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Polymerases that synthesize artificial genetic polymers hold great promise for advancing future applications in synthetic biology. However, engineering natural polymerases to replicate unnatural genetic polymers is a challenging problem. Here we present droplet-based optical polymerase sorting (DrOPS) as a general strategy for expanding polymerase function that employs an optical sensor to monitor polymerase activity inside the microenvironment of a uniform synthetic compartment generated by microfluidics. We validated this approach by performing a complete cycle of encapsulation, sorting and recovery on a doped library and observed an enrichment of ∼1,200-fold for a model engineered polymerase. We then applied our method to …

Contributors

Larsen, Andrew, Dunn, Matthew, Hatch, Andrew, et al.

Created Date

2016-04-05

There is mounting evidence to suggest that the urban built form plays a crucial role in household energy consumption, hence planning energy efficient cities requires thoughtful design at multiple scales - from buildings, to neighborhoods, to urban regions. While data on household energy use are essential for examining the energy implications of different built forms, few utilities providing power and gas offer such information at a granular scale. Therefore, researchers have used various estimation techniques to determine household and neighborhood scale energy use. In this study we develop a novel method for estimating household energy demand that can be applied …

Contributors

Zhang, Wenwen, Guhathakurta, Subhrajit, Pendyala, Ram, et al.

Created Date

2018-01-05

The common formula used for converting a chi-square test into a correlation coefficient for use as an effect size in meta-analysis has a hidden assumption which may be violated in specific instances, leading to an overestimation of the effect size. A corrected formula is provided.

Contributors

Rosenberg, Michael, Biodesign Institute, Center for Evolution and Medicine, et al.

Created Date

2010-04-07

The termites evolved eusociality and complex societies before the ants, but have been studied much less. The recent publication of the first two termite genomes provides a unique comparative opportunity, particularly because the sequenced termites represent opposite ends of the social complexity spectrum. Zootermopsis nevadensis has simple colonies with totipotent workers that can develop into all castes (dispersing reproductives, nest-inheriting replacement reproductives, and soldiers). In contrast, the fungus-growing termite Macrotermes natalensis belongs to the higher termites and has very large and complex societies with morphologically distinct castes that are life-time sterile. Here we compare key characteristics of genomic architecture, focusing …

Contributors

Korb, Judith, Poulsen, Michael, Hu, Haofu, et al.

Created Date

2015-03-04

In spite of the recent interest and advances in linear controllability of complex networks, controlling nonlinear network dynamics remains an outstanding problem. Here we develop an experimentally feasible control framework for nonlinear dynamical networks that exhibit multistability. The control objective is to apply parameter perturbation to drive the system from one attractor to another, assuming that the former is undesired and the latter is desired. To make our framework practically meaningful, we consider restricted parameter perturbation by imposing two constraints: it must be experimentally realizable and applied only temporarily. We introduce the concept of attractor network, which allows us to …

Contributors

Wang, Le-Zhi, Su, Riqi, Huang, Zi-Gang, et al.

Created Date

2016-04-14

Maximally random jammed (MRJ) particle packings can be viewed as prototypical glasses in that they are maximally disordered while simultaneously being mechanically rigid. The prediction of the MRJ packing density ϕMRJ, among other packing properties of frictionless particles, still poses many theoretical challenges, even for congruent spheres or disks. Using the geometric-structure approach, we derive for the first time a highly accurate formula for MRJ densities for a very wide class of two-dimensional frictionless packings, namely, binary convex superdisks, with shapes that continuously interpolate between circles and squares. By incorporating specific attributes of MRJ states and a novel organizing principle, …

Contributors

Tian, Jianxiang, Xu, Yaopengxiao, Jiao, Yang, et al.

Created Date

2015-11-16

Tree-like structures are ubiquitous in nature. In particular, neuronal axons and dendrites have tree-like geometries that mediate electrical signaling within and between cells. Electrical activity in neuronal trees is typically modeled using coupled cable equations on multi-compartment representations, where each compartment represents a small segment of the neuronal membrane. The geometry of each compartment is usually defined as a cylinder or, at best, a surface of revolution based on a linear approximation of the radial change in the neurite. The resulting geometry of the model neuron is coarse, with non-smooth or even discontinuous jumps at the boundaries between compartments. We …

Contributors

Herrera-Valdez, Marco A., Suslov, Sergei, Vega-Guzman, Jose M., et al.

Created Date

2014-07-09

Essential or enduring understandings are often defined as the underlying core concepts or “big ideas” we’d like our students to remember when much of the course content has been forgotten. The central dogma of molecular biology and how cellular information is stored, used, and conveyed is one of the essential understandings students should retain after a course or unit in molecular biology or genetics. An additional enduring understanding is the relationships between DNA sequence, RNA sequence, mRNA production and processing, and the resulting polypeptide/protein product. A final big idea in molecular biology is the relationship between DNA mutation and polypeptide …

Contributors

Marshall, Pamela, New College of Interdisciplinary Arts and Sciences, School of Mathematical and Natural Sciences

Created Date

2017-08-11

A high-sensitivity, fully passive neurosensing system is presented for wireless brain signal monitoring. The proposed system is able to detect very low-power brain-like signals, viz. as low as -82 dBm (50 μVpp) at fneuro > 1 kHz. It is also able to read emulated neural signals as low as -70 dBm (200 μVpp) at fneuro > 100 Hz. This is an improvement of up to 22 dB in sensitivity as compared with previously reported neural signals. The system is comprised of an implanted neurosensor and an exterior interrogator. The neurosensor receives an external carrier signal and mixes it with the …

Contributors

Lee, Cedric W. L., Kiourti, Asimina, Chae, Junseok, et al.

Created Date

2015-06-01

In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. …

Contributors

Kim, Hanseong, Zou, Taisong, Modi, Chintan, et al.

Created Date

2015-01-06