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  1. Article ; Online: A Förster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR.

    Nguyen, Thuy T / Chern, Margaret / Baer, R C / Galagan, James / Dennis, Allison M

    Small (Weinheim an der Bergstrasse, Germany)

    2020  Volume 16, Issue 17, Page(s) e1907522

    Abstract: A recent description of an antibody-free assay is significantly extended for small molecule analytes using allosteric transcription factors (aTFs) and Förster resonance energy transfer (FRET). The FRET signal indicates the differential binding of an aTF- ... ...

    Abstract A recent description of an antibody-free assay is significantly extended for small molecule analytes using allosteric transcription factors (aTFs) and Förster resonance energy transfer (FRET). The FRET signal indicates the differential binding of an aTF-DNA pair with a dose-dependent response to its effector molecule, i.e., the analyte. The new sensors described here, based on the well-characterized aTF TetR, demonstrate several new features of the assay approach: 1) the generalizability of the sensors to additional aTF-DNA-analyte systems, 2) sensitivity modulation through the choice of donor fluorophore (quantum dots or fluorescent proteins, FPs), and 3) sensor tuning using aTF variants with differing aTF-DNA binding affinities. While all of these modular sensors self-assemble, the design reported here based on a recombinant aTF-FP chimera with commercially available dye-labeled DNA uses readily accessible sensor components to facilitate easy adoption of the sensing approach by the broader community.
    MeSH term(s) Biosensing Techniques/instrumentation ; DNA/metabolism ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; Quantum Dots ; Transcription Factors/metabolism
    Chemical Substances Fluorescent Dyes ; Transcription Factors ; DNA (9007-49-2)
    Language English
    Publishing date 2020-04-06
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2168935-0
    ISSN 1613-6829 ; 1613-6810
    ISSN (online) 1613-6829
    ISSN 1613-6810
    DOI 10.1002/smll.201907522
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  2. Article ; Online: Transcription Factor Based Small-Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay.

    Chern, Margaret / Garden, Padric M / Baer, R C / Galagan, James E / Dennis, Allison M

    Angewandte Chemie (International ed. in English)

    2020  Volume 59, Issue 48, Page(s) 21597–21602

    Abstract: Recently, allosteric transcription factors (TFs) were identified as a novel class of biorecognition elements for in vitro sensing, whereby an indicator of the differential binding affinity between a TF and its cognate DNA exhibits dose-dependent ... ...

    Abstract Recently, allosteric transcription factors (TFs) were identified as a novel class of biorecognition elements for in vitro sensing, whereby an indicator of the differential binding affinity between a TF and its cognate DNA exhibits dose-dependent responsivity to an analyte. Described is a modular bead-based biosensor design that can be applied to such TF-DNA-analyte systems. DNA-functionalized beads enable efficient mixing and spatial separation, while TF-labeled semiconductor quantum dots serve as bright fluorescent indicators of the TF-DNA bound (on bead) and unbound states. The prototype sensor for derivatives of the antibiotic tetracycline exhibits nanomolar sensitivity with visual detection of bead fluorescence. Facile changes to the sensor enable sensor response tuning without necessitating changes to the biomolecular affinities. Assay components self-assemble, and readout by eye or digital camera is possible within 5 minutes of analyte addition, making sensor use facile, rapid, and instrument-free.
    MeSH term(s) Anti-Bacterial Agents/analysis ; Biosensing Techniques ; Cell Phone ; DNA/chemistry ; Fluorescent Dyes/chemistry ; Quantum Dots/chemistry ; Semiconductors ; Tetracycline/analysis ; Transcription Factors/chemistry
    Chemical Substances Anti-Bacterial Agents ; Fluorescent Dyes ; Transcription Factors ; DNA (9007-49-2) ; Tetracycline (F8VB5M810T)
    Language English
    Publishing date 2020-09-18
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202007575
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  3. Article: The quantum dot

    Grazon, Chloé / Chern, Margaret / Lally, Patrick / Baer, R C / Fan, Andy / Lecommandoux, Sébastien / Klapperich, Catherine / Dennis, Allison M / Galagan, James E / Grinstaff, Mark W

    Chemical science

    2022  Volume 13, Issue 22, Page(s) 6715–6731

    Abstract: Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of ... ...

    Abstract Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye,
    Language English
    Publishing date 2022-05-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/d1sc06921g
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  4. Article ; Online: SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion.

    Leuzzi, Giuseppe / Vasciaveo, Alessandro / Taglialatela, Angelo / Chen, Xiao / Firestone, Tessa M / Hickman, Allison R / Mao, Wendy / Thakar, Tanay / Vaitsiankova, Alina / Huang, Jen-Wei / Cuella-Martin, Raquel / Hayward, Samuel B / Kesner, Jordan S / Ghasemzadeh, Ali / Nambiar, Tarun S / Ho, Patricia / Rialdi, Alexander / Hebrard, Maxime / Li, Yinglu /
    Gao, Jinmei / Gopinath, Saarang / Adeleke, Oluwatobi A / Venters, Bryan J / Drake, Charles G / Baer, Richard / Izar, Benjamin / Guccione, Ernesto / Keogh, Michael-Christopher / Guerois, Raphael / Sun, Lu / Lu, Chao / Califano, Andrea / Ciccia, Alberto

    Cell

    2024  Volume 187, Issue 4, Page(s) 861–881.e32

    Abstract: Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA ... ...

    Abstract Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 limits endogenous DNA damage, thereby suppressing cGAS-STING-dependent signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a PD-L1 transcriptional regulatory element, thereby promoting PD-L1 expression in cancer cells. SMARCAL1 loss hinders the ability of tumor cells to induce PD-L1 in response to genomic instability, enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a promising target for cancer immunotherapy.
    MeSH term(s) Animals ; Mice ; B7-H1 Antigen/metabolism ; Genomic Instability ; Immunity, Innate ; Melanoma/immunology ; Melanoma/metabolism ; Tumor Escape ; DNA Helicases/metabolism
    Chemical Substances B7-H1 Antigen ; Smarcal1 protein, mouse (EC 2.7.7.-) ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2024-01-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2024.01.008
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1167: Show issues Location:
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    Zs.MG 58: Show issues

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  5. Article ; Online: Achieving Exemplary Attributes With AccrualNet.

    Baer, Allison R / Hajovsky, Jane / Zon, Robin

    Journal of oncology practice

    2011  Volume 7, Issue 6, Page(s) e40–1

    Abstract: The AccrualNet Web site is a helpful compilation of resources for sites aspiring to improve trial accrual. ...

    Abstract The AccrualNet Web site is a helpful compilation of resources for sites aspiring to improve trial accrual.
    Language English
    Publishing date 2011-10-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2236338-5
    ISSN 1935-469X ; 1554-7477
    ISSN (online) 1935-469X
    ISSN 1554-7477
    DOI 10.1200/JOP.2011.000446
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  6. Article ; Online: A new look at informed consent for cancer clinical trials.

    Baer, Allison R / Good, Marge / Schapira, Lidia

    Journal of oncology practice

    2011  Volume 7, Issue 4, Page(s) 267–270

    Abstract: Informed consent is fundamental to the conduct of clinical trials. Prospective participants need to be adequately informed and given the opportunity to ask questions and consult with relatives or friends without feeling pressured or rushed. ...

    Abstract Informed consent is fundamental to the conduct of clinical trials. Prospective participants need to be adequately informed and given the opportunity to ask questions and consult with relatives or friends without feeling pressured or rushed.
    Language English
    Publishing date 2011-06-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2236338-5
    ISSN 1935-469X ; 1554-7477
    ISSN (online) 1935-469X
    ISSN 1554-7477
    DOI 10.1200/JOP.2011.000347
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  7. Article ; Online: Donating tissue for research: patient and provider perspectives.

    Baer, Allison R / Smith, Mary Lou / Bendell, Johanna C

    Journal of oncology practice

    2011  Volume 7, Issue 5, Page(s) 334–337

    Abstract: This article illustrates common patient and provider concerns about donating tissue for the purpose of research, discusses best practices, and provides answers to common patient questions. ...

    Abstract This article illustrates common patient and provider concerns about donating tissue for the purpose of research, discusses best practices, and provides answers to common patient questions.
    Language English
    Publishing date 2011-08-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2236338-5
    ISSN 1935-469X ; 1554-7477
    ISSN (online) 1935-469X
    ISSN 1554-7477
    DOI 10.1200/JOP.2011.000399
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  8. Article ; Online: Surface Immobilized Nucleic Acid-Transcription Factor Quantum Dots for Biosensing.

    Chen, Mingfu / Nguyen, Thuy T / Varongchayakul, Nitinun / Grazon, Chloé / Chern, Margaret / Baer, R C / Lecommandoux, Sébastien / Klapperich, Catherine M / Galagan, James E / Dennis, Allison M / Grinstaff, Mark W

    Advanced healthcare materials

    2020  Volume 9, Issue 17, Page(s) e2000403

    Abstract: Immobilization of biosensors on surfaces is a key step toward development of devices for real-world applications. Here the preparation, characterization, and evaluation of a surface-bound transcription factor-nucleic acid complex for analyte detection as ...

    Abstract Immobilization of biosensors on surfaces is a key step toward development of devices for real-world applications. Here the preparation, characterization, and evaluation of a surface-bound transcription factor-nucleic acid complex for analyte detection as an alternative to conventional systems employing aptamers or antibodies are described. The sensor consists of a gold surface modified with thiolated Cy5 fluorophore-labeled DNA and an allosteric transcription factor (TetR) linked to a quantum dot (QD). Upon addition of anhydrotetracycline (aTc)-the analyte-the TetR-QDs release from the surface-bound DNA, resulting in loss of the Förster resonance energy transfer signal. The sensor responds in a dose-dependent manner over the relevant range of 0-200 µm aTc with a limit of detection of 80 nm. The fabrication of the sensor and the subsequent real-time quantitative measurements establish a framework for the design of future surface-bound, affinity-based biosensors using allosteric transcription factors for molecular recognition.
    MeSH term(s) Biosensing Techniques ; Fluorescence Resonance Energy Transfer ; Nucleic Acids ; Quantum Dots ; Transcription Factors
    Chemical Substances Nucleic Acids ; Transcription Factors
    Language English
    Publishing date 2020-07-21
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2649576-4
    ISSN 2192-2659 ; 2192-2640
    ISSN (online) 2192-2659
    ISSN 2192-2640
    DOI 10.1002/adhm.202000403
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6966: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  9. Article ; Online: Hydrogel-Embedded Quantum Dot-Transcription Factor Sensors for Quantitative Progesterone Detection.

    Chen, Mingfu / Grazon, Chloé / Sensharma, Prerana / Nguyen, Thuy T / Feng, Yunpeng / Chern, Margaret / Baer, R C / Varongchayakul, Nitinun / Cook, Katherine / Lecommandoux, Sébastien / Klapperich, Catherine M / Galagan, James E / Dennis, Allison M / Grinstaff, Mark W

    ACS applied materials & interfaces

    2020  Volume 12, Issue 39, Page(s) 43513–43521

    Abstract: Immobilization of biosensors in or on a functional material is critical for subsequent device development and translation to wearable technology. Here, we present the development and assessment of an immobilized quantum dot-transcription factor-nucleic ... ...

    Abstract Immobilization of biosensors in or on a functional material is critical for subsequent device development and translation to wearable technology. Here, we present the development and assessment of an immobilized quantum dot-transcription factor-nucleic acid complex for progesterone detection as a first step toward such device integration. The sensor, composed of a polyhistidine-tagged transcription factor linked to a quantum dot and a fluorophore-modified cognate DNA, is embedded within a hydrogel as an immobilization matrix. The hydrogel is optically transparent, soft, and flexible as well as traps the quantum dot-transcription factor DNA assembly but allows free passage of the analyte, progesterone. Upon progesterone exposure, DNA dissociates from the quantum dot-transcription factor DNA assembly resulting in an attenuated ratiometric fluorescence output
    MeSH term(s) DNA/chemistry ; Hydrogels/chemistry ; Molecular Structure ; Particle Size ; Progesterone/analysis ; Quantum Dots/chemistry ; Surface Properties ; Transcription Factors/chemistry
    Chemical Substances Hydrogels ; Transcription Factors ; Progesterone (4G7DS2Q64Y) ; DNA (9007-49-2)
    Language English
    Publishing date 2020-09-18
    Publishing country United States
    Document type Journal Article
    ISSN 1944-8252
    ISSN (online) 1944-8252
    DOI 10.1021/acsami.0c13489
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  10. Article ; Online: Implementing a Healthy Food Distribution Program: A Supply Chain Strategy to Increase Fruit and Vegetable Access in Underserved Areas.

    DeFosset, Amelia R / Kwan, Allison / Rizik-Baer, Daniel / Gutierrez, Luis / Gase, Lauren N / Kuo, Tony

    Preventing chronic disease

    2018  Volume 15, Page(s) E61

    Abstract: Increasing access to fresh produce in small retail venues could improve the diet of people in underserved communities. However, small retailers face barriers to stocking fresh produce. In 2014, an innovative distribution program, Community Markets ... ...

    Abstract Increasing access to fresh produce in small retail venues could improve the diet of people in underserved communities. However, small retailers face barriers to stocking fresh produce. In 2014, an innovative distribution program, Community Markets Purchasing Real and Affordable Foods (COMPRA), was launched in Los Angeles with the aim of making it more convenient and profitable for small retailers to stock fresh produce. Our case study describes the key processes and lessons learned in the first 2 years of implementing COMPRA. Considerable investments in staff capacity and infrastructure were needed to launch COMPRA. Early successes included significant week-to-week increases in the volume of produce distributed. Leveraging partnerships, maintaining a flexible operational and funding structure, and broadly addressing store owners' needs contributed to initial gains. We describe key challenges and next steps to scaling the program. Lessons learned from implementing COMPRA could inform other jurisdictions considering supply-side approaches to increase access to healthy food.
    MeSH term(s) California ; Commerce ; Food Supply/economics ; Fruit ; Humans ; Medically Underserved Area ; Vegetables
    Language English
    Publishing date 2018-05-24
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2135684-1
    ISSN 1545-1151 ; 1545-1151
    ISSN (online) 1545-1151
    ISSN 1545-1151
    DOI 10.5888/pcd15.170291
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