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Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Brunk, Elizabeth,Chang, Roger L.,Xia, Jing,Hefzi, Hooman,Yurkovich, James T.,Kim, Donghyuk,Buckmiller, Evan,Wang, Harris H.,Cho, Byung-Kwan,Yang, Chen,Palsson, Bernhard O.,Church, George M.,Lewis, Nat National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.43
<P>Understanding the complex interactions of protein posttranslational modifications (PTMs) represents a major challenge in metabolic engineering, synthetic biology, and the biomedical sciences. Here, we present a workflow that integrates multiplex automated genome editing (MAGE), genome-scale metabolic modeling, and atomistic molecular dynamics to study the effects of PTMs on metabolic enzymes and microbial fitness. This workflow incorporates complementary approaches across scientific disciplines; provides molecular insight into how PTMs influence cellular fitness during nutrient shifts; and demonstrates how mechanistic details of PTMs can be explored at different biological scales. As a proof of concept, we present a global analysis of PTMs on enzymes in the metabolic network of Escherichia coll. Based on our workflow results, we conduct a more detailed, mechanistic analysis of the PTMs in three proteins: enolase, serine hydroxymethyltransferase, and transaldolase. Application of this workflow identified the roles of specific PTMs in observed experimental phenomena and demonstrated how individual PTMs regulate enzymes, pathways, and, ultimately, cell phenotypes.</P>
Self-aligned deterministic coupling of single quantum emitter to nanofocused plasmonic modes
Gong, Su-Hyun,Kim, Je-Hyung,Ko, Young-Ho,Rodriguez, Christophe,Shin, Jonghwa,Lee, Yong-Hee,Dang, Le Si,Zhang, Xiang,Cho, Yong-Hoon National Academy of Sciences 2015 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.112 No.17
<P><B>Significance</B></P><P>Control and optimization of interaction between light and single quantum emitters are a crucial issue for cavity quantum electrodynamics studies and quantum information science. Although considerable efforts have been made, reliable and reproducible coupling between quantum emitter and cavity mode still remains a grand challenge due to the uncertainty of the size, i.e., the emission wavelength, and position of the quantum emitter. Here, we demonstrate an unprecedented approach of the self-aligned deterministic coupling of single quantum dots (QDs) to nanofocused plasmonic modes on an entire wafer. Spatial precision is better than any nanopositioning techniques, and almost all processed QDs exhibit outstanding spontaneous emission rate enhancement. This reliable approach eliminates a major obstacle in the implementation of practical solid-state quantum emitters.</P><P>The quantum plasmonics field has emerged and been growing increasingly, including study of single emitter–light coupling using plasmonic system and scalable quantum plasmonic circuit. This offers opportunity for the quantum control of light with compact device footprint. However, coupling of a single emitter to highly localized plasmonic mode with nanoscale precision remains an important challenge. Today, the spatial overlap between metallic structure and single emitter mostly relies either on chance or on advanced nanopositioning control. Here, we demonstrate deterministic coupling between three-dimensionally nanofocused plasmonic modes and single quantum dots (QDs) without any positioning for single QDs. By depositing a thin silver layer on a site-controlled pyramid QD wafer, three-dimensional plasmonic nanofocusing on each QD at the pyramid apex is geometrically achieved through the silver-coated pyramid facets. Enhancement of the QD spontaneous emission rate as high as 22 ± 16 is measured for all processed QDs emitting over ∼150-meV spectral range. This approach could apply to high fabrication yield on-chip devices for wide application fields, e.g., high-efficiency light-emitting devices and quantum information processing.</P>
RNA design rules from a massive open laboratory
Lee, Jeehyung,Kladwang, Wipapat,Lee, Minjae,Cantu, Daniel,Azizyan, Martin,Kim, Hanjoo,Limpaecher, Alex,Yoon, Sungroh,Treuille, Adrien,Das, Rhiju National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.6
<P>Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems. However, imperfect in silico models—even at the secondary structure level—hinder the design of new RNAs that function properly when synthesized. Here, we present a unique and potentially general approach to such empirical problems: the Massive Open Laboratory. The EteRNA project connects 37,000 enthusiasts to RNA design puzzles through an online interface. Uniquely, EteRNA participants not only manipulate simulated molecules but also control a remote experimental pipeline for high-throughput RNA synthesis and structure mapping. We show herein that the EteRNA community leveraged dozens of cycles of continuous wet laboratory feedback to learn strategies for solving in vitro RNA design problems on which automated methods fail. The top strategies—including several previously unrecognized negative design rules—were distilled by machine learning into an algorithm, EteRNABot. Over a rigorous 1-y testing phase, both the EteRNA community and EteRNABot significantly outperformed prior algorithms in a dozen RNA secondary structure design tests, including the creation of dendrimer-like structures and scaffolds for small molecule sensors. These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science.</P>
Graphene transistor based on tunable Dirac fermion optics
Wang, Ke,Elahi, Mirza M.,Wang, Lei,Habib, K. M. Masum,Taniguchi, Takashi,Watanabe, Kenji,Hone, James,Ghosh, Avik W.,Lee, Gil-Ho,Kim, Philip National Academy of Sciences 2019 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.116 No.14
<P><B>Significance</B></P><P>We report an electrically tunable graphene quantum switch based on Dirac fermion optics (DFO), with electrostatically defined analogies of mirror and collimators utilizing angle-dependent Klein tunneling. The device design allows a previously unreported quantitative characterization of the net DFO contribution and leads to improved device performance resilient to abrupt change in temperature, bias, doping, and electrostatic environment. The electrically tunable collimator and reflector demonstrated in this work, and the capability of accurate in situ characterization of their performance, provide the building blocks toward more complicated functional quantum device architecture such as highly integrated electron-optical circuits.</P><P>We present a quantum switch based on analogous Dirac fermion optics (DFO), in which the angle dependence of Klein tunneling is explicitly utilized to build tunable collimators and reflectors for the quantum wave function of Dirac fermions. We employ a dual-source design with a single flat reflector, which minimizes diffusive edge scattering and suppresses the background incoherent transmission. Our gate-tunable collimator–reflector device design enables the quantitative measurement of the net DFO contribution in the switching device operation. We obtain a full set of transmission coefficients between multiple leads of the device, separating the classical contribution from the coherent transport contribution. The DFO behavior demonstrated in this work requires no explicit energy gap. We demonstrate its robustness against thermal fluctuations up to 230 K and large bias current density up to 10<SUP>2</SUP> A/m, over a wide range of carrier densities. The characterizable and tunable optical components (collimator–reflector) coupled with the conjugated source electrodes developed in this work provide essential building blocks toward more advanced DFO circuits such as quantum interferometers. The capability of building optical circuit analogies at a microscopic scale with highly tunable electron wavelength paves a path toward highly integrated and electrically tunable electron-optical components and circuits.</P>
Cho, Chung-Hyun,Sung, Hoon-Ki,Kim, Kyung-Tae,Cheon, Hyae Gyeong,Oh, Goo Taeg,Hong, Hyo Jeong,Yoo, Ook-Joon,Koh, Gou Young National Academy of Sciences 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.103 No.13
<P>Microvascular dysfunction is a major cause of impaired wound healing seen in diabetic patients. Therefore, reestablishment of structural and functional microvasculature could be beneficial to promote wound healing in these patients. Angiopoietin-1 (Ang1) is a specific growth factor functioning to generate a stable and functional vasculature through the Tie2 and Tie1 receptors. Here we determined the effectiveness of cartilage oligomeric matrix protein (COMP)-Ang1, a soluble, stable, and potent form of Ang1, on promotion of healing in cutaneous wounds of diabetic mice. An excisional full-thickness wound was made in the dorsal side of the tail of diabetic (db/db) mice, and mice were then treated systemically with adenovirus (Ade) encoding COMP-Ang1 or with control virus encoding beta-gal (Ade-beta-gal) or treated topically with recombinant COMP-Ang1 protein or BSA. Time course observations revealed that mice treated with Ade-COMP-Ang1 or COMP-Ang1 protein showed accelerated wound closure and epidermal and dermal regeneration, enhanced angiogenesis and lymphangiogenesis, and higher blood flow in the wound region compared with mice treated with control virus or BSA. COMP-Ang1 promotion of wound closure and angiogenesis was not dependent on endothelial nitric oxide synthase or inducible nitric oxide synthase alone. Taken together, these findings indicate that COMP-Ang1 can promote wound healing in diabetes through enhanced angiogenesis, lymphangiogenesis, and blood flow.</P>