A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology

Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system's structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator

Dual Band Electrodes in Generator-Collector Mode: Simultaneous Measurement of Two Species

A computational model for the simulation of a double band collector-generator experiment is applied to the situation where two electrochemical reactions occur concurrently. It is shown that chronoamperometric measurements can be used to take advantage of differences in diffusion coefficients to measure the concentrations of both electroactive species simultaneously, by measuring the time at which the collection efficiency reaches a specific value. The separation of the electrodes is shown to not affect the sensitivity of the method (in terms of percentage changes in the measured time to reach the specified collection efficiency), but wider gaps can provide a greater range of (larger) absolute values of this characteristic time. It is also shown that measuring the time taken to reach smaller collection efficiencies can allow for the detection of smaller amounts of whichever species diffuses faster. The case of a system containing both ascorbic acid and opamine in water is used to exemplify the method, and it is shown that mole fractions of ascorbic acid between 0.055 and 0.96 can, in principle, be accurately measured.Comment: 34 pages, 8 figure

Impact of Education on Grandparents’ Actions in Raising Grandchildren

Grandparents raising grandchildren represent a population of adults who confront complex interpersonal and environmental challenges. The intent of this case study was to gather and interpret evaluative data to better understand the impact of a 1-day community education program for grandparents who raise their grandchildren. Extension\u27s philosophy of systematic program evaluation to improve supports for families and communities furnished the framework for the project. Elements felt to be essential for a well-designed, 1-day grandparent education program have been extracted from past evaluation cycles and offered here as recommendations

Assessment of fat-mass loss during weight reduction in obese women.

Urho Kaleva Kekkonen Institute for Health Promotion Research, Tampere, Finland.Methods for assessing body fat mass (FM) loss were compared in 32 obese (body mass index [BMI], 29 to 41 kg/m2) premenopausal women before and after a weight loss of 13.0 +/- 3.4 kg (mean +/- SD). A four-component (4C) model was used as the criterion. The other methods were as follows: three-component models (body density with total body water [3W] or bone minerals [3M]), underwater weighing, dual-energy x-ray absorptiometry ([DXA] XR-26, software 2.5.2; Norland, Ft Atkinson, WI), bioelectric impedance analysis (BIA) with an obese-specific equation [Segal et al), skinfolds (Durnin and Womersley), and an equation with BMI (Deurenberg et al). The 3W model (bias +/- SD, 0.5 +/- 0.4 kg), XR-26 (0.6 +/- 2.1 kg), and BMI equation (-0.3 +/- 2.1 kg) gave practically unbiased mean estimations of fat loss. All other methods underestimated fat loss by at least 1.6 kg (range of bias, -2.7 to -1.6 kg). The small bias (0.7 +/- 1.0 kg) between underwater weighing and model 4C before weight reduction indicates that the two-component assumptions were valid in premenopausal, weight-stable obese women. However, particularly the water fraction of the fat-free body component (4C model) was increased after weight reduction (before, 72.9% +/- 1.4%; after, 75.7% +/- 2.2%), making both underwater weighing and the 3M model uncertain for assessment of body composition changes. A general tendency for overestimating FM was seen before and more clearly after weight reduction. However, most methods underestimated fat loss, apparently because of unexpected changes in hydration of the fat-free body component

A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology

Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system's structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator

Modulation of thermogenesis and metabolic health:a built environment perspective

\u3cp\u3eLifestyle interventions, obviating the increasing prevalence of the metabolic syndrome, generally focus on nutrition and physical activity. Environmental factors are hardly covered. Because we spend on average more that 90% of our time indoors, it is, however, relevant to address these factors. In the built environment, the attention has been limited to the (assessment and optimization of) building performance and occupant thermal comfort for a long time. Only recently well-being and health of building occupants are also considered to some extent, but actual metabolic health aspects are not generally covered. In this review, we draw attention to the potential of the commonly neglected lifestyle factor ‘indoor environment’. More specifically, we review current knowledge and the developments of new insights into the effects of ambient temperature, light and the interaction of the two on metabolic health. The literature shows that the effects of indoor environmental factors are important additional factors for a healthy lifestyle and have an impact on metabolic health.\u3c/p\u3

Genome engineering of isogenic human ES cells to model autism disorders.

Isogenic pluripotent stem cells are critical tools for studying human neurological diseases by allowing one to study the effects of a mutation in a fixed genetic background. Of particular interest are the spectrum of autism disorders, some of which are monogenic such as Timothy syndrome (TS); others are multigenic such as the microdeletion and microduplication syndromes of the 16p11.2 chromosomal locus. Here, we report engineered human embryonic stem cell (hESC) lines for modeling these two disorders using locus-specific endonucleases to increase the efficiency of homology-directed repair (HDR). We developed a system to: (1) computationally identify unique transcription activator-like effector nuclease (TALEN) binding sites in the genome using a new software program, TALENSeek, (2) assemble the TALEN genes by combining golden gate cloning with modified constructs from the FLASH protocol, and (3) test the TALEN pairs in an amplification-based HDR assay that is more sensitive than the typical non-homologous end joining assay. We applied these methods to identify, construct, and test TALENs that were used with HDR donors in hESCs to generate an isogenic TS cell line in a scarless manner and to model the 16p11.2 copy number disorder without modifying genomic loci with high sequence similarity

Addressable, "Packet-Based" Intercellular Communication through Plasmid Conjugation

We develop a system for implementing "packet-based" intercellular communication in an engineered bacterial population via conjugation. Our system uses gRNA-based identification markers that allow messages to be addressed to specific strains via Cas9-mediated cleavage of messages sent to the wrong recipient, which we show reduces plasmid transfer by four orders of magnitude. Integrase-mediated editing of the address on the message plasmid allows cells to dynamically update the message's recipients in vivo. As a proof-of-concept demonstration of our system, we propose a linear path scheme that would propagate a message sequentially through the strains of a population in a defined order