David E. Volk

Robert Bosch (Germany)

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David G. Gorenstein

The University of Texas Health Science Center at Houston

Bruce A. Luxon

Georgetown University

Varatharasa Thiviyanathan

The University of Texas Health Science Center at Houston

G.L. Lokesh

Brown Foundation

Alan D.T. Barrett

The University of Texas Medical Branch at Galveston

Muniasamy Neerathilingam

Institute of Bioinformatics

Anoma Somasunderam

The University of Texas Health Science Center at Houston

David W. C. Beasley

The University of Texas Medical Branch at Galveston

Anil K. Sood

The University of Texas MD Anderson Cancer Center

Todd M. Alam

Sandia National Laboratories

Cooperative Institutions

The University of Texas MD Anderson Cancer Center

The University of Texas Health Science Center at Houston

The University of Texas Medical Branch at Galveston

Houston Methodist

National Institutes of Health

The University of Texas at Austin

Rice University

University of Oklahoma Health Sciences Center

Cornell University

Baylor College of Medicine

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1H NMR metabonomic study of rat response to tri-phenyl phosphate and tri-butyl phosphate exposure

Metabolomics (2010)

Todd M. Alam Mary Kathleen Alam Muniasamy Neerathilingam David E. Volk Swapna Sarkar

10.1007/s11306-010-0205-z

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Citations (18)

Thymosins

Elsevier eBooks (2019)

Haruka Kobayashi Yue Yu David E. Volk

Thymosin

10.1016/b978-0-12-813814-4.00013-4

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Citations (1)

Morph-X-Select: Morphology-based tissue aptamer selection for ovarian cancer biomarker discovery

BioTechniques (2016)

Hongyu Wang Xin Li David E. Volk G.L. Lokesh Miguel-Angel Elizondo-Riojas

High affinity aptamer-based biomarker discovery has the advantage of simultaneously discovering an aptamer affinity reagent and its target biomarker protein. Here, we demonstrate a morphology-based tissue aptamer selection method that enables us to use tissue sections from individual patients and identify high-affinity aptamers and their associated target proteins in a systematic and accurate way. We created a combinatorial DNA aptamer library that has been modified with thiophosphate substitutions of the phosphate ester backbone at selected 5´dA positions for enhanced nuclease resistance and targeting. Based on morphological assessment, we used image-directed laser microdissection (LMD) to dissect regions of interest bound with the thioaptamer (TA) library and further identified target proteins for the selected TAs. We have successfully identified and characterized the lead candidate TA, V5, as a vimentin-specific sequence that has shown specific binding to tumor vasculature of human ovarian tissue and human microvascular endothelial cells. This new Morph-X-Select method allows us to select high-affinity aptamers and their associated target proteins in a specific and accurate way, and could be used for personalized biomarker discovery to improve medical decision-making and to facilitate the development of targeted therapies to achieve more favorable outcomes.

Aptamer

Biomarker Discovery

Target protein

Microdissection

Angiogenin

10.2144/000114473

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Citations (25)

Tracking of Nuclear Production using Indigenous Species: Final LDRD Report

Todd M. Alam Mary Kathleen Alam Sarah McIntyre David E. Volk Muniasamy Neerathilingam

Our LDRD research project sought to develop an analytical method for detection of chemicals used in nuclear materials processing. Our approach is distinctly different than current research involving hardware-based sensors. By utilizing the response of indigenous species of plants and/or animals surrounding (or within) a nuclear processing facility, we propose tracking 'suspicious molecules' relevant to nuclear materials processing. As proof of concept, we have examined TBP, tributylphosphate, used in uranium enrichment as well as plutonium extraction from spent nuclear fuels. We will compare TBP to the TPP (triphenylphosphate) analog to determine the uniqueness of the metabonomic response. We show that there is a unique metabonomic response within our animal model to TBP. The TBP signature can further be delineated from that of TPP. We have also developed unique methods of instrumental transfer for metabonomic data sets.

Tracking (education)

Nuclear material

Nuclear Fuel

10.2172/1324990

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Thioaptamer targeted discoidal microparticles increase self immunity and reduce Mycobacterium tuberculosis burden in mice

Journal of Controlled Release (2017)

Fransisca Leonard Ngan P. Ha Preeti Sule Jenolyn F. Alexander David E. Volk

Nanocarriers

10.1016/j.jconrel.2017.09.038

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Therapeutic Targeting of AXL Receptor Tyrosine Kinase Inhibits Tumor Growth and Intraperitoneal Metastasis in Ovarian Cancer Models

Molecular Therapy — Nucleic Acids (2017)

Pınar Kanlikilicer Bülent Özpolat Burcu Aslan Recep Bayraktar Nilgün Gürbüz

Despite substantial improvements in the treatment strategies, ovarian cancer is still the most lethal gynecological malignancy. Identification of drug treatable therapeutic targets and their safe and effective targeting is critical to improve patient survival in ovarian cancer. AXL receptor tyrosine kinase (RTK) has been proposed to be an important therapeutic target for metastatic and advanced-stage human ovarian cancer. We found that AXL-RTK expression is associated with significantly shorter patient survival based on the The Cancer Genome Atlas patient database. To target AXL-RTK, we developed a chemically modified serum nuclease-stable AXL aptamer (AXL-APTAMER), and we evaluated its in vitro and in vivo antitumor activity using in vitro assays as well as two intraperitoneal animal models. AXL-aptamer treatment inhibited the phosphorylation and the activity of AXL, impaired the migration and invasion ability of ovarian cancer cells, and led to the inhibition of tumor growth and number of intraperitoneal metastatic nodules, which was associated with the inhibition of AXL activity and angiogenesis in tumors. When combined with paclitaxel, in vivo systemic (intravenous [i.v.]) administration of AXL-aptamer treatment markedly enhanced the antitumor efficacy of paclitaxel in mice. Taken together, our data indicate that AXL-aptamers successfully target in vivo AXL-RTK and inhibit its AXL activity and tumor growth and progression, representing a promising strategy for the treatment of ovarian cancer.

GAS6

10.1016/j.omtn.2017.06.023

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Citations (63)

Crotyltributylstannane

Encyclopedia of Reagents for Organic Synthesis (2001)

Stephen Castellino David E. Volk

(E) [35998-93-7] C16H34Sn (MW 345.13) InChI = 1S/3C4H9.C4H7.Sn/c4*1-3-4-2;/h3*1,3-4H2,2H3;3-4H,1H2,2H3;/b;;;4-3+; InChIKey = HDDSEBPIVXXGGL-ZQIHSQCASA-N (Z) [35998-94-8] InChI = 1S/3C4H9.C4H7.Sn/c4*1-3-4-2;/h3*1,3-4H2,2H3;3-4H,1H2,2H3;/b;;;4-3-; InChIKey = HDDSEBPIVXXGGL-YOLRLSNNSA-N (allylating reagent for many compounds, including alkyl halides, carbonyl compounds, imines, acetals, thioacetals, and sulfoximides) Alternate Name: 2-butenyltributyltin. Physical Data: bp 100–110 °C/1 mmHg;2f 1H NMR (E) isomer δ 5.95–5.10 (m, 2 H), 2.00–0.70 (m, 32 H); 13C NMR (E) isomer δ 130.5, 120.3, 29.3, 27.5, 27.4, 17.9, 13.8, 9.2;2f 1H NMR (Z) isomer δ 6.84–5.96 (m, 2 H), 3.30–1.43 (m, 32 H); 13C NMR (Z) isomer δ 129.6, 118.2, 29.3, 27.5, 27.4, 13.8, 12.5, 9.4.2f Solubility: sol methylene chloride, diethyl ether, tetrahydrofuran, toluene, and benzene. Form Supplied in: not commercially available. Preparative Methods: several methods have been described.2 Purification: by distillation. Handling, Storage, and Precautions: all organotin compounds are highly toxic. This reagent therefore must be used in a well-ventilated fume hood. Contact with the eyes, skin, and respiratory system should be avoided.

Diethyl ether

Methylene

Tetrahydrofuran

Proton NMR

10.1002/047084289x.rc258m

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X-Aptamers: A Bead-Based Selection Method for Random Incorporation of Druglike Moieties onto Next-Generation Aptamers for Enhanced Binding

Biochemistry (2012)

Weiguo He Miguel-Angel Elizondo-Riojas Xin Li Ganesh Lakshmana Rao Lokesh Anoma Somasunderam

By combining pseudorandom bead-based aptamer libraries with conjugation chemistry, we have created next-generation aptamers, X-aptamers (XAs). Several X-ligands can be added in a directed or random fashion to the aptamers to further enhance their binding affinities for the target proteins. Here we describe the addition of a drug (N-acetyl-2,3-dehydro-2-deoxyneuraminic acid), demonstrated to bind to CD44-HABD, to a complete monothioate backbone-substituted aptamer to increase its binding affinity for the target protein by up to 23-fold, while increasing the drug's level of binding 1-million fold.

Aptamer

Binding affinities

Target protein

SELEX Aptamer Technique

10.1021/bi300471d

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Citations (66)

Letter to the Editor: NMR Structure of the Apo-S100P Protein

Journal of Biomolecular NMR (2004)

Yi-Chien Lee David E. Volk Varatharasa Thiviyanathan Quinn Kleerekoper Alexey V. Gribenko

10.1023/b:jnmr.0000032617.88899.4b

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