Directed evolution methods for overcoming trade‐offs between protein activity and stability

Engineered proteins are being widely developed and employed in applications ranging from enzyme catalysts to therapeutic antibodies. Directed evolution, an iterative experimental process composed of mutagenesis and library screening, is a powerful technique for enhancing existing protein activities and generating entirely new ones not observed in nature. However, the process of accumulating mutations for enhanced protein activity requires chemical and structural changes that are often destabilizing, and low protein stability is a significant barrier to achieving large enhancements in activity during multiple rounds of directed evolution. Here we highlight advances in understanding the origins of protein activity/stability trade‐offs for two important classes of proteins (enzymes and antibodies) as well as innovative experimental and computational methods for overcoming such trade‐offs. These advances hold great potential for improving the generation of highly active and stable proteins that are needed to address key challenges related to human health, energy and the environment.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154495/1/aic16814_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154495/2/aic16814.pd

Optimal classical-communication-assisted local model of n-qubit Greenberger-Horne-Zeilinger correlations

We present a model, motivated by the criterion of reality put forward by Einstein, Podolsky, and Rosen and supplemented by classical communication, which correctly reproduces the quantum-mechanical predictions for measurements of all products of Pauli operators on an n-qubit GHZ state (or ``cat state''). The n-2 bits employed by our model are shown to be optimal for the allowed set of measurements, demonstrating that the required communication overhead scales linearly with n. We formulate a connection between the generation of the local values utilized by our model and the stabilizer formalism, which leads us to conjecture that a generalization of this method will shed light on the content of the Gottesman-Knill theorem.Comment: New version - expanded and revised to address referee comment

Entanglement of Dirac fields in non-inertial frames

We analyze the entanglement between two modes of a free Dirac field as seen by two relatively accelerated parties. The entanglement is degraded by the Unruh effect and asymptotically reaches a non-vanishing minimum value in the infinite acceleration limit. This means that the state always remains entangled to a degree and can be used in quantum information tasks, such as teleportation, between parties in relative uniform acceleration. We analyze our results from the point of view afforded by the phenomenon of entanglement sharing and in terms of recent results in the area of multi-qubit complementarity.Comment: 15 pages, with 8 figures (Mar 2006); accepted to Physical Review A, July 2006 - slightly revise

Response to ‘A well-established fact: Rapid mineralization of organic inputs is an important factor for soil carbon sequestration’ by Angers et al.

Letter to the edito

Soil physical properties affected by soil management and crop rotation in a long term experiment in Southern Brazil

The main objective of this work is to evaluate soil physical properties affected by cover crop rotations and soil management after 19 years of applying NoTill and Conventional Tillage systems with different winter species on a clayey Oxisol in South Brazil

Long-term effect of different soil management systems and winter crops on soil acidity and vertical distribution of nutrients in a Brazilian Oxisol

“Strategies” to sustain crop productivity by reducing the fertilizer and lime demands must be developed. The use of plant species that use more efficiently the soil nutrients and tillage systems that provide nutrients accumulation in more labile forms are prerequisites for sustainable agroecosystems. This study aimed to evaluate the long period effect of cultivating different winter species under different soil management systems on vertical distribution of soil nutrients and the soil acidity distribution in soil profile. The experiment was established in 1986 with six winter treatments (blue lupine, hairy vetch, oat, radish, wheat and fallow) under conventional tillage (CT) and no-tillage (NT) in a very clayey Rhodic Hapludox in Southern Brazil. As a result of 19 years of no soil disturbance, soil chemical attributes related to soil acidity and the availability of P and K were more favorable to crops growth up to 10 cm in the soil under no-tillage than in the conventional tillage. On other hand, lime applications in low doses on the soil surface were not efficient in neutralizing the aluminum toxicity below 10 cm depth. It shows that repeated use of lime on the soil surface under NT system can be a viable alternative strategy only when soil acidity and aluminum toxicity in subsurface has been previously eliminated using the adequate amount of lime and incorporating it into the arable layer. Moreover, in the conventional tillage system P and K availability were higher below 10 cm depth compared to the no-tillage system. Even after 19 years of no soil disturbance in the NT system the available P content below 10 cm soil layer was lower than the optimal content of available P recommended to cash crops. The reduced surface K application over time was sufficient to gain adequate crop yields and to maintain the optimal content of soil available K in both soil management systems. The effects of soil management systems were predominant on the soil acidity attributes, and no effects of winter cover crops were observed on soil acidity attributes. Black oat and blue lupine were more efficient in P cycling, increasing the soil available P content especially in the surface soil under NT. The lower amount of biomass produced over time when no cover crops were used in the winter period resulted in lower P and K availability in the soil, showing the important role of growing winter species to maintain soil fertility

Computing prime factors with a Josephson phase qubit quantum processor

A quantum processor (QuP) can be used to exploit quantum mechanics to find the prime factors of composite numbers[1]. Compiled versions of Shor's algorithm have been demonstrated on ensemble quantum systems[2] and photonic systems[3-5], however this has yet to be shown using solid state quantum bits (qubits). Two advantages of superconducting qubit architectures are the use of conventional microfabrication techniques, which allow straightforward scaling to large numbers of qubits, and a toolkit of circuit elements that can be used to engineer a variety of qubit types and interactions[6, 7]. Using a number of recent qubit control and hardware advances [7-13], here we demonstrate a nine-quantum-element solid-state QuP and show three experiments to highlight its capabilities. We begin by characterizing the device with spectroscopy. Next, we produces coherent interactions between five qubits and verify bi- and tripartite entanglement via quantum state tomography (QST) [8, 12, 14, 15]. In the final experiment, we run a three-qubit compiled version of Shor's algorithm to factor the number 15, and successfully find the prime factors 48% of the time. Improvements in the superconducting qubit coherence times and more complex circuits should provide the resources necessary to factor larger composite numbers and run more intricate quantum algorithms.Comment: 5 pages, 3 figure