System identification of gene regulatory networks for perturbation mitigation via feedback control

In Synthetic Biology, the idea of using feedback control for the mitigation of perturbations to gene regulatory networks due to disease and environmental disturbances is gaining popularity. To facilitate the design of such synthetic control circuits, a suitable model that captures the relevant dynamics of the gene regulatory network is essential. Traditionally, Michaelis-Menten models with Hill-type nonlinearities have often been used to model gene regulatory networks. Here, we show that such models are not suitable for the purposes of controller design, and propose an alternative formalism. Using tools from system identification, we show how to build so-called S-System models that capture the key dynamics of the gene regulatory network and are suitable for controller design. Using the identified S-System model, we design a genetic feedback controller for an example gene regulatory network with the objective of rejecting an external perturbation. Using a sine sweeping method, we show how the S-System model can be approximated by a second order linear transfer function and, based on this transfer function, we design our controller. Simulation results using the full nonlinear S-System model of the network show that the designed controller is able to mitigate the effect of external perturbations. Our findings highlight the usefulness of the S-System modelling formalism for the design of synthetic control circuits for gene regulatory networks

Proportional-Integral Degradation (PI-Deg) control allows accurate tracking of biomolecular concentrations with fewer chemical reactions

We consider the design of synthetic embedded feedback circuits that can implement desired changes in the concentration of the output of a biomolecular process (reference tracking in control terminology). Such systems require the use of a "subtractor", to generate an error signal that captures the difference between the current and desired value of the process output. Unfortunately, standard implementations of the subtraction operator using chemical reaction networks are one-sided, i.e. they cannot produce negative error signals. Previous attempts to deal with this problem by representing signals as the difference in concentrations of two different biomolecular species lead to a doubling of the number of chemical reactions required to generate the circuit, hence sharply increasing the difficulty of experimental implementations and limiting the complexity of potential designs. Here we propose an alternative approach that introduces a degradation term into the classical proportion-integral control scheme. The extra tuning flexibility of the resulting PI-Deg controller compensates for the limitations of the one-sided subtraction operator, providing robust high-performance tracking of concentration changes with a minimal number of chemical reactions

Interpreting ambiguous ‘trace’ results in Schistosoma mansoni CCA Tests: Estimating sensitivity and specificity of ambiguous results with no gold standard

Background The development of new diagnostics is an important tool in the fight against disease. Latent Class Analysis (LCA) is used to estimate the sensitivity and specificity of tests in the absence of a gold standard. The main field diagnostic for Schistosoma mansoni infection, Kato-Katz (KK), is not very sensitive at low infection intensities. A point-of-care circulating cathodic antigen (CCA) test has been shown to be more sensitive than KK. However, CCA can return an ambiguous ‘trace’ result between ‘positive’ and ‘negative’, and much debate has focused on interpretation of traces results. Methodology/Principle findings We show how LCA can be extended to include ambiguous trace results and analyse S. mansoni studies from both Côte d’Ivoire (CdI) and Uganda. We compare the diagnostic performance of KK and CCA and the observed results by each test to the estimated infection prevalence in the population. Prevalence by KK was higher in CdI (13.4%) than in Uganda (6.1%), but prevalence by CCA was similar between countries, both when trace was assumed to be negative (CCAtn: 11.7% in CdI and 9.7% in Uganda) and positive (CCAtp: 20.1% in CdI and 22.5% in Uganda). The estimated sensitivity of CCA was more consistent between countries than the estimated sensitivity of KK, and estimated infection prevalence did not significantly differ between CdI (20.5%) and Uganda (19.1%). The prevalence by CCA with trace as positive did not differ significantly from estimates of infection prevalence in either country, whereas both KK and CCA with trace as negative significantly underestimated infection prevalence in both countries. Conclusions Incorporation of ambiguous results into an LCA enables the effect of different treatment thresholds to be directly assessed and is applicable in many fields. Our results showed that CCA with trace as positive most accurately estimated infection prevalence

Negative pressure wound therapy: Potential publication bias caused by lack of access to unpublished study results data

<p>Abstract</p> <p>Background</p> <p>Negative pressure wound therapy (NPWT) is widely applied, although the evidence base is weak. Previous reviews on medical interventions have shown that conclusions based on published data alone may no longer hold after consideration of unpublished data. The main objective of this study was to identify unpublished randomised controlled trials (RCTs) on NPWT within the framework of a systematic review.</p> <p>Methods</p> <p>RCTs comparing NPWT with conventional wound therapy were identified using MEDLINE, EMBASE, CINAHL and The Cochrane Library. Every database was searched from inception to May 2005. The search was updated in December 2006. Reference lists of original articles and systematic reviews, as well as congress proceedings and online trial registers, were screened for clues to unpublished RCTs. Manufacturers of NPWT devices and authors of conference abstracts were contacted and asked to provide study information. Trials were considered nonrandomised if concealment of allocation to treatment groups was classified as "inadequate". The study status was classified as "completed", "discontinued", "ongoing" or "unclear". The publication status of completed or discontinued RCTs was classified as "published" if a full-text paper on final study results (completed trials) or interim results (discontinued trials) was available, and "unpublished" if this was not the case. The type of sponsorship was also noted for all trials.</p> <p>Results</p> <p>A total of 28 RCTs referring to at least 2755 planned or analysed patients met the inclusion criteria: 13 RCTs had been completed, 6 had been discontinued, 6 were ongoing, and the status of 3 RCTs was unclear. Full-text papers were available on 30% of patients in the 19 completed or discontinued RCTs (495 analysed patients in 10 published RCTs vs. 1154 planned patients in 9 unpublished RCTs). Most information about conference abstracts and unpublished study information referring to trials that were unpublished at the time these documents were generated was obtained from the manufacturer Kinetic Concepts Inc. (KCI) (19 RCTs), followed by The Cochrane Library (18) and a systematic review (15). We were able to obtain some information on the methods of unpublished RCTs, but results data were either not available or requests for results data were not answered; the results of unpublished RCTs could therefore not be considered in the review. One manufacturer, KCI, sponsored the majority of RCTs (19/28; 68%). The sponsorship of the remaining trials was unclear.</p> <p>Conclusion</p> <p>Multi-source comprehensive searches identify unpublished RCTs. However, lack of access to unpublished study results data raises doubts about the completeness of the evidence base on NPWT.</p

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente

Purification and Characterization of Enterovirus 71 Viral Particles Produced from Vero Cells Grown in a Serum-Free Microcarrier Bioreactor System

[[abstract]]Background: Enterovirus 71 (EV71) infections manifest most commonly as a childhood exanthema known as hand-foot-and-mouth disease (HFMD) and can cause neurological disease during acute infection. Principal Finding: In this study, we describe the production, purification and characterization of EV71 virus produced from Vero cells grown in a five-liter serum-free bioreactor system containing 5 g/L Cytodex 1 microcarrier. The viral titer was >106 TCID50/mL by 6 days post infection when a MOI of 10?5 was used at the initial infection. Two EV71 virus fractions were separated and detected when the harvested EV71 virus concentrate was purified by sucrose gradient zonal ultracentrifugation. The EV71 viral particles detected in the 24–28% sucrose fractions had an icosahedral structure 30–31 nm in diameter and had low viral infectivity and RNA content. Three major viral proteins (VP0, VP1 and VP3) were observed by SDS-PAGE. The EV71 viral particles detected in the fractions containing 35–38% sucrose were 33–35 nm in size, had high viral infectivity and RNA content, and were composed of four viral proteins (VP1, VP2, VP3 and VP4), as shown by SDS-PAGE analyses. The two virus fractions were formalin-inactivated and induced high virus neutralizing antibody responses in mouse immunogenicity studies. Both mouse antisera recognized the immunodominant linear neutralization epitope of VP1 (residues 211–225). Conclusion:These results provide important information for cell-based EV71 vaccine development, particularly for the preparation of working standards for viral antigen quantification

H5N1 Whole-Virus Vaccine Induces Neutralizing Antibodies in Humans Which Are Protective in a Mouse Passive Transfer Model

BACKGROUND: Vero cell culture-derived whole-virus H5N1 vaccines have been extensively tested in clinical trials and consistently demonstrated to be safe and immunogenic; however, clinical efficacy is difficult to evaluate in the absence of wide-spread human disease. A lethal mouse model has been utilized which allows investigation of the protective efficacy of active vaccination or passive transfer of vaccine induced sera following lethal H5N1 challenge. METHODS: We used passive transfer of immune sera to investigate antibody-mediated protection elicited by a Vero cell-derived, non-adjuvanted inactivated whole-virus H5N1 vaccine. Mice were injected intravenously with H5N1 vaccine-induced rodent or human immune sera and subsequently challenged with a lethal dose of wild-type H5N1 virus. RESULTS: Passive transfer of H5N1 vaccine-induced mouse, guinea pig and human immune sera provided dose-dependent protection of recipient mice against lethal challenge with wild-type H5N1 virus. Protective dose fifty values for serum H5N1 neutralizing antibody titers were calculated to be ≤1∶11 for all immune sera, independently of source species. CONCLUSIONS: These data underpin the confidence that the Vero cell culture-derived, whole-virus H5N1 vaccine will be effective in a pandemic situation and support the use of neutralizing serum antibody titers as a correlate of protection for H5N1 vaccines

Seroepidemiology of coxsackievirus A6, coxsackievirus A16, and Enterovirus 71 infections among children and adolescents in Singapore, 2008-2010

10.1371/journal.pone.0127999PLoS ONE105e012799

Southern Ocean pteropods at risk from ocean warming and acidification

Early life stages of marine calcifiers are particularly vulnerable to climate change. In the Southern Ocean aragonite undersaturation events and areas of rapid warming already occur and are predicted to increase in extent. Here, we present the first study to successfully hatch the polar pteropod Limacina helicina antarctica and observe the potential impact of exposure to increased temperature and aragonite undersaturation resulting from ocean acidification (OA) on the early life stage survival and shell morphology. High larval mortality (up to 39%) was observed in individuals exposed to perturbed conditions. Warming and OA induced extensive shell malformation and dissolution, respectively, increasing shell fragility. Furthermore, shell growth decreased, with variation between treatments and exposure time. Our results demonstrate that short-term exposure through passing through hotspots of OA and warming poses a serious threat to pteropod recruitment and long-term population viability

Universal asymptotic clone size distribution for general population growth

Deterministically growing (wild-type) populations which seed stochastically developing mutant clones have found an expanding number of applications from microbial populations to cancer. The special case of exponential wild-type population growth, usually termed the Luria-Delbr\"uck or Lea-Coulson model, is often assumed but seldom realistic. In this article we generalise this model to different types of wild-type population growth, with mutants evolving as a birth-death branching process. Our focus is on the size distribution of clones - that is the number of progeny of a founder mutant - which can be mapped to the total number of mutants. Exact expressions are derived for exponential, power-law and logistic population growth. Additionally for a large class of population growth we prove that the long time limit of the clone size distribution has a general two-parameter form, whose tail decays as a power-law. Considering metastases in cancer as the mutant clones, upon analysing a data-set of their size distribution, we indeed find that a power-law tail is more likely than an exponential one.Comment: 22 pages, 4 figures. To appear in the Bulletin of Mathematical Biology doi:10.1007/s11538-016-0221-