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  1. Article ; Online: Mixed Ligand Passivation as the Origin of Near-Unity Emission Quantum Yields in CsPbBr

    Ding, Yang / Zhang, Zhuoming / Toso, Stefano / Gushchina, Irina / Trepalin, Vadim / Shi, Kejia / Peng, Jeffrey W / Kuno, Masaru

    Journal of the American Chemical Society

    2023  Volume 145, Issue 11, Page(s) 6362–6370

    Abstract: Key features of syntheses, involving the quaternary ammonium passivation of ... ...

    Abstract Key features of syntheses, involving the quaternary ammonium passivation of CsPbBr
    Language English
    Publishing date 2023-03-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.2c13527
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  2. Article: Enhanced lattice perfection by low temperature thermal annealing in photoelectric (CH

    Li, Wen-Hsien / Lee, Chi-Hung / Ling, Tsu-Yin / Ma, Ma-Hsuan / Wei, Pai-Chun / He, Jr-Hau / Wu, Chun-Min / Peng, Jen-Chih / Xu, Guangyong / Zhao, Yang / Lynn, Jeffrey W

    Physical review materials

    2023  Volume 5, Issue 2

    Abstract: The coupling between the organic ... ...

    Abstract The coupling between the organic CH
    Language English
    Publishing date 2023-11-07
    Publishing country United States
    Document type Journal Article
    ISSN 2475-9953
    ISSN 2475-9953
    DOI 10.1103/PhysRevMaterials.5.025401
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  3. Article: Occupant-Based Injury Severity Prediction.

    Owen, Susan H / Joyner, Jeffrey W / Zhang, Peng / Wang, Stewart C

    Stapp car crash journal

    2022  Volume 65, Page(s) 17–28

    Abstract: Road traffic injuries continue to be a leading cause of death around the world. Rapid emergency response is a key factor in improving occupant outcomes. Over the past ten years, Injury Severity Prediction (ISP) models have been developed and deployed to ... ...

    Abstract Road traffic injuries continue to be a leading cause of death around the world. Rapid emergency response is a key factor in improving occupant outcomes. Over the past ten years, Injury Severity Prediction (ISP) models have been developed and deployed to assist in effective dispatch of emergency medical services (EMS). Prior versions of ISP have relied on driver-based scenarios that are not relevant in many of the possible autonomous vehicle (AV) contexts. This paper describes the development and validation of occupant-based ISP models that predict injury severity for specific vehicle seat positions. Models show improved predictive performance, sensitivity 80% and specificity over 95%, for front row occupants. Second row occupant models have similar specificity, but sensitivity scores dropped due to occupant heterogeneity and small sample sizes of seriously injured occupants.
    MeSH term(s) Accidents, Traffic ; Humans ; Wounds and Injuries
    Language English
    Publishing date 2022-04-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2037200-0
    ISSN 1532-8546 ; 0585-086X
    ISSN 1532-8546 ; 0585-086X
    DOI 10.4271/2021-22-0002
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  4. Article ; Online: Characterizing Protein Dynamics with NMR R

    Massi, Francesca / Peng, Jeffrey W

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1688, Page(s) 205–221

    Abstract: The measurement of ... ...

    Abstract The measurement of R
    MeSH term(s) Magnetic Resonance Spectroscopy/methods ; Models, Molecular ; Motion ; Protein Conformation ; Proteins/chemistry ; Thermodynamics
    Chemical Substances Proteins
    Language English
    Publishing date 2017-11-17
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7386-6_10
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  5. Article: Investigating Dynamic Interdomain Allostery in Pin1.

    Peng, Jeffrey W

    Biophysical reviews

    2015  Volume 7, Issue 2, Page(s) 239–249

    Abstract: Signaling proteins often sequester complementary functional sites in separate domains. How do the different domains communicate with one another? An attractive system to address this question is the mitotic regulator, human Pin1 (Lu et al. 1996). Pin-1 ... ...

    Abstract Signaling proteins often sequester complementary functional sites in separate domains. How do the different domains communicate with one another? An attractive system to address this question is the mitotic regulator, human Pin1 (Lu et al. 1996). Pin-1 consists of two tethered domains: a WW domain for substrate binding, and a catalytic domain for peptidyl-prolyl isomerase (PPIase) activity. Pin1 accelerates the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs within proteins regulating the cell cycle and neuronal development. The early x-ray (Ranganathan et al. 1997; Verdecia et al. 2000) and solution NMR studies (Bayer et al. 2003; Jacobs et al. 2003) of Pin1 indicated inter- and intradomain motion. We became interested in exploring how such motions might affect interdomain communication, using NMR. Our accumulated results indicate substrate binding to Pin1 WW domain changes the intra/inter domain mobility, thereby altering substrate activity in the distal PPIase domain catalytic site. Thus, Pin1 shows evidence of dynamic allostery, in the sense of Cooper and Dryden (Cooper and Dryden 1984). We highlight our results supporting this conclusion, and summarize them via a simple speculative model of conformational selection.
    Language English
    Publishing date 2015-04-22
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-015-0171-9
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  6. Article ; Online: Orchestration of virulence factor expression and modulation of biofilm dispersal in Erwinia amylovora through activation of the Hfq-dependent small RNA RprA.

    Peng, Jingyu / Schachterle, Jeffrey K / Sundin, George W

    Molecular plant pathology

    2020  Volume 22, Issue 2, Page(s) 255–270

    Abstract: Erwinia amylovora is the causative agent of the devastating disease fire blight of pome fruit trees. After infection of host plant leaves at apple shoot tips, E. amylovora cells form biofilms in xylem vessels, restrict water flow, and cause wilting ... ...

    Abstract Erwinia amylovora is the causative agent of the devastating disease fire blight of pome fruit trees. After infection of host plant leaves at apple shoot tips, E. amylovora cells form biofilms in xylem vessels, restrict water flow, and cause wilting symptoms. Although E. amylovora is well known to be able to cause systemic infection, how biofilm cells of E. amylovora transit from the sessile mode of growth in xylem to the planktonic mode of growth in cortical parenchyma remains unknown. Increasing evidence has suggested the important modulatory roles of Hfq-dependent small RNAs (sRNAs) in the pathogenesis of E. amylovora. Here, we demonstrate that the sRNA RprA acts as a positive regulator of amylovoran exopolysaccharide production, the type III secretion system (T3SS), and flagellar-dependent motility, and as a negative regulator of levansucrase activity and cellulose production. We also show that RprA affects the promoter activity of multiple virulence factor genes and regulates hrpS, a critical T3SS regulator, at the posttranscriptional level. We determined that rprA expression can be activated by the Rcs phosphorelay, and that expression is active during T3SS-mediated host infection in an immature pear fruit infection model. We further showed that overexpression of rprA activated the in vitro dispersal of E. amylovora cells from biofilms. Thus, our investigation of the varied role of RprA in affecting E. amylovora virulence provides important insights into the functions of this sRNA in biofilm control and systemic infection.
    MeSH term(s) Biofilms ; Cellulose/genetics ; Erwinia amylovora/genetics ; Erwinia amylovora/metabolism ; Erwinia amylovora/pathogenicity ; Hexosyltransferases/genetics ; Movement ; Polysaccharides, Bacterial/genetics ; Promoter Regions, Genetic ; RNA, Bacterial/physiology ; Type III Secretion Systems/genetics ; Virulence Factors/genetics ; Virulence Factors/metabolism
    Chemical Substances Polysaccharides, Bacterial ; RNA, Bacterial ; Type III Secretion Systems ; Virulence Factors ; amylovoran ; Cellulose (9004-34-6) ; Hexosyltransferases (EC 2.4.1.-) ; levansucrase (EC 2.4.1.10)
    Language English
    Publishing date 2020-12-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2020755-4
    ISSN 1364-3703 ; 1464-6722
    ISSN (online) 1364-3703
    ISSN 1464-6722
    DOI 10.1111/mpp.13024
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  7. Article ; Online: A gratuitous β-Lactamase inducer uncovers hidden active site dynamics of the Staphylococcus aureus BlaR1 sensor domain.

    Frederick, Thomas E / Peng, Jeffrey W

    PloS one

    2018  Volume 13, Issue 5, Page(s) e0197241

    Abstract: Increasing evidence shows that active sites of proteins have non-trivial conformational dynamics. These dynamics include active site residues sampling different local conformations that allow for multiple, and possibly novel, inhibitor binding poses. Yet, ...

    Abstract Increasing evidence shows that active sites of proteins have non-trivial conformational dynamics. These dynamics include active site residues sampling different local conformations that allow for multiple, and possibly novel, inhibitor binding poses. Yet, active site dynamics garner only marginal attention in most inhibitor design efforts and exert little influence on synthesis strategies. This is partly because synthesis requires a level of atomic structural detail that is frequently missing in current characterizations of conformational dynamics. In particular, while the identity of the mobile protein residues may be clear, the specific conformations they sample remain obscure. Here, we show how an appropriate choice of ligand can significantly sharpen our abilities to describe the interconverting binding poses (conformations) of protein active sites. Specifically, we show how 2-(2'-carboxyphenyl)-benzoyl-6-aminopenicillanic acid (CBAP) exposes otherwise hidden dynamics of a protein active site that binds β-lactam antibiotics. When CBAP acylates (binds) the active site serine of the β-lactam sensor domain of BlaR1 (BlaRS), it shifts the time scale of the active site dynamics to the slow exchange regime. Slow exchange enables direct characterization of inter-converting protein and bound ligand conformations using NMR methods. These methods include chemical shift analysis, 2-d exchange spectroscopy, off-resonance ROESY of the bound ligand, and reduced spectral density mapping. The active site architecture of BlaRS is shared by many β-lactamases of therapeutic interest, suggesting CBAP could expose functional motions in other β-lactam binding proteins. More broadly, CBAP highlights the utility of identifying chemical probes common to structurally homologous proteins to better expose functional motions of active sites.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; Catalytic Domain ; Escherichia coli ; Ligands ; Metalloendopeptidases/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Penicillanic Acid/analogs & derivatives ; Penicillanic Acid/chemistry ; Penicillanic Acid/pharmacology ; Protein Conformation ; Staphylococcus aureus ; beta-Lactamases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Ligands ; 2-(2'-carboxyphenyl)benzoyl-6-aminopenicillanic acid (14796-35-1) ; Penicillanic Acid (87-53-6) ; BlaR1 protein, Staphylococcus aureus (EC 3.4.24.-) ; Metalloendopeptidases (EC 3.4.24.-) ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2018-05-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0197241
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  8. Article ; Online: Genetic Dissection of the

    Kharadi, Roshni R / Schachterle, Jeffrey K / Yuan, Xiaochen / Castiblanco, Luisa F / Peng, Jingyu / Slack, Suzanne M / Zeng, Quan / Sundin, George W

    Annual review of phytopathology

    2021  Volume 59, Page(s) 191–212

    Abstract: Fire blight, caused by the bacterial ... ...

    Abstract Fire blight, caused by the bacterial phytopathogen
    MeSH term(s) Dissection ; Erwinia amylovora/genetics ; Malus ; Plant Diseases ; Pyrus
    Language English
    Publishing date 2021-05-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 207934-3
    ISSN 1545-2107 ; 0066-4286
    ISSN (online) 1545-2107
    ISSN 0066-4286
    DOI 10.1146/annurev-phyto-020620-095540
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  9. Article: Multifaceted roles of cohesin in regulating transcriptional loops.

    Kim, Minji / Wang, Ping / Clow, Patricia A / Chien, I Eli / Wang, Xiaotao / Peng, Jianhao / Chai, Haoxi / Liu, Xiyuan / Lee, Byoungkoo / Ngan, Chew Yee / Yue, Feng / Milenkovic, Olgica / Chuang, Jeffrey H / Wei, Chia-Lin / Casellas, Rafael / Cheng, Albert W / Ruan, Yijun

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live- ... ...

    Abstract Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
    Language English
    Publishing date 2024-03-27
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.25.586715
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  10. Article ; Online: Linear, Graft, and Beyond

    Jeffrey L. Self / Aristotle J. Zervoudakis / Xiayu Peng / William R. Lenart / Christopher W. Macosko / Christopher J. Ellison

    JACS Au, Vol 2, Iss 2, Pp 310-

    Multiblock Copolymers as Next-Generation Compatibilizers

    2022  Volume 321

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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