@article{moore_escudero-abarca_suh_jaykus_2015, title={Generation and characterization of nucleic acid aptamers targeting the capsid P domain of a human norovirus GII.4 strain}, volume={209}, ISSN={["1873-4863"]}, DOI={10.1016/j.jbiotec.2015.06.389}, abstractNote={Human noroviruses (NoV) are the leading cause of acute viral gastroenteritis worldwide. Significant antigenic diversity of NoV strains has limited the availability of broadly reactive ligands for design of detection assays. The purpose of this work was to produce and characterize single stranded (ss)DNA aptamers with binding specificity to human NoV using an easily produced NoV target—the P domain protein. Aptamer selection was done using SELEX (Systematic Evolution of Ligands by EXponential enrichment) directed against an Escherichia coli-expressed and purified epidemic NoV GII.4 strain P domain. Two of six unique aptamers (designated M1 and M6-2) were chosen for characterization. Inclusivity testing using an enzyme-linked aptamer sorbent assay (ELASA) against a panel of 14 virus-like particles (VLPs) showed these aptamers had broad reactivity and exhibited strong binding to GI.7, GII.2, two GII.4 strains, and GII.7 VLPs. Aptamer M6-2 exhibited at least low to moderate binding to all VLPs tested. Aptamers significantly (p < 0.05) bound virus in partially purified GII.4 New Orleans outbreak stool specimens as demonstrated by ELASA and aptamer magnetic capture (AMC) followed by RT-qPCR. This is the first demonstration of human NoV P domain protein as a functional target for the selection of nucleic acid aptamers that specifically bind and broadly recognize diverse human NoV strains.}, journal={JOURNAL OF BIOTECHNOLOGY}, author={Moore, Matthew D. and Escudero-Abarca, Blanca I. and Suh, Soo Hwan and Jaykus, Lee-Ann}, year={2015}, month={Sep}, pages={41–49} }
 @article{suh_dwivedi_jaykus_2014, title={Development and evaluation of aptamer magnetic capture assay in conjunction with real-time PCR for detection of Campylobacter jejuni}, volume={56}, ISSN={["1096-1127"]}, DOI={10.1016/j.lwt.2013.12.012}, abstractNote={A prototype method for the concentration and detection of Campylobacter jejuni was developed using a previously reported biotinylated DNA aptamer in conjunction with qPCR. The so-called aptamer-based magnetic capture-qPCR (AMC-qPCR) assay was compared to a similar immunomagnetic separation (IMS)-qPCR assay. In small volume experiments (300 μl) applied to serially diluted C. jejuni suspended in buffer containing a mixed culture of other common food borne pathogens, the lower detection limit of the AMC-qPCR method was 1.1 log10/300 μl C. jejuni cells, one log10 better (lower) than that of IMS-qPCR (2.1 log10 CFU/300 μl). AMC-qPCR capture efficiency was 10–13% at assay detection limit. In 10 ml scale-up experiments, the lower detection limit of AMC-qPCR was 2.0 log10 CFU/10 ml with corresponding capture efficiency of 4–7%. Nucleic acid aptamers are promising alternatives to antibodies for magnetic bead-based capture followed by qPCR detection.}, number={2}, journal={LWT-FOOD SCIENCE AND TECHNOLOGY}, author={Suh, Soo Hwan and Dwivedi, Had P. and Jaykus, Lee-Ann}, year={2014}, month={May}, pages={256–260} }
 @article{choi_kim_suh_kim_kim_kim_park_park_shin_2014, title={Ligularia fischeri Extract Protects Against Oxidative-Stress-Induced Neurotoxicity in Mice and PC12 Cells}, volume={17}, ISSN={["1557-7600"]}, DOI={10.1089/jmf.2013.3014}, abstractNote={Alzheimer's disease (AD) is pathologically characterized by the presence of amyloid plaques in brain and the overproduction of amyloid beta (Aβ), leading to learning and memory impairment and intense oxidative stress. In this study, the protective effect of Ligularia fischeri extract was investigated using PC12 cells. L. fischeri extract attenuated hydrogen-peroxide-induced DNA fragmentation in cells. In vivo behavioral tests were performed to examine the effects of the extract on amyloid-β peptide1-42-induced impairment of learning and memory in mice. A diet containing the extract increased alternation behaviors in the Y-maze test and step-through latency of passive avoidance task. Moreover, we found that consumption of the extract decreased lipid peroxidation in a biochemical study of brain tissue in mice. High-performance liquid chromatography was used to identify the active compounds in the extract. These results suggest that L. fischeri extract could be protective against Aβ-induced neurotoxicity, possibly due to the antioxidative capacity of its constituent, 3-O-caffeoylquinic acid.}, number={11}, journal={JOURNAL OF MEDICINAL FOOD}, author={Choi, Soo Jung and Kim, Jae Kyeom and Suh, Soo Hwan and Kim, Cho Rong and Kim, Hye Kyung and Kim, Chang-Ju and Park, Gwi Gun and Park, Cheung-Seog and Shin, Dong-Hoon}, year={2014}, month={Nov}, pages={1222–1231} }
 @article{escudero-abarca_rawsthorne_goulter_suh_jaykus_2014, title={Molecular methods used to estimate thermal inactivation of a prototype human norovirus: More heat resistant than previously believed?}, volume={41}, ISSN={["1095-9998"]}, DOI={10.1016/j.fm.2014.01.009}, abstractNote={Two molecular-based methods for estimating capsid integrity as a proxy for virus infectivity were used to produce thermal inactivation profiles of Snow Mountain virus (SMV), a prototype human norovirus (HuNoV). Monodispersed virus suspensions were exposed to 77, 80, 82 and 85 °C for various times, pre-treated with either propidium monoazide (PMA) or RNase, and subjected to RNA isolation followed by RT-qPCR amplification. D-values were 25.6 ± 2.8, 3.1 ± 0.1, 0.7 ± 0.04 and 0.2 ± 0.07 min at 77, 80, 82 and 85 °C, respectively for PMA-treated SMV; and 16.4 ± 0.4, 3.9 ± 0.2 0.9 ± 0.3 and 0.12 ± 0.00 min at 77, 80, 82 and 85 °C, respectively for RNase-treated SMV. Corresponding zD values were 3.80 °C and 3.71 °C for PMA and RNase-treated virus, respectively. Electron microscopy data applied to heat-treated virus-like particles supported this relatively high degree of thermal resistance. The data suggest that SMV is more heat resistant than common cultivable HuNoV surrogates. Standardized thermal inactivation methods (such as milk pasteurization) may not be stringent enough to eliminate this virus and perhaps other HuNoV.}, journal={FOOD MICROBIOLOGY}, author={Escudero-Abarca, B. I. and Rawsthorne, H. and Goulter, R. M. and Suh, S. H. and Jaykus, L. A.}, year={2014}, month={Aug}, pages={91–95} }
 @article{suh_dwivedi_choi_jaykus_2014, title={Selection and characterization of DNA aptamers specific for Listeria species}, volume={459}, ISSN={["1096-0309"]}, DOI={10.1016/j.ab.2014.05.006}, abstractNote={Single-stranded (ss) DNA aptamers with binding affinity to Listeria spp. were selected using a whole-cell SELEX (Systematic Evolution of Ligands by EXponential enrichment) method. Listeria monocytogenes cells were grown at 37 °C and harvested at mid-log phase or early stationary phase to serve as the targets in SELEX. A total of 10 unique aptamer sequences were identified, six associated with log phase cells and four with stationary phase cells. Binding affinity of the aptamers was determined using flow cytometry and ranged from 10% to 44%. Four candidates having high binding affinity were further studied and found to show genus-specific binding affinity when screened against five different species within the Listeria genus. Using sequential binding assays combined with flow cytometry, it was determined that three of the aptamers (LM6-2, LM12-6, and LM12-13) bound to one apparent cell surface moiety, while a fourth aptamer (LM6-116) appeared to bind to a different cell surface region. This is the first study in which SELEX targeted bacterial cells at different growth phases. When used together, aptamers that bind to different cell surface moieties could increase the analytical sensitivity of future capture and detection assays.}, journal={ANALYTICAL BIOCHEMISTRY}, author={Suh, Soo Hwan and Dwivedi, Hari P. and Choi, Soo Jung and Jaykus, Lee-Ann}, year={2014}, month={Aug}, pages={39–45} }
 @article{escudero-abarca_suh_moore_dwivedi_jaykus_2014, title={Selection, Characterization and Application of Nucleic Acid Aptamers for the Capture and Detection of Human Norovirus Strains}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0106805}, abstractNote={Human noroviruses (HuNoV) are the leading cause of acute viral gastroenteritis and an important cause of foodborne disease. Despite their public health significance, routine detection of HuNoV in community settings, or food and environmental samples, is limited, and there is a need to develop alternative HuNoV diagnostic reagents to complement existing ones. The purpose of this study was to select and characterize single-stranded (ss)DNA aptamers with binding affinity to HuNoV. The utility of these aptamers was demonstrated in their use for capture and detection of HuNoV in outbreak-derived fecal samples and a representative food matrix. SELEX (Systematic Evolution of Ligands by EXponential enrichment) was used to isolate ssDNA aptamer sequences with broad reactivity to the prototype GII.2 HuNoV strain, Snow Mountain Virus (SMV). Four aptamer candidates (designated 19, 21, 25 and 26) were identified and screened for binding affinity to 14 different virus-like particles (VLPs) corresponding to various GI and GII HuNoV strains using an Enzyme-Linked Aptamer Sorbant Assay (ELASA). Collectively, aptamers 21 and 25 showed affinity to 13 of the 14 VLPs tested, with strongest binding to GII.2 (SMV) and GII.4 VLPs. Aptamer 25 was chosen for further study. Its binding affinity to SMV-VLPs was equivalent to that of a commercial antibody within a range of 1 to 5 µg/ml. Aptamer 25 also showed binding to representative HuNoV strains present in stool specimens obtained from naturally infected individuals. Lastly, an aptamer magnetic capture (AMC) method using aptamer 25 coupled with RT-qPCR was developed for recovery and detection of HuNoV in artificially contaminated lettuce. The capture efficiency of the AMC was 2.5–36% with an assay detection limit of 10 RNA copies per lettuce sample. These ssDNA aptamer candidates show promise as broadly reactive reagents for use in HuNoV capture and detection assays in various sample types.}, number={9}, journal={PLOS ONE}, author={Escudero-Abarca, Blanca I. and Suh, Soo Hwan and Moore, Matthew D. and Dwivedi, Hari P. and Jaykus, Lee-Ann}, year={2014}, month={Sep} }
 @article{suh_jaykus_2013, title={Nucleic acid aptamers for capture and detection of Listeria spp}, volume={167}, ISSN={["1873-4863"]}, DOI={10.1016/j.jbiotec.2013.07.027}, abstractNote={The purpose of this study was to identify biotinylated single-stranded (ss) DNA aptamers with binding specificity to Listeria and use these for capture and subsequent qPCR detection of the organism. For aptamer selection, SELEX (systematic evolution of ligands by exponential enrichment) was applied to a biotin-labeled ssDNA combinatorial library. After multiple rounds of selection and counter-selection, aptamers separated, sequenced, and characterized by flow cytometry showed binding affinities to L. monocytogenes of 18-23%. Although selected for using L. monocytogenes, these aptamers showed similar binding affinity for other members of the Listeria genus and low binding affinity for non-Listeria species. One aptamer, Lbi-17, was chosen for development of a prototype capture and detection assay. When Lbi-17 was conjugated to magnetic beads and used in a combined aptamer magnetic capture (AMC)-qPCR assay, the pathogen could be detected at concentrations <60 CFU/500 μl buffer in the presence of a heterogeneous cocktail of non-Listeria bacterial cells, with a capture efficiency of 26-77%. Parallel experiments using immunomagnetic separation (IMS)-qPCR produced the same detection limit but lower capture efficiency (16-21%). Increasing assay volume to 10 and 50 ml resulted in reduced capture efficiency and higher limits of detection, at 2.7 and 4.8 log₁₀ CFU L. monocytogenes per sample, respectively, for the AMC-qPCR assay. Biotinylated ssDNA aptamers are promising ligands for food-borne pathogen concentration prior to detection using molecular methods.}, number={4}, journal={JOURNAL OF BIOTECHNOLOGY}, author={Suh, Soo Hwan and Jaykus, Lee-Ann}, year={2013}, month={Sep}, pages={454–461} }