The Dynamics of Hybrid Metabolic-Genetic Oscillators

The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological models of a family of hybrid metabolic-genetic circuits known as "metabolators." Under mild assumptions on the kinetics, we use GM to analytically prove that all explicit kinetic models which are topologically analogous to one such circuit, the "core metabolator," cannot undergo Hopf bifurcations. Then, we examine more detailed models of the metabolator. Inspired by the experimental observation of a Hopf bifurcation in a synthetically constructed circuit related to the core metabolator, we apply GM to identify the critical components of the synthetically constructed metabolator which must be reintroduced in order to recover the Hopf bifurcation. Next, we study the dynamics of a re-wired version of the core metabolator, dubbed the "reverse" metabolator, and show that it exhibits a substantially richer set of dynamical behaviors, including both local and global oscillations. Prompted by the observation of relaxation oscillations in the reverse metabolator, we study the role that a separation of genetic and metabolic time scales may play in its dynamics, and find that widely separated time scales promote stability in the circuit. Our results illustrate a generic pipeline for vetting the potential success of a potential circuit design, simply by studying the dynamics of the corresponding generalized model

Measuring well-being in aphasia: The GHQ-28 versus the NHP

This study aimed to get the opinions of people with aphasia on two subjective well-being measures: the General Health Questionnaire 28-item version (GHQ-28) (Goldberg & Hillier, 1979) and the Nottingham Health Profile (NHP) (Hunt, McKenna, McEwen, Williams, & Papp, 1981). Twelve persons with moderate to mild aphasia of at least 2-years duration completed the GHQ-28 and the NHP. In a semistructured intenriew, they gave their feedback on the two questionnaires. All participants were able to complete both instruments. Nine out of 12 participants showed high psychological distress (> 5/28) in the GHQ-28. The NHP (part 1 less the physical abilities section) had a correlation of 0.78 (p < .01) with the GHQ-28. The social dysfunction subscale of the NHP identified more problems in the participants with aphasia than the social isolation subscale of the GHQ-28. The majority of the participants (10 out of 12) preferred the NHP, as they found it easier to understand and respond to. This small-scale study indicated that both the GHQ-28 and the NHP can be administered to people with moderate to mild aphasia and provide useful information on their well-being. Participants reported that the NHP was easier to do, and it asked questions more relevant to their situation

A method for the reconstruction of unknown non-monotonic growth functions in the chemostat

We propose an adaptive control law that allows one to identify unstable steady states of the open-loop system in the single-species chemostat model without the knowledge of the growth function. We then show how one can use this control law to trace out (reconstruct) the whole graph of the growth function. The process of tracing out the graph can be performed either continuously or step-wise. We present and compare both approaches. Even in the case of two species in competition, which is not directly accessible with our approach due to lack of controllability, feedback control improves identifiability of the non-dominant growth rate.Comment: expansion of ideas from proceedings paper (17 pages, 8 figures), proceedings paper is version v

Short-Term Retinoic Acid Treatment Increases In Vivo, but Decreases In Vitro, Epidermal Transglutaminase-K Enzyme Activity and Immunoreactivity

Epidermal transglutaminase-K is believed to catalyze the covalent linking of loricrin and involucrin to form cross-linked (CE) envelopes. In normal skin, transglutaminase-K is expressed as a band immediately below the stratum corneum, whereas in psoriasis and healing skin its expression is considerably expanded throughout the suprabasal layers. We have investigated whether the hyperproliferative state induced by short-term application of topical retinoic acid is similarly characterized by an increase in transglutaminase-K enzyme activity and immunoreactivity.Retinoic acid (0.1% cream) or vehicle were applied to human skin and occluded for 4 d. Skin biopsies were obtained for measurement of transglutaminase-K and transglutaminase-C activity and immunoreactivity. For comparison, cultured normal human keratinocytes were incubated for 4 d in the presence of 1 μM retinoic acid and the subsequent transglutaminase-K activity and immunoreactivity measured. Transglutaminase-K activity was increased 2.8 times in retinoic acid compared to vehicle-treated skin (p < 0.005, n = 12) whereas there was no significant difference in transglutaminase-C activity. However, transglutaminase-K mRNA levels were not significantly different between retinoic acid- and vehicle-treated skin. In vehicle-treated skin, transglutaminase-K immunoreactivity was limited to a narrow, substratum corneal band, but was considerably expanded in a diffuse suprabasal pattern in retinoic acid-treated epidermis. In contrast, transglutaminase-K immunostaining was decreased and its enzymatic activity reduced sixfold in retinoic acid-treated keratinocytes (p < 0.01, n = 4).These results demonstrate that retinoic acid treatment in vivo, in contrast to in vitro, leads to not only increased transglutaminase-K protein expression but also increased enzymatic activity in the absence of detectable increases in mRNA levels.These data, taken with the previously reported lack of in vivo modulation of the differentiation markers keratins 1 and 10 by retinoic acid, indicate that certain aspects of keratinocyte terminal differentiation that are altered in vitro by retinoic acid do not occur in vivo in human skin

Frequency Locking of an Optical Cavity using LQG Integral Control

This paper considers the application of integral Linear Quadratic Gaussian (LQG) optimal control theory to a problem of cavity locking in quantum optics. The cavity locking problem involves controlling the error between the laser frequency and the resonant frequency of the cavity. A model for the cavity system, which comprises a piezo-electric actuator and an optical cavity is experimentally determined using a subspace identification method. An LQG controller which includes integral action is synthesized to stabilize the frequency of the cavity to the laser frequency and to reject low frequency noise. The controller is successfully implemented in the laboratory using a dSpace DSP board.Comment: 18 pages, 9 figure

A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia

BACKGROUND: Somatic cytidine mutations in normal mammalian nuclear genes occur during antibody diversification in B lymphocytes and generate an isoform of apolipoprotein B in intestinal cells by RNA editing. Here, I describe that succinate dehydrogenase (SDH; mitochondrial complex II) subunit B gene (SDHB) is somatically mutated at a cytidine residue in normal peripheral blood mononuclear cells (PBMCs) and T-cell acute leukemia. Germ line mutations in the SDHB, SDHC or SDHD genes cause hereditary paraganglioma (PGL) tumors which show constitutive activation of homeostatic mechanisms induced by oxygen deprivation (hypoxia). PRINCIPAL FINDINGS: To determine the prevalence of a mutation identified in the SDHB mRNA, 180 samples are tested. An SDHB stop-codon mutation c.136C>T (R46X) is present in a significant fraction (average = 5.8%, range = less than 1 to 30%, n = 52) of the mRNAs obtained from PBMCs. In contrast, the R46X mutation is present in the genomic DNA of PBMCs at very low levels. Examination of the PBMC cell-type subsets identifies monocytes and natural killer (NK) cells as primary sources of the mutant transcript, although lesser contributions also come from B and T lymphocytes. Transcript sequence analyses in leukemic cell lines derived from monocyte, NK, T and B cells indicate that the mutational mechanism targeting SDHB is operational in T-cell acute leukemia. Accordingly, substantial levels (more than 3%) of the mutant SDHB transcripts are detected in five of 20 primary childhood T-cell acute lymphoblastic leukemia (T-ALL) bone marrow samples, but in none of 20 B-ALL samples. In addition, distinct heterozygous SDHB missense DNA mutations are identified in Jurkat and TALL-104 cell lines which are derived from T-ALLs. CONCLUSIONS: The identification of a recurrent, inactivating stop-codon mutation in the SDHB gene in normal blood cells suggests that SDHB is targeted by a cytidine deaminase enzyme. The SDHB mutations in normal PBMCs and leukemic T cells might play a role in cellular pre-adaptation to hypoxia

Rejection of mismatched disturbances for systems with input delay via a predictive extended state observer

[EN] The problem of output stabilization and disturbance rejection for input-delayed systems is tackled in this work. First, a suitable transformation is introduced to translate mismatched disturbances into an equivalent input disturbance. Then, an extended state observer is combined with a predictive observer structure to obtain a future estimation of both the state and the disturbance. A disturbance model is assumed to be known but attenuation of unmodeled components is also considered. The stabilization is proved via Lyapunov-Krasovskii functionals, leading to sufficient conditions in terms of linear matrix inequalities for the closed-loop analysis and parameter tuning. 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Hybridization in parasites: consequences for adaptive evolution, pathogenesis and public health in a changing world

[No abstract available