted by clinic trackers, had been absent from the clinic for three months or more, and gave consent to be re-contacted by the researchers. The researchers interviewed participants, using their local language, on several topics, including their experiences of care at the clinic and of tracking, and the circumstances of missed appointments. The detailed accounts were transcribed, and then the researchers categorized the reasons for missing appointments into intentional and unintentional reasons.
Eight-hundred-ninety patients in the three countries were tracked during the study period, but only 287 were located, of whom 91 participated in the study. Of the 91 participants, 76 were being prescribed ART, and 15 had not started treatment. The main unintentional reason for missing clinic visits was a conflicting demand on the patients' time, which was often unexpected and for complex reasons, such as caring for a dying relative, going to a funeral, or traveling to work. These reasons were often transient and changed over time. Intentional reasons were often related to dissatisfaction with the care received at the clinic, especially “the harsh treatment” they received from health workers, which typically referred to behavior perceived by patients to be rude. For example, participants reported being spoken to “roughly” or feeling that the clinic staff “didn't care.” Such behavior made patients feel hurt, humiliated, and angry, and reluctant to return to the clinic. The researchers found that, overall, disengagement from care appeared to be a process through which missed visits and subsequent reluctance to return over time eroded patients' sense of connectedness to care.
What Do These Findings Mean?
Absences from care will be inevitable over a lifetime course of treatment for HIV/AIDS. These findings indicate that absences may be unintentional as well as intentional, and that the reasons are complex and can change over time. Initial reasons for missing may disappear, leaving patients free, but reluctant, to return to care. Reasons for reluctance include shame at having been absent and the anticipation of a negative response to return from care providers. Patient education for ART initiation in sub-Saharan Africa often includes stern warnings about the lifelong commitment beginning ART represents. Paradoxically, educational efforts intended to maximize the benefits of ART for patients may be driving some away from care. Therefore, efforts to prevent missed clinic visits coupled with strategies to minimize any obstacles to coming back to care are necessary to keep patients' missed visits from turning into long-term disengagement from treatment.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001369.
This study is further discussed in a PLOS Medicine Perspective by Edward Mills
The World Health Organization has the latest data on access to ART
The US National Institute of Allergy and Infectious Diseases has more information on types of ART, and also on adherence to treatment
The US Centers for Disease Control and Prevention has some information about interventions to help improve adherence
doi:10.1371/journal.pmed.1001369
PMCID: PMC3541407  PMID: 23341753
21.  A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells 
PLoS Computational Biology  2011;7(7):e1002122.
The reciprocal differentiation of T helper 17 (TH17) cells and induced regulatory T (iTreg) cells plays a critical role in both the pathogenesis and resolution of diverse human inflammatory diseases. Although initial studies suggested a stable commitment to either the TH17 or the iTreg lineage, recent results reveal remarkable plasticity and heterogeneity, reflected in the capacity of differentiated effectors cells to be reprogrammed among TH17 and iTreg lineages and the intriguing phenomenon that a group of naïve precursor CD4+ T cells can be programmed into phenotypically diverse populations by the same differentiation signal, transforming growth factor beta. To reconcile these observations, we have built a mathematical model of TH17/iTreg differentiation that exhibits four different stable steady states, governed by pitchfork bifurcations with certain degrees of broken symmetry. According to the model, a group of precursor cells with some small cell-to-cell variability can differentiate into phenotypically distinct subsets of cells, which exhibit distinct levels of the master transcription-factor regulators for the two T cell lineages. A dynamical control system with these properties is flexible enough to be steered down alternative pathways by polarizing signals, such as interleukin-6 and retinoic acid and it may be used by the immune system to generate functionally distinct effector cells in desired fractions in response to a range of differentiation signals. Additionally, the model suggests a quantitative explanation for the phenotype with high expression levels of both master regulators. This phenotype corresponds to a re-stabilized co-expressing state, appearing at a late stage of differentiation, rather than a bipotent precursor state observed under some other circumstances. Our simulations reconcile most published experimental observations and predict novel differentiation states as well as transitions among different phenotypes that have not yet been observed experimentally.
Author Summary
In order to perform complex functions upon pathogenic challenges, the immune system needs to efficiently deploy a repertoire of specialized cells by inducing the differentiation of precursor cells into effector cells. In a critical process of the adaptive immune system, one common type of precursor cell can give rise to both T helper 17 cells and regulatory T cells, which have distinct phenotypes and functions. Recent discoveries have revealed a certain heterogeneity in this reciprocal differentiation system. In particular, treating precursor cells with a single differentiation signal can result in a remarkably diverse population. An understanding of such variable responses is limited by a lack of quantitative models. Our mathematical model of this cell differentiation system reveals how the control system generates phenotypic diversity and how its final state can be regulated by various signals. The model suggests a new quantitative explanation for the scenario in which the master regulators of two different T cell lineages can be highly expressed in a single cell. The model provides a new framework for understanding the dynamic properties of this type of regulatory network and the mechanisms that help to maintain a balance of effector cells during the inflammatory response to infection.
doi:10.1371/journal.pcbi.1002122
PMCID: PMC3145653  PMID: 21829337
22.  Interplay between innate and adaptive immunity in the development of non infectious uveitis 
In vertebrates, the innate and adaptive immune systems have evolved seamlessly to protect the host by rapidly responding to danger signals, eliminating pathogens and creating immunological memory as well as immunological tolerance to self. The innate immune system harnesses receptors that recognize conserved pathogen patterns and alongside the more specific recognition systems and memory of adaptive immunity, their interplay is evidenced by respective roles during generation and regulation of immune responses. The hallmark of adaptive immunity which requires engagement of innate immunity is an ability to discriminate between self and non-self (and eventually between pathogen and symbiont) as well as peripheral control mechanisms maintaining immunological health and appropriate responses. Loss of control mechanisms and/or regulation of either the adaptive or the innate immune system lead to autoimmunity and autoinflammation respectively. Although autoimmune pathways have been largely studied to date in the context of development of non-infectious intraocular inflammation, the recruitment and activation of innate immunity is required for full expression of the varied phenotypes of non-infectious uveitis. Since autoimmunity and autoinflammation implicate different molecular pathways, even though some convergence occurs, increasing our understanding of their respective roles in the development of uveitis will highlight treatment targets and influence our understanding of immune mechanisms operative in other retinal diseases. Herein, we extrapolate from the basic mechanisms of activation and control of innate and adaptive immunity to how autoinflammatory and autoimmune pathways contribute to disease development in non-infectious uveitis patients.
doi:10.1016/j.preteyeres.2011.11.004
PMCID: PMC3288447  PMID: 22120610
23.  Memory-like Responses of Natural Killer Cells 
Immunological reviews  2010;235(1):297-305.
Summary
Natural killer (NK) cells are lymphocytes with the capacity to produce cytokines and kill target cells upon activation. NK cells have long been categorized as members of the innate immune system and as such have been thought to follow the ‘rules’ of innate immunity, including the principle that they have no immunologic memory, a property thought to be strictly limited to adaptive immunity. However, recent studies have suggested that NK cells have the capacity to alter their behavior based on prior activation. This property is analogous to adaptive immune memory; however, some NK cell memory-like functions are not strictly antigen-dependent and can be demonstrated following cytokine stimulation. Here we discuss the recent evidence that NK cells can exhibit properties of immunologic memory, focusing on the ability of cytokines to non-specifically induce memory-like NK cells with enhanced responses to restimulation.
doi:10.1111/j.0105-2896.2010.00891.x
PMCID: PMC2907109  PMID: 20536571
natural killer cell; innate immunity; memory; cytokines; interferon γ
24.  Mechanisms of GII.4 Norovirus Persistence in Human Populations  
PLoS Medicine  2008;5(2):e31.
Background
Noroviruses are the leading cause of viral acute gastroenteritis in humans, noted for causing epidemic outbreaks in communities, the military, cruise ships, hospitals, and assisted living communities. The evolutionary mechanisms governing the persistence and emergence of new norovirus strains in human populations are unknown. Primarily organized by sequence homology into two major human genogroups defined by multiple genoclusters, the majority of norovirus outbreaks are caused by viruses from the GII.4 genocluster, which was first recognized as the major epidemic strain in the mid-1990s. Previous studies by our laboratory and others indicate that some noroviruses readily infect individuals who carry a gene encoding a functional alpha-1,2-fucosyltransferase (FUT2) and are designated “secretor-positive” to indicate that they express ABH histo-blood group antigens (HBGAs), a highly heterogeneous group of related carbohydrates on mucosal surfaces. Individuals with defects in the FUT2 gene are termed secretor-negative, do not express the appropriate HBGA necessary for docking, and are resistant to Norwalk infection. These data argue that FUT2 and other genes encoding enzymes that regulate processing of the HBGA carbohydrates function as susceptibility alleles. However, secretor-negative individuals can be infected with other norovirus strains, and reinfection with the GII.4 strains is common in human populations. In this article, we analyze molecular mechanisms governing GII.4 epidemiology, susceptibility, and persistence in human populations.
Methods and Findings
Phylogenetic analyses of the GII.4 capsid sequences suggested an epochal evolution over the last 20 y with periods of stasis followed by rapid evolution of novel epidemic strains. The epidemic strains show a linear relationship in time, whereby serial replacements emerge from the previous cluster. Five major evolutionary clusters were identified, and representative ORF2 capsid genes for each cluster were expressed as virus-like particles (VLPs). Using salivary and carbohydrate-binding assays, we showed that GII.4 VLP-carbohydrate ligand binding patterns have changed over time and include carbohydrates regulated by the human FUT2 and FUT3 pathways, suggesting that strain sensitivity to human susceptibility alleles will vary. Variation in surface-exposed residues and in residues that surround the fucose ligand interaction domain suggests that antigenic drift may promote GII.4 persistence in human populations. Evidence supporting antigenic drift was obtained by measuring the antigenic relatedness of GII.4 VLPs using murine and human sera and demonstrating strain-specific serologic and carbohydrate-binding blockade responses. These data suggest that the GII.4 noroviruses persist by altering their HBGA carbohydrate-binding targets over time, which not only allows for escape from highly penetrant host susceptibility alleles, but simultaneously allows for immune-driven selection in the receptor-binding region to facilitate escape from protective herd immunity.
Conclusions
Our data suggest that the surface-exposed carbohydrate ligand binding domain in the norovirus capsid is under heavy immune selection and likely evolves by antigenic drift in the face of human herd immunity. Variation in the capsid carbohydrate-binding domain is tolerated because of the large repertoire of similar, yet distinct HBGA carbohydrate receptors available on mucosal surfaces that could interface with the remodeled architecture of the capsid ligand-binding pocket. The continuing evolution of new replacement strains suggests that, as with influenza viruses, vaccines could be targeted that protect against norovirus infections, and that continued epidemiologic surveillance and reformulations of norovirus vaccines will be essential in the control of future outbreaks.
Through phylogenetic analysis of norovirus isolates, Ralph Baric and colleagues show that new epidemic strains arise as the variety of available cellular receptors permits antigenic drift in the viral capsid.
Editors' Summary
Background.
Noroviruses are the leading cause of viral gastroenteritis (stomach flu), the symptoms of which include nausea, vomiting, and diarrhea. There is no treatment for infection with these highly contagious viruses. While most people recover within a few days, the very young and old may experience severe disease. Like influenza, large outbreaks (epidemics) of norovirus infection occur periodically (often in closed communities such as cruise ships), and most people have several norovirus infections during their lifetime. Currently, 100,000–200,000 people are being infected each week in England with a new GII.4 variant. There are several reasons for this pattern of infection and reinfection. First, the immune response induced by a norovirus infection is short-lived in some people, but not all. Second, there are many different noroviruses. Based on their genomes (genetic blueprints), noroviruses belong to five “genogroups,” which are further subdivided into “genotypes.” An immune response to one norovirus provides little protection against noroviruses of other genogroups or genotypes. Third, like influenza viruses, noroviruses frequently acquire small changes in their genome. This process is called antigenic drift (antigens are the molecules on the surface of infectious agents that stimulate the production of antibodies, proteins that help the immune system recognize and deal with foreign invaders). Norovirus epidemics occur when virus variants emerge to which the human population has no immunity.
Why Was This Study Done?
It is unknown exactly how noroviruses change over time or how they persist in human populations. In addition, little is known about susceptibility to norovirus infections except that secretor-positive individuals—people who express “histoblood group antigens” (HBGAs, a heterogeneous group of sugar molecules by which noroviruses attach themselves to human cells) on the cells that line their mouths and guts—are more susceptible than secretor-negative people, who express these antigens only on red blood cells. Information of this sort is needed to devise effective intervention strategies, therapies, and vaccines to reduce the illness and economic costs associated with norovirus outbreaks. In this study, the researchers investigate the molecular mechanisms governing the emergence and persistence of epidemic norovirus strains in human populations by analyzing how GII.4 norovirus strains (the genotype usually associated with epidemics) have changed over time.
What Did the Researchers Do and Find?
The researchers analyzed the relationships among the sequences of the gene encoding the capsid protein of GII.4 norovirus strains isolated over the past 20 years. The capsid protein forms a shell around noroviruses and is involved in their binding to HBGAs and their recognition by the human immune system. The researchers found that the virus evolved in fits and starts. That is, for several years, one cluster of strains was predominant but then new epidemic strains emerged rapidly from the cluster. In all, the researchers identified five major evolutionary clusters. They then created “virus-like particles” (VLPs) using representative capsid genes from each cluster and showed that these VLPs bound to different HBGAs. Finally they measured the antigenic relatedness of the different VLPs using human blood collected during a 1988 GII.4 outbreak. Antibodies in these samples recognized the VLPs representing early GII.4 strains better than VLPs representing recent GII.4 strains. The ability of the blood samples to block the interaction of VLPs with their matching HBGAs showed a similar pattern.
What Do These Findings Mean?
These findings suggest that the part of the norovirus capsid protein that binds to sugars on host cells is under heavy immune selection and evolves over time by antigenic drift. They show that, like influenza viruses, GII.4 viruses evolve through serial changes in the capsid sequence that occur sporadically after periods of stability, probably to evade the build up of immunity within the human population. Variation in this region of the viral genome is possible because human populations express a great variety of HBGA molecules so there is always likely to be a subpopulation of people that is susceptible to the altered virus. Overall, these findings suggest that it should be possible to develop vaccines to protect against norovirus infections but, just as with influenza virus, surveillance systems will have to monitor how the virus is changing and vaccines will need to be reformulated frequently to provide effective protection against norovirus outbreaks.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050031.
See a related PLoS Medicine Perspective article
The MedlinePlus encyclopedia has a page on viral gastroenteritis (in English and Spanish)
The US Centers for Disease Control and Prevention provides information on viral gastroenteritis (in English and Spanish) and on noroviruses
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doi:10.1371/journal.pmed.0050031
PMCID: PMC2235898  PMID: 18271619
25.  Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch 
We designed and constructed a genetic sequential logic circuit that can function as a push-on push-off switch. The circuit consists of a bistable switch module and a NOR gate module.The bistable switch module and NOR gate module were rationally designed and constructed.The two above modules were coupled by two interconnecting parts, cIind- and lacI. When optimizing the defined function, we fine-tuned the expression of the two interconnecting parts by directed evolution.Three control circuits were constructed to show the interconnecting parts are essential for achieving the defined function.
Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of genetic information-processing systems.
As in electronics, combinational and sequential logic circuits are two kinds of fundamental processors in cells. In a combinational logic circuit, the output depends only on the present inputs, whereas in a sequential logic circuit, the output also depends on the history of the input due to its own memory. If we can successfully construct the two kinds of basic logic circuits in a cell, they can serve as building blocks to be assembled into high-order genetic circuits and implement more sophisticated computation.
Construction of genetic combinational logic circuits (GSLCs), such as AND, OR, and NOR gates, has been frequently reported in the last decade (Guet et al, 2002; Dueber et al, 2003; Anderson et al, 2007; Win and Smolke, 2008). Meanwhile toggle switches, which can function as memory modules, have been implemented in prokaryotic and eukaryotic cells (Becskei et al, 2001; Kramer et al, 2004; Ajo-Franklin et al, 2007).
Here, we constructed a novel GSLC that functions as a push-on push-off switch by coupling a combinational logic module with a bistable switch module (Figure 1A). When the internal state of the memory is in the ‘ON' state, the external UV input makes the circuit's output promoter PNOR generate an ‘OFF' pulse signal and register the ‘OFF' state into the memory; when the internal state is in the ‘OFF' state, the same external UV input induces the circuit's output promoter PNOR to generate an ‘ON' pulse signal and register the ‘ON' state into the memory.
In our design, the combinatorial logic gate is a NOR gate and the switch module is a clearable bistable switch (Figure 1C). Two interconnecting parts are designed to connect the NOR gate and the bistable switch (Figure 1D). UV irradiation was used as both an external input signal and a reset signal for the clearable bistable switch (Figure 1B).
Before implementing the experimental construction, we used a set of ordinary differential equations to simulate the dynamic process. With a set of reasonable parameters, the simulation results showed that the circuit could function as a push-on push-off switch (Figure 1E). Then the bistable switch module and NOR gate module were rationally designed and constructed. Our experimental results showed that the corresponding functions were implemented very well.
After the construction of the memory and the NOR gate module, we coupled the two modules together by fine-tuning the expression of two interconnecting parts lacI and cIind−. The two libraries for the ribosome-binding sites (RBSs) of lacI and cIind− were simultaneously transformed into Escherichia coli cells harboring the memory module plasmid. After growth on agar plates with appropriate antibiotics, colonies containing all three plasmids were selected.
With efficient mutation libraries, we developed a new screening method to select the functional circuits. The experimental process is described in Figure 4A. It consists of two rounds of selection. In the first round of selection, approximatelybout 300 mutants out of 1000 were chosen. In the second round, only three mutants were selected. As shown in Figure 4B, if the initial state was ‘OFF' with green color, the fraction of green cells in the population was near 100% before UV stimulus, whereas less than 10% of cells remained in the green ‘OFF' state after UV stimulus (Figure 4B). This result indicates that the switch from ‘OFF' to ‘ON' is quite complete. Unfortunately, the switch from ‘ON' to ‘OFF' was not as efficient: only about one-third of the population switched to the ‘OFF' state after UV triggering (Figure 4C). Nonetheless, the switch is still significant compared with that of the population not exposed to UV irradiation (Figure 4B and C). These results show that the fine-tuned GSLC can generate different output signals under the same input on the basis of the internal state of its memory, and register the output signal into its memory as the new internal state.
To show that decoupled circuits cannot achieve the sequential logic function, we also constructed three control circuits. The bistable switch module and the NOR gate module were decoupled by removing either or both of the interconnecting parts. In the first control circuit, LacI was removed; without LacI, LexA becomes the only effective input for the NOR gate. As a consequence, upon UV stimulus, promoter PNOR always generates a high output signal, and the ‘ON' state (high CI and low CI434) is latched in the memory with the help of CIind−. Correspondingly, the color of the cells will change to red. In the other two control circuits, CIind− or both LacI and CIind− were removed. Owing to the lack of the feedback part CIind−, when the output of the promoter PNOR is ‘ON', no output signal can be registered into the memory. In this case, the memory module will spontaneously enter into the low CI/high CI434 state after UV stimulus. All experimental results are consistent with the above expectation.
Finally, to show the property of the push-on push-off switch of the circuit, we sequentially stimulated a homogeneous population of cells with the same dose of UV signal multiple times. The first UV stimulus caused the fraction of green cells in the population to decrease from 99.3% to 8.4%, so that more than 90% of the population switched from the ‘OFF' to the ‘ON' state. The second UV stimulus resulted in the fraction of green cells increasing from 8.4% to 34.5%. Therefore, only 26.1% of the population switched back to the ‘OFF' state. These results are comparable to the results of switching efficiency measurement shown in Figure 4B and C. With repeated exposure to UV irradiation, the population increasingly appeared like a mixture of the two states, the ratio of which gradually reached a steady state. The push-on–push-off function of the circuit was thus lost at the population level.
In summary, we successfully assembled a bistable switch module and a combinatorial NOR gate module into a functional sequential logic circuit. We combined rational design with directed evolution to generate the desired system behavior. In this work, we showed that simultaneous mutation of multiple RBS targets, followed by directed evolution, is a powerful tool to search the in vivo parameter space to generate functional circuits from multiple rationally designed synthetic device modules. We anticipate that this approach will lend itself well to the next step in synthetic biology, combining multiple circuits, each composed of several device modules, to create useful synthetic systems that perform sophisticated computation.
Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and ‘memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch.
doi:10.1038/msb.2010.2
PMCID: PMC2858441  PMID: 20212522
bistable switch; coupling modules; genetic sequential logic circuit; NOR gate; push-on push-off switch

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