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3eciphering the protein-DNA code of bacteria Ninged helix-turn-helix transcription factors

Frontiers of Electrical and Electronic Engineering in China 2018年第1期6卷 68-84页

作者： Adam p. joyce james j. Havranek program in Developmental Regenerative and Stem Cell Biology Washington University in St. Louis St. Louis MO 63110 USA Department of Biochemistry and Molecular Biophysics Washington University in St. Louis St. Louis MO 63110 USA

Background： Sequence-specific binding by transcription factors （TFs） plays a significant role in the selection and regulation of target genes. At the protein：DNA interface, amino acid side-chains construct a diverse physicochemical network of specific and non-specific interactions, and seemingly subtle changes in amino acid identity at certain positions may dramatically impact TF：DNA binding. Variation of these specificity-determining residues （SDRs） is a major mechanism of functional divergence between TFs with strong structural or sequence homology. Methods： In this study, we employed a combination of high-throughput specificity profiling by SELEX and Spec-seq, structural modeling, and evolutionary analysis to probe the binding preferences of winged helix-turn-helix TFs belonging to the OmpR sub-family in Escherichia coil Results： We found that E. coli OmpR paralogs recognize tandem, variably spaced repeats composed of＂GT-A＂ or ＂GCT＂-containing half-sites. Some divergent sequence preferences observed within the ＂GT-A＂ mode correlate with amino acid similarity; conversely, ＂GCT＂-based motifs were observed for a subset of paralogs with low sequence homology. Direct specificity profiling of a subset of OmpR homologues （CpxR, RstA, and OmpR） as well as predicted ＂SDR-swap＂ variants revealed that individual SDRs may impact sequence preferences locally through direct contact with DNA bases or distally via the DNA backbone. Conclusions： Overall, our work provides evidence for a common structural code for sequence-specific wHTH：DNA interactions, and demonstrates that surprisingly modest residue changes can enable recognition of highly divergent sequence motifs. Further examination of SDR predictions will likely reveal additional mechanisms controlling the evolutionary divergence of this important class of transcriptional regulators.

关键词： transcription factor SELEX winged helix-turn-helix specificity detenlainants two-component signaling

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Long-term, in vivo therapeutic effects of a single dose of miR-145 micelles for atherosclerosis

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Bioactive Materials 2023年第9期27卷 327-336页

作者： Deborah D.Chin Neil patel Woori Lee Sonali Kanaya jackson Cook Eun ji Chung Department of Biomedical Engineering University of Southern CaliforniaLos AngelesCA90089United States Division of Vascular Surgery and Endovascular Therapy Department of SurgeryKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCA90033United States Mork Family Department of Chemical Engineering and Materials Science University of Southern CaliforniaLos AngelesCA90089United States Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell research Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA90033United States Division of Nephrology and Hypertension Department of MedicineKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCA90033United States Norris Comprehensive Cancer Center Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA90089United States

Atherosclerosis is a chronic inflammatory disease that is characterized by the build-up of lipid-rich plaques in the arterial walls. The standard treatment for patients with atherosclerosis is statin therapy aimed to lower serum lipid levels. Despite its widespread use, many patients taking statins continue to experience acute events. Thus, to develop improved and alternative therapies, we previously reported on microRNA-145 (miR-145 micelles) and its ability to inhibit atherosclerosis by targeting vascular smooth muscle cells (VSMCs). Importantly, one dose of miR-145 micelles significantly abrogated disease progression when evaluated two weeks post-administration. Thus, in this study, to evaluate how long the sustained effects of miR-145 micelles can be maintained and towards identifying a dosing regimen that is practical for patients with chronic disease, the therapeutic effects of a single dose of miR-145 micelles were evaluated for up to two months in vivo. After one and two months post-treatment, miR-145 micelles were found to reduce plaque size and overall lesion area compared to all other controls including statins without causing adverse effects. Furthermore, a single dose of miR-145 micelle treatment inhibited VSMC transdifferentiation into pathogenic macrophage-like and osteogenic cells in plaques. Together, our data shows the long-term efficacy and sustained effects of miR-145 micelles that is amenable using a dosing frequency relevant to chronic disease patients.

关键词： MicroRNA-145 Atherosclerosis Vascular smooth muscle cell Nanoparticle Gene therapy

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High-throughput discovery of fluoride-ion conductors via a decoupled,dynamic,and iterative(DDI)framework

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npj Computational Materials 2022年第1期8卷 983-991页

作者： jack D.Sundberg Daniel L.Druffel Lauren M.McRae Matthew G.Lanetti jacob T.pawlik Scott C.Warren Department of Chemistry The University of North Carolina at Chapel HillChapel HillNC27599United States

Fluoride–ion batteries are a promising alternative to lithium–ion batteries with higher theoretical capacities and working voltages,but they have experienced limited success due to the poor ionic conductivities of known electrolytes and ***,we report a high-throughput computational screening of 9747 fluoride-containing materials in search of fluoride-ion *** a combination of empirical,lightweight DFT,and nudged elastic band(NEB)calculations,we identified>10 crystal systems with high fluoride *** applied a search strategy where calculations are performed in any order(decoupled),computational resources are reassigned based on need(dynamic),and predictive models are repeatedly updated(iterative).Unlike hierarchical searches,our decoupled,dynamic,and iterative framework(DDI)began by calculating high-quality barrier heights for fluoride-ion mobility in a large and diverse group of *** high-quality dataset provided a benchmark against which a rapid calculation method could be *** accurate method was then used to measure the barrier heights for 6797 fluoride–ion *** final dataset has allowed us to discover many fascinating,high-performance conductors and to derive the design rules that govern their *** materials will accelerate experimental research into fluoride–ion batteries,while the design rules will provide an improved foundation for understanding ionic conduction.

关键词： fluoride dynamic repeatedly

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Bioelectronic protein nanowire sensors for ammonia detection

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Nano research 2020年第5期13卷 1479-1484页

作者： Alexander F.Smith Xiaomeng Liu Trevor L.Woodard Tianda Fu Todd Emrick juan M.jiménez Derek R.Lovley jun Yao Department of Biomedical Engineering University of MassachusettsAmherstMA 01003USA Department of Electrical and Computer Engineering University of MassachusettsAmherstMA 01003USA Department of Microbiology University of MassachusettsAmherstMA 01003USA Department of polymer Science and Engineering University of MassachusettsAmherstMA 01003USA Department of Mechanical and Industrial Engineering University of MassachusettsAmherstMA 01003USA Institute for Applied Life Sciences(IALS) University of MassachusettsAmherstMA 01003USA

Electronic sensors based on biomaterials can lead to novel green technologies that are low cost,renewable,and *** we demonstrate bioelectronic ammonia sensors made from protein nanowires harvested from the microorganism Geobacter *** nanowire sensor responds to a broad range of ammonia concentrations(10 to 10^6 ppb),which covers the range relevant for industrial,environmental,and biomedical *** sensor also demonstrates high selectivity to ammonia compared to moisture and other common gases found in human *** results provide a proof-of-concept demonstration for developing protein nanowire based gas sensors for applications in industry,agriculture,environmental monitoring,and healthcare.

关键词： nanowire protein nanowire biomaterial bioelectronics biosensor ammonia sensor

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Multi-scale investigation of short-range order and dislocation glide in MoNbTi and TaNbTi multi-principal element alloys

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npj Computational Materials 2023年第1期9卷 1430-1442页

作者： Hui Zheng Lauren T.W.Fey Xiang-Guo Li Yong-jie Hu Liang Qi Chi Chen Shuozhi Xu Irene j.Beyerlein Shyue ping Ong Department of NanoEngineering University of California San DiegoLa JollaCA 92093-0448USA Materials Department University of CaliforniaSanta BarbaraCA 93106-5050USA Department of Materials Science and Engineering University of MichiganAnn ArborMI 48109USA Department of Materials Science and Engineering Drexel UniversityPhiladelphiaPA 19104USA Department of Mechanical Engineering University of CaliforniaSanta BarbaraCA 93106-5070USA

Refractory multi-principal element alloys(RMpEAs)are promising materials for high-temperature structural ***,we investigate the role of short-range ordering(SRO)on dislocation glide in the MoNbTi and TaNbTi RMpEAs using a multi-scale modeling *** carlo/molecular dynamics simulations with a moment tensor potential show that MoNbTi exhibits a much greater degree of SRO than TaNbTi and the local composition has a direct effect on the unstable stacking fault energies(USFEs).From mesoscale phase-field dislocation dynamics simulations,we find that increasing SRO leads to higher mean USFEs and stress required for dislocation *** gliding dislocations experience significant hardening due to pinning and depinning caused by random compositional fluctuations,with higher SRO decreasing the degree of USFE dispersion and hence,amount of ***,we show how the morphology of an expanding dislocation loop is affected by the applied stress.

关键词： alloys dislocation element

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A Convergent Understanding of Charged Defects

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Accounts of Materials research 2022年第7期3卷 685-696页

作者： Shashwat Anand Michael Y.Toriyama Chris Wolverton Sossina M.Haile G.jeffrey Snyder Department of Materials Science and Engineering Northwestern UniversityEvanstonIllinois 60208United States Materials Sciences Division Lawrence Berkeley National LaboratoryBerkeleyCalifornia 94720United States

CONSpECTUS:Historically,defects in semiconductors and ionic conductors have been studied using very different *** the solid-state ionics community,nonstoichiometry and defect thermochemistry are often probed directly through *** dependency of defect concentrations on chemical conditions(typically oxygen pressure)are modeled using a physical chemistry framework and compactly represented by the well-known Brouwer diagrams.

关键词： defect chemistry ionic

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Microfabricated platforms to investigate cell mechanical properties

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Medicine in Novel Technology and Devices 2022年第1期13卷 49-58页

作者： Amir M.Esfahani Grayson Minnick jordan Rosenbohm Haiwei Zhai Xiaowei jin Bahareh Tajvidi Safa justin Brooks Ruiguo Yang Department of Mechanical and Materials Engineering University of Nebraska-LincolnLincolnNE68516USA Nebraska Center for Integrated Biomolecular Communication University of Nebraska-LincolnLincolnNE68588USA Mary and Dick Holland Regenerative Medicine program University of Nebraska Medical CenterOmahaNE68198USA Department of Bioengineering School of MedicineJohns Hopkins UniversityBaltimoreMD21205USA

Mechanical stimulation has been imposed on living cells using several *** early investigations were conducted on groups of cells,utilizing techniques such as substrate deformation and flow-induced *** investigate the properties of cells individually,many conventional techniques were utilized,such as AFM,optical traps/optical tweezers,magnetic beads,and micropipette *** specific mechanical interrogations,microelectro-mechanical systems(MEMS)have been designed to probe single cells in different interrogation *** exert loads on the cells,these devices often comprise piezo-electric driven actuators that attach directly to the cell or move a structure on which cells are *** and biaxial pullers,micropillars,and cantilever beams are examples of MEMS *** this review,the methodologies to analyze single cell activity under external loads using microfabricated devices will be *** will focus on the mechanical interrogation in three different regimes:compression,traction,and tension,and discuss different microfabricated platforms designed for these purposes.

关键词： BioMEMS Single cell Mechanical properties Microdevices

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Spatially and spectrally resolved orbital angular momentum interactions in plasmonic vortex generators

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Light(Science & Applications) 2019年第1期8卷 907-915页

作者： jordan A.Hachtel Sang-Yeon Cho Roderick B.Davidson II Matthew A.Feldman Matthew F.Chisholm Richard F.Haglund juan Carlos Idrobo Sokrates T.pantelides Benjamin j.Lawrie Center for Nanophase Materials Science Oak Ridge National LaboratoryOak RidgeTN 37831USA Klipsch School of Electrical and Computer Engineering New Mexico State UniversityLas CrucesNM 88003USA Department of physics and Astronomy Vanderbilt UniversityNashvilleTN 37235USA Quantum Information Science Group Oak Ridge National LaboratoryOak RidgeTN 37831USA Materials Science and Technology Division Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Electrical Engineering and Computer Science Vanderbilt University NashvilleNashvilleTN 37235USA Chemistry Division U.S.Naval Research LaboratoryWashingtonD.C.20375USA

Understanding the near-field electromagnetic interactions that produce optical orbital angular momentum(OAM)is crucial for integrating twisted light into ***,we examine the cathodoluminescence(CL)of plasmonic vortices carrying OAM generated in spiral *** nanospiral geometry defines a photonic local density of states that is sampled by the electron probe in a scanning transmission electron microscope(STEM),thus accessing the optical response of the plasmonic vortex with high spatial and spectral *** map the full spectral dispersion of the plasmonic vortex in spiral structures designed to yield increasing topological ***,we fabricate nested nanospirals and demonstrate that OAM from one nanospiral can be coupled to the nested nanospiral,resulting in enhanced luminescence in concentric spirals of like handedness with respect to concentric spirals of opposite *** results illustrate the potential for generating and coupling plasmonic vortices in chiral nanostructures for sensitive detection and manipulation of optical OAM.

关键词： momentum spectral angular

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Learning Matter:Materials Design with Machine Learning andAtomistic Simulations

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Accounts of Materials research 2022年第3期3卷 343-357页

作者： Simon Axelrod Daniel Schwalbe-Koda Somesh Mohapatra james Damewood Kevin p.Greenman Rafael Gómez-Bombarelli Department of Chemistry and Chemical Biology Harvard UniversityCambridgeMassachusetts 02138United States Department of Materials Science and Engineering Massachusetts Institute of TechnologyCambridgeMassachusetts 02139United States

CONSpECTUS:Designing new materials is vital for addressing pressing societal challenges in health,energy,and *** combination of physicochemical laws and empirical trial and error has long guided material design,but this approach is limited by the cost of experiments and the difficulty of deriving complex guiding *** space of hypothetical materials to be considered is incredibly large,and only a small fraction of possible compounds can ever be tested *** computational techniques of atomistic simulation and machine learning(ML)offer an avenue to rapidly invent new materials and navigate this enormous ***,they can be used to infer complex design principles and identify high-quality candidates more rapidly than trial-and-error *** this Account,we review our group’s recent contributions to simulation and ML for materials *** begin by discussing the numerical representation of materials for use in *** can be produced through deterministic algorithms,learnable encodings,or physics-based methods and lead to vector,graph,and matrix *** describe how these different approaches offer distinct material-and application-specific *** provide demonstrations from our own work on small-molecule drugs,macromolecules,dyes,electrolytes,and *** several cases,we show how the appropriate representation led to guiding principles that facilitated experimental materials ***,we highlight the development of ML methods for enhancing atomistic *** advances help to improve simulation accuracy and expand the time and length scales that can be *** include differentiable atomistic simulations in which ensemble-averaged quantities are differentiated with respect to system parameters,and novel autoregressive methods for enhanced sampling of challenging physical *** developments include learnable coarse-grained models,which can accelerate molecula

关键词： zeolite differentiable latter

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Interfacial Charge Transfer in Nanoscale polymer Transistors

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Nano research 2008年第4期1卷 341-350页

作者： jeffrey H.Worne Rajiv Giridharagopal Kevin F.Kelly Douglas Natelson Department of Electrical and Computer Engineering Rice University6100 Main St.HoustonTX 77005USA Department of physics and Astronomy Rice University6100 Main St.HoustonTX 77005USA

Interfacial charge transfer plays an essential role in establishing the relative alignment of the metal Fermi level and the energy bands of organic *** the details remain elusive in many systems,this charge transfer has been inferred in a number of photoemission *** present electronic transport measurements in very short channel(Lpoly(3-hexylthiophene)(p3HT).As channel length is reduced,the evolution of the contact resistance and the zero gate voltage conductance are consistent with such charge *** channel conduction in devices with pt contacts is greatly enhanced compared to analogous devices with Au contacts,consistent with charge transfer *** current scanning tunneling microscopy(ACSTM)provides further evidence that holes are transferred from pt into p3HT,while much less charge transfer takes place at the Au/p3HT interface.

关键词： Organic semiconductors band alignment charge transfer organic field-effect transistor scanning tunneling microscopy

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