Proximity extension of circular DNA aptamers with real-time protein detection

Multivalent circular aptamers or ‘captamers’ have recently been introduced through the merger of aptameric recognition functions with the basic principles of DNA nanotechnology. Aptamers have strong utility as protein-binding motifs for diagnostic applications, where their ease of discovery, thermal stability and low cost make them ideal components for incorporation into targeted protein assays. Here we report upon a property specific to circular DNA aptamers: their intrinsic compatibility with a highly sensitive protein detection method termed the ‘proximity extension’ assay. The circular DNA architecture facilitates the integration of multiple functional elements into a single molecule: aptameric target recognition, nucleic acid hybridization specificity and rolling circle amplification. Successful exploitation of these properties is demonstrated for the molecular analysis of thrombin, with the assay delivering a detection limit nearly three orders of magnitude below the dissociation constants of the two contributing aptamer–thrombin interactions. Real-time signal amplification and detection under isothermal conditions points towards potential clinical applications, with both fluorescent and bioelectronic methods of detection achieved. This application elaborates the pleiotropic properties of circular DNA aptamers beyond the stability, potency and multitargeting characteristics described earlier

A Unified Account of the Moral Standing to Blame

Recently, philosophers have turned their attention to the question, not when a given agent is blameworthy for what she does, but when a further agent has the moral standing to blame her for what she does. Philosophers have proposed at least four conditions on having “moral standing”: 1. One’s blame would not be “hypocritical”. 2. One is not oneself “involved in” the target agent’s wrongdoing. 3. One must be warranted in believing that the target is indeed blameworthy for the wrongdoing. 4. The target’s wrongdoing must some of “one’s business”. These conditions are often proposed as both conditions on one and the same thing, and as marking fundamentally different ways of “losing standing.” Here I call these claims into question. First, I claim that conditions (3) and (4) are simply conditions on different things than are conditions (1) and (2). Second, I argue that condition (2) reduces to condition (1): when “involvement” removes someone’s standing to blame, it does so only by indicating something further about that agent, viz., that he or she lacks commitment to the values that condemn the wrongdoer’s action. The result: after we clarify the nature of the non-hypocrisy condition, we will have a unified account of moral standing to blame. Issues also discussed: whether standing can ever be regained, the relationship between standing and our "moral fragility", the difference between mere inconsistency and hypocrisy, and whether a condition of standing might be derived from deeper facts about the "equality of persons"

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data

Validating the Adidas miCoach for estimating pace, distance, and energy expenditure during outdoor over-ground exercise accelerometer

The Adidas miCoach was developed as a personal training system to estimate pace, distance and energy expenditure (EE) but has yet to be validated. PURPOSE: To validate the Adidas miCoach for estimating pace (min/km), distance (km) and EE (kcal/min) during outdoor over-ground walking and running for two different sensor configurations. METHODS: Six male and 8 female moderately endurance trained participants (mean ± SD age: 28.2 ± 8.5 y; height: 167.4 ± 7.8 cm; mass: 60.9 ± 11.1 kg; VO2max: 54.4 ± 5.5 mL/kg/min) completed this validation study. The protocol consisted of walking at 53.6, 80.4, and 107.2 m/min and running at 134.0, 160.8, 187.6, and 214.0 m/min on an outdoor track while wearing a portable metabolic measurement unit (Cosmed K4b2). A miCoach sensor was attached to the right shoelaces (Laces) and a second miCoach sensor was inserted in the right insole of the shoe (Midsole). Estimated pace, distance and EE were compared to values determined by criterion methods (Actual). Data were analyzed using a repeated-measure ANOVA (pace, distance) or ANCOVA (EE) to evaluate significant differences. RESULTS: A significant main effect (P \u3c 0.035) was observed for speed indicating an increase in measured values at each subsequent speed for pace, distance, and EE. For pace at all speeds, the laces and midsole miCoach estimated pace were significantly different from each other (P \u3c 0.01), and from actual pace (P \u3c 0.02). For distance, the laces and midsole miCoach estimates were similar for all speeds; however, significant differences were observed for the midsole at 53.6 m/min (P = 0.003) and for both laces and midsole at 80.4 and 107.2 m/min (P ≤ 0.05) compared to actual distance. For walking speeds, miCoach estimated EE was significantly different between laces and midsole (P \u3c 0.04), and compared to actual EE (P \u3c 0.001); however, midsole at 160.8 m/min (P = 0.035) and both laces and midsole at 187.6 and 214.4 m/min (P \u3c 0.01) were significantly different from actual EE. CONCLUSION: These data indicate that the Adidas miCoach is accurate for estimating distance. However, it lacks the ability to accurately estimate pace and EE across a range of walking and running speeds. Additionally, it appears that the laces configuration produced more accurate estimates than the midsole

Renormalization group and perfect operators for stochastic differential equations

We develop renormalization group methods for solving partial and stochastic differential equations on coarse meshes. Renormalization group transformations are used to calculate the precise effect of small scale dynamics on the dynamics at the mesh size. The fixed point of these transformations yields a perfect operator: an exact representation of physical observables on the mesh scale with minimal lattice artifacts. We apply the formalism to simple nonlinear models of critical dynamics, and show how the method leads to an improvement in the computational performance of Monte Carlo methods.Comment: 35 pages, 16 figure

The C-Band All-Sky Survey: Instrument design, status, and first-look data

The C-Band All-Sky Survey (C-BASS) aims to produce sensitive, all-sky maps of diffuse Galactic emission at 5 GHz in total intensity and linear polarization. These maps will be used (with other surveys) to separate the several astrophysical components contributing to microwave emission, and in particular will allow an accurate map of synchrotron emission to be produced for the subtraction of foregrounds from measurements of the polarized Cosmic Microwave Background. We describe the design of the analog instrument, the optics of our 6.1 m dish at the Owens Valley Radio Observatory, the status of observations, and first-look data.Comment: 10 pages, 11 figures, published in Proceedings of SPIE MIllimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy V (2010), Vol. 7741, 77411I-1 - 77411I-1

α7 Nicotinic Acetylcholine Receptor Interaction with G Proteins in Breast Cancer Cell Proliferation, Motility, and Calcium Signaling

Chronic smoking is a primary risk factor for breast cancer due to the presence of various toxins and carcinogens within tobacco products. Nicotine is the primary addictive component of tobacco products and has been shown to promote breast cancer cell proliferation and metastases. Nicotine activates nicotinic acetylcholine receptors (nAChRs) that are expressed in cancer cell lines. Here, we examine the role of the α7 nAChR in coupling to heterotrimeric G proteins within breast cancer MCF-7 cells. Pharmacological activation of the α7 nAChR using choline or nicotine was found to increase proliferation, motility, and calcium signaling in MCF-7 cells. This effect of α7 nAChR on cell proliferation was abolished by application of Gαi/o and Gαq protein blockers. Specifically, application of the Gαi/o inhibitor pertussis toxin was found to abolish choline-mediated cell proliferation and intracellular calcium transient response. These findings were corroborated by expression of a G protein binding dominant negative nAChR subunit (α7345-348A), which resulted in significantly attenuating calcium signaling and cellular proliferation in response to choline. Our study shows a new role for G protein signaling in the mechanism of α7 nAChR-associated breast cancer growth

Inclusion of quasi-vertex views in a brain-dedicated multi-pinhole SPECT system for improved imaging performance

With brain-dedicated multi-detector systems employing pinhole apertures the usage of detectors facing the top of the patient\u27s head (i.e., quasi-vertex views) can provide the advantage of additional viewing from close to the brain for improved detector coverage. In this paper, we report the results of simulation and reconstruction studies to investigate the impact of the quasi-vertex views on the imaging performance of AdaptiSPECT-C, a brain-dedicated stationary SPECT system under development. In this design, both primary and scatter photons from regions located inferior to the brain can contribute to SPECT projections acquired by the quasi-vertex views, and thus degrade AdaptiSPECT-C imaging performance. In this work, we determined the proportion, origin, and nature (i.e., primary, scatter, and multiple-scatter) of counts emitted from structures within the head and throughout the body contributing to projections from the different AdaptiSPECT-C detector rings, as well as from a true vertex view detector. We simulated phantoms used to assess different aspects of image quality (i.e., uniform sphere and Derenzo), as well as anthropomorphic phantoms with multiple count levels emulating clinical(123)I activity distributions (i.e., DaTscan and perfusion). We determined that attenuation and scatter in the patient\u27s body greatly diminish the probability of the photons emitted outside the volume of interest reaching to detectors and being recorded within the 15% photopeak energy window. In addition, we demonstrated that the inclusion of the residual of such counts in the system acquisition does not degrade visual interpretation or quantitative analysis. The addition of the quasi-vertex detectors increases volumetric sensitivity, angular sampling, and spatial resolution leading to significant enhancement in image quality, especially in the striato-thalamic and superior regions of the brain. Besides, the use of quasi-vertex detectors improves the recovery of clinically relevant metrics such as the striatal binding ratio and mean activity in selected cerebral structures