35 results on '"Salena BJ"'
Search Results
2. Higher Affinity Enables More Accurate Detection of SARS-CoV-2 in Human Saliva Using Aptamer-Based Litmus Test.
- Author
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Liu R, Li J, Gu J, Salena BJ, and Li Y
- Subjects
- Humans, Spike Glycoprotein, Coronavirus analysis, Spike Glycoprotein, Coronavirus metabolism, Spike Glycoprotein, Coronavirus chemistry, Colorimetry methods, Aptamers, Nucleotide chemistry, SARS-CoV-2 isolation & purification, Saliva virology, Saliva chemistry, COVID-19 diagnosis, COVID-19 virology, SELEX Aptamer Technique
- Abstract
Many aptamers have been generated by systematic evolution of ligands by exponential enrichment (SELEX) to recognize spike proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2&ek), some of which have been engineered into dimeric and trimeric versions for enhanced affinity for diagnostic applications. However, no studies have been conducted to compare the utilities of monomeric, dimeric and trimeric aptamers in diagnostic assays with real clinical samples to answer the question of what levels of affinity an aptamer must have for accurate clinical diagnostics. Herein, we carried out a comparative study with two monomeric aptamers MSA1 and MSA5, one dimeric aptamer and two homotrimeric aptamers constructed with MSA1 and MSA5, with affinity varying by 1000-fold. Using a colorimetric sandwich assay to analyze 48 human saliva samples, we found that the trimeric aptamer assay (K
d ≈10 pM) can identify the SARS-CoV-2 infection much more accurately than the dimeric aptamer assay (Kd ≈100 pM) and monomeric aptamer assay (Kd ≈10,000 pM). Based on the experimental data, we theoretically predict the levels of affinity an aptamer needs to possess to achieve 80-100 % sensitivity and 100 % specificity. The findings from this study highlight the need for deriving very high affinity aptamers to enable highly accurate detection of viral infection for future pandemics., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)- Published
- 2024
- Full Text
- View/download PDF
3. Aptamer and DNAzyme Based Colorimetric Biosensors for Pathogen Detection.
- Author
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Liu R, Li J, Salena BJ, and Li Y
- Abstract
The detection of pathogens is critical for preventing and controlling health hazards across clinical, environmental, and food safety sectors. Functional nucleic acids (FNAs), such as aptamers and DNAzymes, have emerged as versatile molecular tools for pathogen detection due to their high specificity and affinity. This review focuses on the in vitro selection of FNAs for pathogens, with emphasis on the selection of aptamers for specific biomarkers and intact pathogens, including bacteria and viruses. Additionally, the selection of DNAzymes for bacterial detection is discussed. The integration of these FNAs into colorimetric biosensors has enabled the development of simple, cost-effective diagnostic platforms. Both non-catalytic and catalytic colorimetric biosensors are explored, including those based on gold nanoparticles, polydiacetylenes, protein enzymes, G-quadruplexes, and nanozymes. These biosensors offer visible detection through color changes, making them ideal for point-of-care diagnostics. The review concludes by highlighting current challenges and future perspectives for advancing FNA-based colorimetric biosensing technologies for pathogen detection., (© 2024 The Author(s). Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2024
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4. Fighting Mutations with Mutations: Evolutionarily Adapting a DNA Aptamer for High-Affinity Recognition of Mutated Spike Proteins of SARS-CoV-2.
- Author
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Wang Q, Li J, Zhang Z, Amini R, Derdall A, Gu J, Xia J, Salena BJ, Yamamura D, Soleymani L, and Li Y
- Abstract
An on-going challenge with COVID-19, which has huge implications for future pandemics, is the rapid emergence of viral variants that makes diagnostic tools less accurate, calling for rapid identification of recognition elements for detecting new variants caused by mutations. We hypothesize that we can fight mutations of the viruses with mutations of existing recognition elements. We demonstrate this concept via rapidly evolving an existing DNA aptamer originally selected for the spike protein (S-protein) of wildtype SARS-CoV-2 to enhance the interaction with the same protein of the Omicron variants. The new aptamer, MBA5SA1, has acquired 22 mutations within its 40-nucleotide core sequence and improved its binding affinity for the S-proteins of diverse Omicron subvariants by >100-fold compared to its parental aptamer (improved from nanomolar to picomolar affinity). Deep sequencing analysis reveals dynamic competitions among several MBA5SA1 variants in response to increasing selection pressure imposed during in vitro selection, with MBA5SA1 being the final winner of the competition. Additionally, MBA5SA1 was implemented into an enzyme-linked aptamer binding assay (ELABA), which was applied for detecting Omicron variants in the saliva of infected patients. The assay produced a sensitivity of 86.5 % and a specificity of 100 %, which were established with 83 clinical samples., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2024
- Full Text
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5. High-Precision Viral Detection Using Electrochemical Kinetic Profiling of Aptamer-Antigen Recognition in Clinical Samples and Machine Learning.
- Author
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Sen P, Zhang Z, Sakib S, Gu J, Li W, Adhikari BR, Motsenyat A, L'Heureux-Hache J, Ang JC, Panesar G, Salena BJ, Yamamura D, Miller MS, Li Y, and Soleymani L
- Subjects
- Humans, Kinetics, Influenza A virus, Antigens, Viral analysis, Antigens, Viral immunology, Biosensing Techniques methods, Aptamers, Nucleotide chemistry, SARS-CoV-2 isolation & purification, SARS-CoV-2 immunology, Machine Learning, Electrochemical Techniques methods, COVID-19 diagnosis, COVID-19 virology
- Abstract
High-precision viral detection at point of need with clinical samples plays a pivotal role in the diagnosis of infectious diseases and the control of a global pandemic. However, the complexity of clinical samples that often contain very low viral concentrations makes it a huge challenge to develop simple diagnostic devices that do not require any sample processing and yet are capable of meeting performance metrics such as very high sensitivity and specificity. Herein we describe a new single-pot and single-step electrochemical method that uses real-time kinetic profiling of the interaction between a high-affinity aptamer and an antigen on a viral surface. This method generates many data points per sample, which when combined with machine learning, can deliver highly accurate test results in a short testing time. We demonstrate this concept using both SARS-CoV-2 and Influenza A viruses as model viruses with specifically engineered high-affinity aptamers. Utilizing this technique to diagnose COVID-19 with 37 real human saliva samples results in a sensitivity and specificity of both 100 % (27 true negatives and 10 true positives, with 0 false negative and 0 false positive), which showcases the superb diagnostic precision of this method., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2024
- Full Text
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6. A Fluorogenic DNAzyme for A Thermally Stable Protein Biomarker from Fusobacterium nucleatum, a Human Bacterial Pathogen.
- Author
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Feng Q, Zakaria S, Morrison D, Tram K, Gu J, Salena BJ, and Li Y
- Subjects
- Pregnancy, Female, Humans, RNA metabolism, Fusobacterium nucleatum, DNA, Catalytic metabolism
- Abstract
Fusobacterium nucleatum has been correlated to many poor human conditions including oral infections, adverse pregnancies and cancer, and thus molecular tools capable of detecting this human pathogen can be used to develop diagnostic tests for them. Using a new selection method targeting thermally stable proteins without a counter-selection step, we derived an fluorogenic RNA-cleaving DNAzyme, named RFD-FN1, that can be activated by a thermally stable protein target that is unique to F. nucleatum subspecies. High thermal stability of protein targets is a very desirable attribute for DNAzyme-based biosensing directly with biological samples because nucleases found inherently in these samples can be heat-inactivated. We further demonstrate that RFD-FN1 can function as a fluorescent sensor in both human saliva and human stool samples. The discovery of RFD-FN1 paired with a highly thermal stable protein target presents opportunities for developing simpler diagnostic tests for this important pathogen., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2023
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7. In Vitro Selection and Characterization of a DNAzyme Probe for Diverse Pathogenic Strains of Clostridium difficile.
- Author
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Qian S, Chang D, Gu J, Salena BJ, and Li Y
- Subjects
- Humans, Rapid Diagnostic Tests, Clostridioides difficile genetics, DNA, Catalytic, Clostridium Infections diagnosis
- Abstract
Clostridium difficile frequently causes an infectious disease known as Clostridium difficile infection (CDI), and there is an urgent need for the development of more effective rapid diagnostic tests for CDI. Previously we have developed an RNA-cleaving fluorogenic DNAzyme (RFD) probe, named RFD-CD1, that is capable of detecting a specific strain of C. difficile but is too specific to recognize other pathogenic C. difficile strains. To overcome this issue, herein we report RFD-CD2, another RFD that is not only highly specific to C. difficile but also capable of recognizing diverse pathogenic C. difficile strains. Extensive sequence and structure characterization establishes a pseudoknot structure and a significantly minimized sequence for RFD-CD2. As a fluorescent sensor, RFD-CD2 can detect C. difficile at a concentration as low as 100 CFU/mL, thus making this DNAzyme an attractive molecular probe for rapid diagnosis of CDI caused by diverse strains of C. difficile., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)
- Published
- 2023
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8. Detection of Large Genomic RNA via DNAzyme-Mediated RNA Cleavage and Rolling Circle Amplification: SARS-CoV-2 as a Model.
- Author
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Gu J, Mathai A, Nurmi C, White D, Panesar G, Yamamura D, Balion C, Gubbay J, Mossman K, Capretta A, Salena BJ, Soleymani L, Filipe CDM, Brennan JD, and Li Y
- Subjects
- Humans, RNA, SARS-CoV-2 genetics, SARS-CoV-2 metabolism, RNA Cleavage, Nucleic Acid Amplification Techniques methods, Genomics, DNA, Catalytic metabolism, COVID-19 diagnosis, Biosensing Techniques methods
- Abstract
A new method for the detection of genomic RNA combines RNA cleavage by the 10-23 DNAzyme and use of the cleavage fragments as primers to initiate rolling circle amplification (RCA). 230 different 10-23 DNAzyme variants were screened to identify those that target accessible RNA sites within the highly structured RNA transcripts of SARS-CoV-2. A total of 28 DNAzymes were identified with >20 % cleavage, 5 with >40 % cleavage and one with >60 % in 10 min. The cleavage fragments from these reactions were then screened for coupling to an RCA reaction, leading to the identification of several cleavage fragments that could efficiently initiate RCA. Using a newly developed quasi-exponential RCA method with a detection limit of 500 aM of RNA, 14 RT-PCR positive and 15 RT-PCR negative patient saliva samples were evaluated for SARS-CoV-2 genomic RNA, achieving a clinical sensitivity of 86 % and specificity of 100 % for detection of the virus in <2.5 h., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)
- Published
- 2023
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9. Engineering a Ligase Binding DNA Aptamer into a Templating DNA Scaffold to Guide the Selective Synthesis of Circular DNAzymes and DNA Aptamers.
- Author
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Yan Y, Chang D, Xu Y, Chang Y, Zhang Q, Yuan Q, Salena BJ, Li Y, and Liu M
- Subjects
- Ligases metabolism, Nucleic Acid Amplification Techniques, DNA chemistry, DNA, Circular, DNA, Single-Stranded, DNA, Catalytic metabolism, Aptamers, Nucleotide chemistry, Biosensing Techniques
- Abstract
Functional nucleic acids (FNAs), such as DNAzymes and DNA aptamers, can be engineered into circular forms for improved performance. Circular FNAs are promising candidates for bioanalytical and biomedical applications due to their intriguing properties of enhanced biological stability and compatibility with rolling circle amplification. They are typically made from linear single-stranded (ss) DNA molecules via ligase-mediated ligation. However, it remains a great challenge to synthesize circular ssDNA molecules in high yield due to inherent side reactions where two or more of the same ssDNA molecules are ligated. Herein, we present a strategy to overcome this issue by first using in vitro selection to search from a random-sequence DNA library a ligatable DNA aptamer that binds a DNA ligase and then by engineering this aptamer into a general-purpose templating DNA scaffold to guide the ligase to execute selective intramolecular circularization. We demonstrate the broad utility of this approach via the creation of several species of circular DNA molecules, including a circular DNAzyme sensor for a bacterium and a circular DNA aptamer sensor for a protein target with excellent detection sensitivity and specificity.
- Published
- 2023
- Full Text
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10. Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer.
- Author
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Li J, Zhang Z, Gu J, Amini R, Mansfield AG, Xia J, White D, Stacey HD, Ang JC, Panesar G, Capretta A, Filipe CDM, Mossman K, Salena BJ, Gubbay JB, Balion C, Soleymani L, Miller MS, Yamamura D, Brennan JD, and Li Y
- Subjects
- Humans, Spike Glycoprotein, Coronavirus, Biological Assay, Oligonucleotides, SARS-CoV-2, COVID-19 diagnosis
- Abstract
Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva with a limit of detection as low as 6.3 × 10
3 copies/mL. The ELABA was also used to test 50 SARS-CoV-2-positive and 60 SARS-CoV-2-negative patient saliva samples, providing sensitivity and specificity values of 84.0 and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.- Published
- 2022
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11. A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern.
- Author
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Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, White D, Filipe CDM, Mossman K, Miller MS, Salena BJ, Yamamura D, Sen P, Soleymani L, Brennan JD, and Li Y
- Abstract
Invited for the cover of this issue are John Brennan, Yingfu Li, and co-workers at McMaster University. The image depicts MSA52 as a universal DNA aptamer that recognizes spike proteins of diverse SARS-CoV-2 variants of concern. Read the full text of the article at 10.1002/chem.202200078., (© 2022 Wiley-VCH GmbH.)
- Published
- 2022
- Full Text
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12. Investigation of discordant SARS-CoV-2 RT-PCR results using minimally processed saliva.
- Author
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White D, Gu J, Steinberg CJ, Yamamura D, Salena BJ, Balion C, Filipe CDM, Capretta A, Li Y, and Brennan JD
- Subjects
- False Negative Reactions, Healthy Volunteers, Humans, Point-of-Care Testing, COVID-19 Nucleic Acid Testing, SARS-CoV-2 isolation & purification, Saliva virology
- Abstract
Saliva is an attractive sample for coronavirus disease 2019 testing due its ease of collection and amenability to detect viral RNA with minimal processing. Using a direct-to-RT-PCR method with saliva self-collected from confirmed COVID-19 positive volunteers, we observed 32% false negative results. Confirmed negative and healthy volunteer samples spiked with 10
6 genome copies/mL of heat-inactivated severe acute respiratory syndrome coronavirus 2 showed false negative results of 10% and 13%, respectively. Additional sample heating or dilution of the false negative samples conferred only modest improvements. These results highlight the potential to significantly underdiagnose COVID-19 infections when testing directly from minimally processed heterogeneous saliva samples., (© 2022. The Author(s).)- Published
- 2022
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13. High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva.
- Author
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Zhang Z, Pandey R, Li J, Gu J, White D, Stacey HD, Ang JC, Steinberg CJ, Capretta A, Filipe CDM, Mossman K, Balion C, Miller MS, Salena BJ, Yamamura D, Soleymani L, Brennan JD, and Li Y
- Subjects
- Humans, Saliva chemistry, Antigens, Viral analysis, Aptamers, Nucleotide chemistry, Biosensing Techniques, COVID-19 Serological Testing, Electrochemical Techniques, SARS-CoV-2 genetics
- Abstract
We report a simple and rapid saliva-based SARS-CoV-2 antigen test that utilizes a newly developed dimeric DNA aptamer, denoted as DSA1N5, that specifically recognizes the spike proteins of the wildtype virus and its Alpha and Delta variants with dissociation constants of 120, 290 and 480 pM, respectively, and binds pseudotyped lentiviruses expressing the wildtype and alpha trimeric spike proteins with affinity constants of 2.1 pM and 2.3 pM, respectively. To develop a highly sensitive test, DSA1N5 was immobilized onto gold electrodes to produce an electrochemical impedance sensor, which was capable of detecting 1000 viral particles per mL in 1:1 diluted saliva in under 10 min without any further sample processing. Evaluation of 36 positive and 37 negative patient saliva samples produced a clinical sensitivity of 80.5 % and specificity of 100 % and the sensor could detect the wildtype virus as well as the Alpha and Delta variants in the patient samples, which is the first reported rapid test that can detect any emerging variant of SARS-CoV-2., (© 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)
- Published
- 2021
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14. Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library.
- Author
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Li J, Zhang Z, Gu J, Stacey HD, Ang JC, Capretta A, Filipe CDM, Mossman KL, Balion C, Salena BJ, Yamamura D, Soleymani L, Miller MS, Brennan JD, and Li Y
- Subjects
- Base Pairing, Base Sequence, COVID-19 diagnosis, Colorimetry methods, Humans, Nucleic Acid Conformation, SELEX Aptamer Technique, Aptamers, Nucleotide chemistry, Aptamers, Nucleotide genetics, COVID-19 virology, Gene Library, Mutation, SARS-CoV-2 genetics, Spike Glycoprotein, Coronavirus genetics
- Abstract
We performed in vitro selection experiments to identify DNA aptamers for the S1 subunit of the SARS-CoV-2 spike protein (S1 protein). Using a pool of pre-structured random DNA sequences, we obtained over 100 candidate aptamers after 13 cycles of enrichment under progressively more stringent selection pressure. The top 10 sequences all exhibited strong binding to the S1 protein. Two aptamers, named MSA1 (Kd = 1.8 nM) and MSA5 (Kd = 2.7 nM), were assessed for binding to the heat-treated S1 protein, untreated S1 protein spiked into 50% human saliva and the trimeric spike protein of both the wildtype and the B.1.1.7 variant, demonstrating comparable affinities in all cases. MSA1 and MSA5 also recognized the pseudotyped lentivirus of SARS-CoV-2 with respective Kd values of 22.7 pM and 11.8 pM. Secondary structure prediction and sequence truncation experiments revealed that both MSA1 and MSA5 adopted a hairpin structure, which was the motif pre-designed into the original library. A colorimetric sandwich assay was developed using MSA1 as both the recognition element and detection element, which was capable of detecting the pseudotyped lentivirus in 50% saliva with a limit of detection of 400 fM, confirming the potential of these aptamers as diagnostic tools for COVID-19 detection., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2021
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15. Ribbon of DNA Lattice on Gold Nanoparticles for Selective Drug Delivery to Cancer Cells.
- Author
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Zhang S, Chen C, Xue C, Chang D, Xu H, Salena BJ, Li Y, and Wu ZS
- Subjects
- Antineoplastic Agents therapeutic use, Cell Line, Tumor, Doxorubicin administration & dosage, Doxorubicin therapeutic use, Humans, Microscopy, Atomic Force, Antineoplastic Agents administration & dosage, DNA chemistry, Drug Delivery Systems, Gold chemistry, Metal Nanoparticles chemistry, Neoplasms drug therapy
- Abstract
Herein, we report on the design of a programmable DNA ribbon using long-chain DNA molecules with a user-defined repetitive padlock sequence. The DNA ribbon can be further combined with gold nanoparticles (AuNPs) to create a composite nanomaterial that contains an AuNP core and a high-density DNA crown carrying a cancer-cell-targeting DNA aptamer, a fluorescent tag for location tracking, and a cell-killing drug. This composite material can be efficiently internalized by cancer cells and its cellular location can be tracked by fluorescence imaging. The system offers several attractive characteristics, including simple design, tunable DNA crown, high drug-loading capacity, selective cell targeting, and pH-sensitive drug release. These features make such a material a promising therapeutic agent., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2020
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16. In Vitro Selection of New DNA Aptamers for Human Vascular Endothelial Growth Factor 165.
- Author
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Manochehry S, Gu J, McConnell EM, Salena BJ, and Li Y
- Subjects
- Aptamers, Nucleotide genetics, Binding Sites, High-Throughput Nucleotide Sequencing, Humans, Vascular Endothelial Growth Factor A genetics, Aptamers, Nucleotide chemistry, Vascular Endothelial Growth Factor A chemistry
- Abstract
Two DNA aptamers that bind the heparin-binding domain (HBD) of the human vascular endothelial growth factor 165 (VEGF-165) have been previously reported. Although VEGF-165 is a homodimeric protein and the two aptamers have different sequences and secondary structures, the aptamers appear to occupy the same binding site and cannot form a 2 : 1 aptamer/protein complex, thus making them unsuitable for creating a higher-affinity dimeric DNA aptamer. This has motivated us to conduct a new in vitro selection experiment to search for new VEGF-165-binding DNA aptamers with different properties. We undertook a multistream selection strategy in which the concentration of VEGF-165 was varied significantly. We carried out 11 rounds of selection, and next-generation sequencing was conducted for every round in each stream. From comprehensive sequence analysis, we identified four classes of DNA aptamers, of which two were reported before, but two are new DNA aptamers. One of the new aptamers exhibits a unique property that has never been observed before: it is capable of forming the 2 : 1 aptamer/protein complex with VEGF-165. This work has expanded the repertoire of VEGF-165-binding DNA aptamers and creates a possibility to engineer a higher affinity homodimeric aptamer for VEGF-165., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2020
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17. Target-Induced Catalytic Assembly of Y-Shaped DNA and Its Application for In Situ Imaging of MicroRNAs.
- Author
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Xue C, Zhang SX, Ouyang CH, Chang D, Salena BJ, Li Y, and Wu ZS
- Subjects
- Biocatalysis, DNA-Directed DNA Polymerase chemistry, HeLa Cells, Humans, In Situ Hybridization, Fluorescence, MCF-7 Cells, MicroRNAs metabolism, Optical Imaging, DNA biosynthesis, DNA chemistry, DNA-Directed DNA Polymerase metabolism, MicroRNAs analysis
- Abstract
DNA is a highly programmable material that can be configured into unique high-order structures, such as DNA branched junctions containing multiple helical arms converging at a center. Herein we show that DNA programmability can deliver in situ growth of a 3-way junction-based DNA structure (denoted Y-shaped DNA) with the use of three hairpin-shaped DNA molecules as precursors, a specific microRNA target as a recyclable trigger, and a DNA polymerase as a driver. We demonstrate that the Y-shaped configuration comes with the benefit of restricted freedom of movement in confined cellular environment, which makes the approach ideally suited for in situ imaging of small RNA targets, such as microRNAs. Comparative analysis illustrates that the proposed imaging technique is superior to both the classic fluorescence in situ hybridization (FISH) method and an analogous amplified imaging method via programmed growth of a double-stranded DNA (rather than Y-shaped DNA) product., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2018
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18. Serendipitous Discovery of a Guanine-rich DNA Molecule with a Highly Stable Structure in Urea.
- Author
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Zhang W, Liu M, Lee C, Salena BJ, and Li Y
- Subjects
- Base Sequence, Ions, Metals pharmacology, Time Factors, G-Quadruplexes drug effects, Urea pharmacology
- Abstract
We have made an accidental discovery of an unusual, single-stranded, guanine-rich DNA molecule that is capable of adopting a folded structure in 7 M urea (7MU) known to denature nucleic acid structures. The folding of this molecule requires Na
+ and Mg2+ and the folded structure remains stable when subjected to denaturing (7MU) polyacrylamide gel electrophoresis. Results from sequence mutagenesis, DNA methylation, and circular dichroism spectroscopy studies suggest that this molecule adopts an intramolecular guanine-quadruplex structure with 5 layers of guanine tetrads. Our finding indicates that DNA has the ability to create extremely stable structural folds despite its limited chemical repertoire, making it possible to develop DNA-based systems for unconventional applications.- Published
- 2018
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19. Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test.
- Author
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Chang D, Tram K, Li B, Feng Q, Shen Z, Lee CH, Salena BJ, and Li Y
- Subjects
- Colorimetry methods, DNA Replication, Nucleic Acid Amplification Techniques, Polymerase Chain Reaction methods
- Abstract
We report on a new colorimetric DNA detection method that takes advantage of the power of polymerase chain reaction (PCR) and the simplicity of the classic litmus test. The strategy makes use of a modified set of primers for PCR to facilitate ensuing manipulations of resultant DNA amplicons: their tagging with urease and immobilization onto magnetic beads. The amplicon/urease-laden beads are then used to hydrolyze urea, resulting in the increase of pH that can be conveniently reported by a pH-sensitive dye. We have successfully applied this strategy for the detection of two hypervirulent strains of the bacterium Clostridium difficile that are responsible for the recent increase in the global incidence and severity of C. difficile infections. Furthermore, the viability of this test for diagnostic applications is demonstrated using clinically validated stool samples from C. difficile infected patients.
- Published
- 2017
- Full Text
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20. Colorimetric Detection of Bacteria Using Litmus Test.
- Author
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Tram K, Manochehry S, Feng Q, Chang D, Salena BJ, and Li Y
- Subjects
- Ammonia analysis, Bacteria enzymology, DNA, Catalytic chemistry, Enzymes, Immobilized chemistry, Hydrogen-Ion Concentration, Point-of-Care Systems, Urease chemistry, Bacteria isolation & purification, Bacteriological Techniques methods, Colorimetry methods
- Abstract
There are increasing demands for simple but still effective methods that can be used to detect specific pathogens for point-of-care or field applications. Such methods need to be user-friendly and produce reliable results that can be easily interpreted by both specialists and non-professionals. The litmus test for pH is simple, quick, and effective as it reports the pH of a test sample via a simple color change. We have developed an approach to take advantage of the litmus test for bacterial detection. The method exploits a bacterium-specific RNA-cleaving DNAzyme to achieve two functions: recognizing a bacterium of interest and providing a mechanism to control the activity of urease. Through the use of magnetic beads immobilized with a DNAzyme-urease conjugate, the presence of bacteria in a test sample is relayed to the release of urease from beads to solution. The released urease is transferred to a test solution to hydrolyze urea into ammonia, resulting in an increase of pH that can be visualized using the classic litmus test.
- Published
- 2016
- Full Text
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21. Topological DNA Assemblies Containing Identical or Fraternal Twins.
- Author
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Wu ZS, Shen Z, Tram K, Salena BJ, and Li Y
- Subjects
- DNA Restriction Enzymes, DNA, Catenated chemical synthesis, DNA, Catenated metabolism, Electrophoresis, Polyacrylamide Gel, Nanostructures chemistry, Nucleic Acid Amplification Techniques, DNA, Catenated chemistry
- Abstract
DNA catenanes are assemblies made up of two or more DNA rings linked together through mechanical bonds, and they are desirable for engineering unique nanoscale devices. However, current methods of synthesizing DNA catenanes rely on the formation of strong linking duplexes between component units to enable interlocking and thus do not permit the synthesis of complex single-stranded DNA structures with freely functioning units. We have recently reported DNA sequences that can thread through a DNA circle without the formation of a linking duplex. Here we show that these unique DNA molecules can be further used to make intricate symmetric or asymmetric DNA [3]catenanes, single-stranded DNA assemblies made up of a central mother ring interlocked to two identical or fraternal twin daughter rings, which have never been reported before. These addressable freely functioning interlocked DNA rings should facilitate the design of elaborate nanoscale machines based on DNA., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2016
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22. A Catalytic DNA Activated by a Specific Strain of Bacterial Pathogen.
- Author
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Shen Z, Wu Z, Chang D, Zhang W, Tram K, Lee C, Kim P, Salena BJ, and Li Y
- Subjects
- Clostridioides difficile pathogenicity, DNA, Catalytic metabolism
- Abstract
Pathogenic strains of bacteria are known to cause various infectious diseases and there is a growing demand for molecular probes that can selectively recognize them. Here we report a special DNAzyme (catalytic DNA), RFD-CD1, that shows exquisite specificity for a pathogenic strain of Clostridium difficile (C. difficile). RFD-CD1 was derived by an in vitro selection approach where a random-sequence DNA library was allowed to react with an unpurified molecular mixture derived from this strain of C. difficle, coupled with a subtractive selection strategy to eliminate cross-reactivities to unintended C. difficile strains and other bacteria species. RFD-CD1 is activated by a truncated version of TcdC, a transcription factor, that is unique to the targeted strain of C. difficle. Our study demonstrates for the first time that in vitro selection offers an effective approach for deriving functional nucleic acid probes that are capable of achieving strain-specific recognition of bacterial pathogens., (© 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)
- Published
- 2016
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23. Optimal DNA templates for rolling circle amplification revealed by in vitro selection.
- Author
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Mao Y, Liu M, Tram K, Gu J, Salena BJ, Jiang Y, and Li Y
- Subjects
- Aptamers, Nucleotide chemistry, Bacillus Phages enzymology, Base Sequence, DNA, Circular metabolism, DNA-Directed DNA Polymerase metabolism, Biosensing Techniques methods, DNA, Circular chemistry, Nucleic Acid Amplification Techniques methods
- Abstract
Rolling circle amplification (RCA) has been widely used as an isothermal DNA amplification technique for diagnostic and bioanalytical applications. Because RCA involves repeated copying of the same circular DNA template by a DNA polymerase thousands of times, we hypothesized there exist DNA sequences that can function as optimal templates and produce more DNA amplicons within an allocated time. Herein we describe an in vitro selection effort conducted to search from a random sequence DNA pool for such templates for phi29 DNA polymerase, a frequently used polymerase for RCA. Diverse DNA molecules were isolated and they were characterized by richness in adenosine (A) and cytidine (C) nucleotides. The top ranked sequences exhibit superior RCA efficiency and the use of these templates for RCA results in significantly improved detection sensitivity. AC-rich sequences are expected to find useful applications for setting up effective RCA assays for biological sensing., (© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2015
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24. Translating bacterial detection by DNAzymes into a litmus test.
- Author
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Tram K, Kanda P, Salena BJ, Huan S, and Li Y
- Subjects
- Coloring Agents analysis, Coloring Agents chemistry, DNA, Catalytic genetics, Hydrogen-Ion Concentration, Paper, RNA, Bacterial analysis, RNA, Bacterial genetics, Species Specificity, Urease metabolism, Bacteria genetics, Bacteria isolation & purification, Bacterial Typing Techniques methods, DNA, Catalytic metabolism, RNA, Bacterial metabolism
- Abstract
Microbial pathogens pose serious threats to public health and safety, and results in millions of illnesses and deaths as well as huge economic losses annually. Laborious and expensive pathogen tests often represent a significant hindrance to implementing effective front-line preventative care, particularly in resource-limited regions. Thus, there is a significant need to develop low-cost and easy-to-use methods for pathogen detection. Herein, we present a simple and inexpensive litmus test for bacterial detection. The method takes advantage of a bacteria-specific RNA-cleaving DNAzyme probe as the molecular recognition element and the ability of urease to hydrolyze urea and elevate the pH value of the test solution. By coupling urease to the DNAzyme on magnetic beads, the detection of bacteria is translated into a pH increase, which can be readily detected using a litmus dye or pH paper. The simplicity, low cost, and broad adaptability make this litmus test attractive for field applications, particularly in the developing world., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2014
- Full Text
- View/download PDF
25. Arrest of rolling circle amplification by protein-binding DNA aptamers.
- Author
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Wang L, Tram K, Ali MM, Salena BJ, Li J, and Li Y
- Subjects
- Nucleic Acid Amplification Techniques methods, Aptamers, Nucleotide biosynthesis, Aptamers, Nucleotide chemistry, DNA-Binding Proteins chemistry, DNA-Directed DNA Polymerase chemistry, Oligonucleotides biosynthesis, Oligonucleotides chemistry
- Abstract
Certain DNA polymerases, such as ϕ29 DNA polymerase, can isothermally copy the sequence of a circular template round by round in a process known as rolling circle amplification (RCA), which results in super-long single-stranded (ss) DNA molecules made of tandem repeats. The power of RCA reflects the high processivity and the strand-displacement ability of these polymerases. In this work, the ability of ϕ29DNAP to carry out RCA over circular templates containing a protein-binding DNA aptamer sequence was investigated. It was found that protein-aptamer interactions can prevent this DNA polymerase from reading through the aptameric domain. This finding indicates that protein-binding DNA aptamers can form highly stable complexes with their targets in solution. This novel observation was exploited by translating RCA arrest into a simple and convenient colorimetric assay for the detection of specific protein targets, which continues to showcase the versatility of aptamers as molecular recognition elements for biosensing applications., (Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2014
- Full Text
- View/download PDF
26. A sensitive DNA enzyme-based fluorescent assay for bacterial detection.
- Author
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Aguirre SD, Ali MM, Salena BJ, and Li Y
- Abstract
Bacterial detection plays an important role in protecting public health and safety, and thus, substantial research efforts have been directed at developing bacterial sensing methods that are sensitive, specific, inexpensive, and easy to use. We have recently reported a novel "mix-and-read" assay where a fluorogenic DNAzyme probe was used to detect model bacterium E. coli. In this work, we carried out a series of optimization experiments in order to improve the performance of this assay. The optimized assay can achieve a detection limit of 1000 colony-forming units (CFU) without a culturing step and is able to detect 1 CFU following as short as 4 h of bacterial culturing in a growth medium. Overall, our effort has led to the development of a highly sensitive and easy-to-use fluorescent bacterial detection assay that employs a catalytic DNA.
- Published
- 2013
- Full Text
- View/download PDF
27. NSAID--induced gastroduodenal ulcers: exploring the silent dilemma.
- Author
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Mohamed AH, Salena BJ, and Hunt RH
- Subjects
- Age Factors, Anti-Inflammatory Agents, Non-Steroidal administration & dosage, Arthritis, Rheumatoid complications, Duodenal Ulcer diagnosis, Duodenal Ulcer prevention & control, Gastric Mucosa drug effects, Gastric Mucosa metabolism, Gastrointestinal Diseases complications, Helicobacter Infections complications, Helicobacter pylori, Histamine H2 Antagonists therapeutic use, Humans, Misoprostol therapeutic use, Prostaglandins biosynthesis, Risk Factors, Sex Factors, Stomach Ulcer diagnosis, Stomach Ulcer prevention & control, Anti-Inflammatory Agents, Non-Steroidal adverse effects, Duodenal Ulcer chemically induced, Stomach Ulcer chemically induced
- Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are effective medications and are very commonly prescribed. They are used by a large proportion of elderly persons who are most prone to adverse events. NSAID gastropathy is the commonest side effect. The relative risk of adverse events is high, but the absolute risk for any individual patient is low. Individualizing the risk/benefit ratio would lead to cost effective care.
- Published
- 1994
28. Effects of chronic NSAIDs on gastric mucosal injury related to mucosal prostanoids, and plasma drug concentrations in human volunteers.
- Author
-
Rainsford KD, James C, Johnson DM, Stetsko PI, Hill RE, Salena BJ, and Hunt RH
- Subjects
- Adult, Anti-Inflammatory Agents, Non-Steroidal pharmacology, Apazone adverse effects, Apazone blood, Apazone pharmacology, Gastric Fundus drug effects, Gastric Fundus metabolism, Gastric Mucosa metabolism, Humans, Indomethacin adverse effects, Indomethacin blood, Indomethacin pharmacology, Male, Naproxen adverse effects, Naproxen blood, Naproxen pharmacology, Piroxicam adverse effects, Piroxicam blood, Piroxicam pharmacology, Pyloric Antrum drug effects, Pyloric Antrum metabolism, 6-Ketoprostaglandin F1 alpha metabolism, Anti-Inflammatory Agents, Non-Steroidal adverse effects, Dinoprostone metabolism, Gastric Mucosa drug effects, Thromboxane B2 metabolism
- Abstract
The relationship between endoscopically observed gastric mucosal damage, elicited following repeated oral intake for 7 d of four NSAIDs, to their effects on antral and fundic production of PGE2, 6-keto-PGF1 alpha and TxB2 (assayed by GC-MS), mucosal histology and plasma concentration profiles was studied in 40 normal males. Subjects received azapropazone (APZ) 600 mg b.i.d., indomethacin (IND) 50 mg t.i.d., naproxen (NAP) 500 mg b.i.d., piroxicam (PIR) 20 mg qq.d., or one placebo capsule t.i.d. (N = 8/group). Plasma NSAIDs (HPLC) levelled at 7 d. Mucosal damage occurred in the antrum region with IND and NAP. APZ and PIR exhibited no differences compared to placebo. NAP and IND reduced all three prostanoids in the antrum while APZ and PIR were ineffective. Fundic PGE2 was reduced by IND, NAP and PIR; APZ had no effects. Thus, mucosal damage relates to effects on prostanoid production in the antrum but not in the fundus.
- Published
- 1993
- Full Text
- View/download PDF
29. Endoscopic therapy for acute nonvariceal upper gastrointestinal hemorrhage: a meta-analysis.
- Author
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Cook DJ, Guyatt GH, Salena BJ, and Laine LA
- Subjects
- Acute Disease, Clinical Trials as Topic, Electrocoagulation adverse effects, Gastrointestinal Hemorrhage etiology, Gastrointestinal Hemorrhage mortality, Humans, Injections, Laser Therapy adverse effects, Meta-Analysis as Topic, Peptic Ulcer complications, Recurrence, Research Design, Risk Factors, Survival Analysis, Gastrointestinal Hemorrhage therapy, Gastroscopy
- Abstract
Endoscopic hemostatic therapy for upper gastrointestinal bleeding is gaining widespread acceptance despite often conflicting results of randomized controlled trials. To examine the effect of endoscopic therapy in acute nonvariceal upper gastrointestinal hemorrhage, a meta-analysis was performed using a computerized search of the English-language literature and a bibliographic review. The methodology, population, intervention, and outcomes of each relevant trial were evaluated by duplicate independent review. Thirty randomized controlled trials evaluating hemostatic endoscopic treatment were identified. Endoscopic therapy significantly reduced rates of further bleeding (odds ratio, 0.38; 95% confidence interval, 0.32-0.45), surgery (odds ratio, 0.36; 95% confidence interval, 0.28-0.45), and mortality (odds ratio, 0.55; 95% confidence interval, 0.40-0.76). When analyzed separately, thermal-contact devices (monopolar and bipolar electrocoagulation and heater probe), laser treatment, and injection therapy all significantly decreased further bleeding and surgery rates. The reductions in mortality were comparable for all three forms of therapy, but the decrease reached statistical significance only for laser therapy. Further examination of subgroups indicated that endoscopic treatment decreased rates of further bleeding, surgery, and mortality in patients with high-risk endoscopic features of active bleeding or nonbleeding visible vessels. Rebleeding was not reduced by endoscopic therapy in patients with ulcers containing flat pigmented spots or adherent clots. Endoscopic hemostatic therapy provides a clinically important reduction in morbidity and mortality in patients with acute nonvariceal upper gastrointestinal hemorrhage.
- Published
- 1992
- Full Text
- View/download PDF
30. Do hourly averaged pH readings correlate with those from point readings of aspiration? Comparison of two different electrode positions with simultaneous aspiration.
- Author
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Chiverton SG, Salena BJ, Burget DW, and Hunt RH
- Subjects
- Adult, Gastric Acid metabolism, Humans, Hydrogen-Ion Concentration, Intubation, Gastrointestinal, Male, Time Factors, Gastric Acidity Determination, Microelectrodes, Monitoring, Physiologic methods, Suction methods
- Abstract
Hourly averaged data from continuous intraluminal pH recording were compared with the point aspiration in five 24-hour studies performed on healthy volunteers. Two different electrode positions were compared simultaneously with aspiration. The correlation was performed using the median from the whole hour's recording of the electrode against the aspiration point. There was a significant correlation between both electrodes and aspiration (p less than 0.001), although both electrodes read consistently lower than aspiration: electrode A (gastric antrum), median pH = 1.4; electrode B (gastric body), pH = 1.9; aspiration, pH = 2.3. These findings show that data reported in clinical trials using different recording techniques are not directly comparable and must be interpreted appropriately. The position of the electrode may also be important.
- Published
- 1990
- Full Text
- View/download PDF
31. Pregnancy and esophageal varices.
- Author
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Salena BJ and Sivak MV Jr
- Subjects
- Adult, Esophagoscopy, Female, Humans, Pregnancy, Esophageal and Gastric Varices therapy, Pregnancy Complications, Cardiovascular therapy, Sclerosing Solutions therapeutic use
- Published
- 1988
- Full Text
- View/download PDF
32. Does misoprostol given as a single large dose improve its antisecretory effect?
- Author
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Chiverton SG, Burget DW, Salena BJ, and Hunt RH
- Subjects
- Adult, Anti-Ulcer Agents administration & dosage, Dose-Response Relationship, Drug, Double-Blind Method, Humans, Male, Misoprostol administration & dosage, Anti-Ulcer Agents pharmacology, Gastric Acid metabolism, Misoprostol pharmacology
- Abstract
H2-receptor antagonists have been shown to be effective in the suppression of nocturnal acidity. This double-blind, randomized, crossover Latin-square study of 24-h intragastric pH in 12 normal volunteers investigated the effect of large single-dose administration of misoprostol on intragastric acidity. Efficacy of 800 micrograms misoprostol h.s., 600 micrograms h.s., 400 micrograms h.s. and 800 micrograms after supper was compared to placebo and 200 micrograms misoprostol q.d.s. Twenty-four hour mean pH +/- s.d. was placebo 2.1 +/- 0.3, misoprostol 200 micrograms q.d.s. Twenty-four hour mean pH +/- s.d. was placebo 2.1 +/- 0.3, misoprostol 200 micrograms q.d.s. 2.2 +/- 0.3, 800 micrograms p.m. 2.6 +/- 1.1, 400 micrograms h.s. 2.6 +/- 0.7, 600 micrograms h.s. 2.6 +/- 0.4, 800 micrograms h.s. 2.6 +/- 0.5. The effect of misoprostol on gastric acidity was short and limited to the nocturnal period. Only misoprostol 800 micrograms and 600 micrograms reduced 24-h acidity compared to placebo (P less than 0.04).
- Published
- 1989
- Full Text
- View/download PDF
33. Adenomyoma of the common bile duct.
- Author
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Cook DJ, Salena BJ, and Vincic LM
- Subjects
- Aged, Aged, 80 and over, Cholestasis etiology, Female, Humans, Common Bile Duct Neoplasms complications, Common Bile Duct Neoplasms pathology, Endometriosis complications, Endometriosis pathology
- Abstract
We report an unusual case of biliary obstruction secondary to adenomyoma of the common bile duct. Adenomyomas are benign tumors, found infrequently in the biliary tree. Clinical presentation, biochemical, radiographic, and endoscopic investigations do not distinguish adenomyomas from malignant or other lesions; diagnosis requires histological examination. The natural history and optimal treatment of these tumors have not been established.
- Published
- 1988
34. Chronic cough and the use of captopril: unmasking asthma.
- Author
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Salena BJ
- Subjects
- Asthma diagnosis, Chronic Disease, Humans, Asthma complications, Captopril adverse effects, Cough etiology
- Published
- 1986
35. The limitations of current therapy in peptic ulcer disease.
- Author
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Salena BJ and Hunt RH
- Subjects
- Antacids adverse effects, Antacids pharmacology, Anti-Ulcer Agents administration & dosage, Anti-Ulcer Agents adverse effects, Gastric Juice metabolism, Humans, Peptic Ulcer physiopathology, Anti-Ulcer Agents therapeutic use, Peptic Ulcer drug therapy
- Abstract
The current therapeutic approach to peptic ulcer disease includes agents that reduce gastric acidity and hence peptic activity, inactivate or adsorb pepsin, create a physical barrier against the effects of acid and pepsin, or enhance mucosal defence. Profound gastric acid reduction may predispose to infection, and it has been suggested that carcinogenesis is possible, although a cause-effect relationship has never been established. The side-effects of therapy are well-described, and may limit the therapeutic approach. Healing rates correlate closely with acid suppression in duodenal ulcer, but not entirely in gastric ulcer. Maintenance therapy lowers the relapse rate, but does not alter the ulcer diathesis. The optimal strategy for long-term management remains unclear, but in the future one should consider outcome measures which include a decrease in pain, improvement in the quality of life, reduction work loss, and a reduction of complications, in addition to ulcer healing. The ideal therapy should be efficacious, safe, and convenient--with no side-effects--and cost-effective. New agents should suppress acid and peptic activity, while enhancing the gastric mucosal defence mechanisms (such as mucosal blood flow, mucus, and bicarbonate secretion) and stimulating gastric cellular regeneration and restitution.
- Published
- 1987
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