DNA and Peptide Aptamer Selection for Diagnostic Applications
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Guide for Common Viral Diseases of Animals in Louisiana
Sampling and Testing Guide for Common Viral Diseases of Animals in Louisiana Please click on the species of interest: Cattle Deer and Small Ruminants The Louisiana Animal Swine Disease Diagnostic Horses Laboratory Dogs A service unit of the LSU School of Veterinary Medicine Adapted from Murphy, F.A., et al, Veterinary Virology, 3rd ed. Cats Academic Press, 1999. Compiled by Rob Poston Multi-species: Rabiesvirus DCN LADDL Guide for Common Viral Diseases v. B2 1 Cattle Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 2 Deer and Small Ruminants Please click on the principle system involvement Generalized viral disease Respiratory viral disease Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 3 Swine Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 4 Horses Please click on the principle system involvement Generalized viral diseases Neurological viral diseases Respiratory viral diseases Enteric viral diseases Abortifacient/neonatal viral diseases Viral infections affecting the skin Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. B2 5 Dogs Please click on the principle system involvement Generalized viral diseases Respiratory viral diseases Enteric viral diseases Reproductive/neonatal viral diseases Back to the Beginning DCN LADDL Guide for Common Viral Diseases v. -
Comparative Analysis, Distribution, and Characterization of Microsatellites in Orf Virus Genome
www.nature.com/scientificreports OPEN Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome Basanta Pravas Sahu1, Prativa Majee 1, Ravi Raj Singh1, Anjan Sahoo2 & Debasis Nayak 1* Genome-wide in-silico identifcation of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036–1,181 microsatellites per strain. The further screening revealed the presence of 83–107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6–8.4 and 53.0–59.5 bp/ kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6–0.8 and 12.1–17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD signifcantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-signifcantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)- x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. -
Aptamer-Mediated Cancer Gene Therapy Dongxi Xiang , Sarah
Aptamer-Mediated Cancer Gene Therapy Dongxi Xiang1*, Sarah Shigdar 1*, Greg Qiao2, Shu-Feng Zhou3, Yong Li4, Ming Q Wei5, 6 1 7 8 9** Liang Qiao , Hadi Al.Shamaileh , Yimin Zhu , Conglong Zheng , Chunwen Pu and Wei Duan1** 1School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria, 3217, Australia. 2 Department of Chemical and Biomolecular Engineering, Melbourne School of Engineering The University of Melbourne, Parkville, Victoria 3010, Australia 3Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33612, USA. 4Cancer Care Centre, St George Hospital, Kogarah, NSW2217, and St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, NSW2052, Australia 5Division of Molecular and Gene Therapies, Griffith Health Institute and School of Medical Science, Griffith University, Gold Coast, QLD 4222, Australia 6Storr Liver Unit, at the Westmead Millennium Institute, the University of Sydney at the Westmead Hospital, Westmead NSW, 2145, Australia 7Suzhou Key Laboratory of Nanobiomedicine, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu, China, 215123 8Department of Biology, Medical College, Dalian University, Liaoning, People’s Republic of China 9The Affiliated Zhongshan Hospital of Dalian University, 6 Jiefang Road, Dalian, Liaoning, The People's Republic of China, 116001. 1 * These authors contributed equally. ** Corresponding authors: E-mail: [email protected] (C. Pu); or [email protected] (W. Duan). 2 Abstract Cancer as a genetic disorder is one of the leading causes of death worldwide. Conventional anticancer options such as chemo- and/or radio-therapy have their own drawbacks and could not provide a cure in most cases at present. -
Modulation of NF-Κb Signalling by Microbial Pathogens
REVIEWS Modulation of NF‑κB signalling by microbial pathogens Masmudur M. Rahman and Grant McFadden Abstract | The nuclear factor-κB (NF‑κB) family of transcription factors plays a central part in the host response to infection by microbial pathogens, by orchestrating the innate and acquired host immune responses. The NF‑κB proteins are activated by diverse signalling pathways that originate from many different cellular receptors and sensors. Many successful pathogens have acquired sophisticated mechanisms to regulate the NF‑κB signalling pathways by deploying subversive proteins or hijacking the host signalling molecules. Here, we describe the mechanisms by which viruses and bacteria micromanage the host NF‑κB signalling circuitry to favour the continued survival of the pathogen. The nuclear factor-κB (NF-κB) family of transcription Signalling targets upstream of NF‑κB factors regulates the expression of hundreds of genes that NF-κB proteins are tightly regulated in both the cyto- are associated with diverse cellular processes, such as pro- plasm and the nucleus6. Under normal physiological liferation, differentiation and death, as well as innate and conditions, NF‑κB complexes remain inactive in the adaptive immune responses. The mammalian NF‑κB cytoplasm through a direct interaction with proteins proteins are members of the Rel domain-containing pro- of the inhibitor of NF-κB (IκB) family, including IκBα, tein family: RELA (also known as p65), RELB, c‑REL, IκBβ and IκBε (also known as NF-κBIα, NF-κBIβ and the NF-κB p105 subunit (also known as NF‑κB1; which NF-κBIε, respectively); IκB proteins mask the nuclear is cleaved into the p50 subunit) and the NF-κB p100 localization domains in the NF‑κB complex, thus subunit (also known as NF‑κB2; which is cleaved into retaining the transcription complex in the cytoplasm. -
Lab-On-A-Chip Systems for Aptamer-Based Biosensing
micromachines Review Lab-on-a-Chip Systems for Aptamer-Based Biosensing Niazul I. Khan 1 and Edward Song 1,2,* 1 Department of Electrical and Computer Engineering, University of New Hampshire, Durham, NH 03824, USA; [email protected] 2 Materials Science Program, University of New Hampshire, Durham, NH 03824, USA * Correspondence: [email protected]; Tel.: +1-603-862-5498 Received: 6 January 2020; Accepted: 17 February 2020; Published: 20 February 2020 Abstract: Aptamers are oligonucleotides or peptides that are selected from a pool of random sequences that exhibit high affinity toward a specific biomolecular species of interest. Therefore, they are ideal for use as recognition elements and ligands for binding to the target. In recent years, aptamers have gained a great deal of attention in the field of biosensing as the next-generation target receptors that could potentially replace the functions of antibodies. Consequently, it is increasingly becoming popular to integrate aptamers into a variety of sensing platforms to enhance specificity and selectivity in analyte detection. Simultaneously, as the fields of lab-on-a-chip (LOC) technology, point-of-care (POC) diagnostics, and personal medicine become topics of great interest, integration of such aptamer-based sensors with LOC devices are showing promising results as evidenced by the recent growth of literature in this area. The focus of this review article is to highlight the recent progress in aptamer-based biosensor development with emphasis on the integration between aptamers and the various forms of LOC devices including microfluidic chips and paper-based microfluidics. As aptamers are extremely versatile in terms of their utilization in different detection principles, a broad range of techniques are covered including electrochemical, optical, colorimetric, and gravimetric sensing as well as surface acoustics waves and transistor-based detection. -
Real-Time PCR for Direct Aptamer Quantification on Functionalized
www.nature.com/scientificreports OPEN Real-time PCR for direct aptamer quantifcation on functionalized graphene surfaces Viviane C. F. dos Santos1,2*, Nathalie B. F. Almeida1,2, Thiago A. S. L. de Sousa1, Eduardo N. D. Araujo3, Antero S. R. de Andrade2 & Flávio Plentz1 In this study, we develop a real-time PCR strategy to directly detect and quantify DNA aptamers on functionalized graphene surfaces using a Staphylococcus aureus aptamer (SA20) as demonstration case. We show that real-time PCR allowed aptamer quantifcation in the range of 0.05 fg to 2.5 ng. Using this quantitative technique, it was possible to determine that graphene functionalization with amino modifed SA20 (preceded by a graphene surface modifcation with thionine) was much more efcient than the process using SA20 with a pyrene modifcation. We also demonstrated that the functionalization methods investigated were selective to graphene as compared to bare silicon dioxide surfaces. The precise quantifcation of aptamers immobilized on graphene surface was performed for the frst time by molecular biology techniques, introducing a novel methodology of wide application. DNA (deoxyribonucleic acid) aptamers are single strand oligonucleotides that presents high afnity and speci- fcity to their binders1. In comparison with traditional ligands, such as antibodies, aptamers present some advan- tages. Tey are chemically stable, cost-efective, more resistant to pH and temperature variations, and are more fexible in the design of their structures2. Due to these characteristics, they have great potential as sensing compo- nents in diagnostic and detection assays. Biosensor platforms based on DNA aptamers are more stable for storage and transport than the antibodies counterparts2. -
Specimen Type, Collection Methods, and Diagnostic Assays Available For
Specimen type, collection methods, and diagnostic assays available for the detection of poxviruses from human specimens by the Poxvirus and Rabies Branch, Centers for Disease Control and Prevention1. Specimen Orthopoxvirus Parapoxvirus Yatapoxvirus Molluscipoxvirus Specimen type collection method PCR6 Culture EM8 IHC9,10 Serology11 PCR12 EM8 IHC9,10 PCR13 EM8 PCR EM8 Lesion material Fresh or frozen Swab 5 Lesion material [dry or in media ] [vesicle / pustule Formalin fixed skin, scab / crust, etc.] Paraffin block Fixed slide(s) Container Lesion fluid Swab [vesicle / pustule [dry or in media5] fluid, etc.] Touch prep slide Blood EDTA2 EDTA tube 7 Spun or aliquoted Serum before shipment Spun or aliquoted Plasma before shipment CSF3,4 Sterile 1. The detection of poxviruses by electron microscopy (EM) and immunohistochemical staining (IHC) is performed by the Infectious Disease Pathology Branch of the CDC. 2. EDTA — Ethylenediaminetetraacetic acid. 3. CSF — Cerebrospinal fluid. 4. In order to accurately interpret test results generated from CSF specimens, paired serum must also be submitted. 5. If media is used to store and transport specimens a minimal amount should be used to ensure as little dilution of DNA as possible. 6. Orthopoxvirus generic real-time polymerase chain reaction (PCR) assays will amplify DNA from numerous species of virus within the Orthopoxvirus genus. Species-specific real-time PCR assays are available for selective detection of DNA from variola virus, vaccinia virus, monkeypox virus, and cowpox virus. 7. Blood is not ideal for the detection of orthopoxviruses by PCR as the period of viremia has often passed before sampling occurs. 8. EM can reveal the presence of a poxvirus in clinical specimens or from virus culture, but this technique cannot differentiate between virus species within the same genus. -
Design Strategies for Aptamer-Based Biosensors
Sensors 2010, 10, 4541-4557; doi:10.3390/s100504541 OPEN ACCESS sensors ISSN 1424-8220 www.mdpi.com/journal/sensors Review Design Strategies for Aptamer-Based Biosensors Kun Han 1,2, Zhiqiang Liang 3 and Nandi Zhou 1,4,* 1 Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China 2 Suzhou Institute of Biomedical Engineering Technology, Chinese Academy of Science, Suzhou 215163, China; E-Mail: [email protected] 3 Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, China; E-Mail: [email protected] 4 School of Biotechnology and the Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-510-8591-8116; Fax: +86-510-8591-8116. Received: 11 February 2010; in revised form: 1 April 2010 / Accepted: 4 April 2010 / Published: 4 May 2010 Abstract: Aptamers have been widely used as recognition elements for biosensor construction, especially in the detection of proteins or small molecule targets, and regarded as promising alternatives for antibodies in bioassay areas. In this review, we present an overview of reported design strategies for the fabrication of biosensors and classify them into four basic modes: target-induced structure switching mode, sandwich or sandwich-like mode, target-induced dissociation/displacement mode and competitive replacement mode. In view of the unprecedented advantages brought about by aptamers and smart design strategies, aptamer-based biosensors are expected to be one of the most promising devices in bioassay related applications. -
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DNA and RNA Nanotechnology 2015; 2: 42–52 Mini review Open Access Martin Panigaj*, Jakob Reiser Aptamer guided delivery of nucleic acid-based nanoparticles DOI 10.1515/rnan-2015-0005 Evolution of Ligands by Exponential enrichment) [4,5]. Received July 15, 2015; accepted October 3, 2015 Nucleic acid-based aptamers are especially well suited Abstract: Targeted delivery of bioactive compounds is a for the delivery of nucleic acid-based therapeutics. Any key part of successful therapies. In this context, nucleic nucleic acid with therapeutic potential can be linked acid and protein-based aptamers have been shown to to an aptamer sequence [6], resulting in a bivalent bind therapeutically relevant targets including receptors. molecule endowed with a targeting aptamer moiety and In the last decade, nucleic acid-based therapeutics a functional RNA/DNA moiety like a small interfering coupled to aptamers have emerged as a viable strategy for RNA (siRNA), a micro RNA (miRNA), a miRNA antagonist cell specific delivery. Additionally, recent developments (antimiR), deoxyribozymes (DNAzymes), etc. In addition in nucleic acid nanotechnology offer an abundance of to the specific binding, many aptamers upon receptor possibilities to rationally design aptamer targeted RNA recognition elicit antagonistic or agonistic responses that, or DNA nanoparticles involving combinatorial use of in combination with conjugated functional nucleic acids various intrinsic functionalities. Although a host of issues have the potential of synergism. Since the first report including stability, safety and intracellular trafficking describing an aptamer-siRNA delivery approach in 2006 remain to be addressed, aptamers as simple functional many functional RNAs and DNAs conjugated to aptamer chimeras or as parts of multifunctional self-assembled sequences have been tested in vitro and in vivo [7-9]. -
Treatment of Metastatic Disease Through Natural Killer Cell Modulation by Infected Cell Vaccines
viruses Review Treatment of Metastatic Disease through Natural Killer Cell Modulation by Infected Cell Vaccines Seyedeh Raheleh Niavarani 1, Christine Lawson 1 and Lee-Hwa Tai 1,2,* 1 Department of Anatomy and Cell Biology, Université de Sherbrooke, Sherbrooke QC J1E 4K8, Canada; [email protected] (S.R.N.); [email protected] (C.L.) 2 Centre de Recherche du Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke QC J1E 4K8, Canada * Correspondence: [email protected]; Tel.: +1-819-821-8000 (ext. 71199) Received: 26 March 2019; Accepted: 10 May 2019; Published: 11 May 2019 Abstract: Oncolytic viruses (OVs) are a form of immunotherapy that release tumor antigens in the context of highly immunogenic viral signals following tumor-targeted infection and destruction. Emerging preclinical and clinical evidence suggests that this in situ vaccine effect is critical for successful viro-immunotherapy. In this review, we discuss the application of OV as an infected cell vaccine (ICV) as one method of enhancing the potency and breadth of anti-tumoral immunity. We focus on understanding and manipulating the critical role of natural killer (NK) cells and their interactions with other immune cells to promote a clinical outcome. With a synergistic tumor killing and immune activating mechanism, ICVs represent a valuable new addition to the cancer fighting toolbox with the potential to treat malignant disease. Keywords: immunotherapy; oncolytic virus; autologous cancer vaccines; infected cell vaccines; natural killer cells; immunomonitoring 1. Introduction While the field of oncology has seen great advances in treating primary solid cancers, malignant cancers that have spread to multiple sites of the body have rarely been cured. -
Characterization of a Bifunctional Synthetic RNA Aptamer
www.nature.com/scientificreports OPEN Characterization of A Bifunctional Synthetic RNA Aptamer and A Truncated Form for Ability to Inhibit Growth of Non-Small Cell Lung Cancer Hanlu Wang1,2, Meng Qin2,3, Rihe Liu1,4, Xinxin Ding1,5, Irvin S. Y. Chen6 & Yongping Jiang1,2* An in vitro-transcribed RNA aptamer (trans-RA16) that targets non-small cell lung cancer (NSCLC) was previously identifed through in vivo SELEX. Trans-RA16 can specifcally target and inhibit human NCI-H460 cells in vitro and xenograft tumors in vivo. Here, in a follow-up study, we obtained a chemically-synthesized version of this RNA aptamer (syn-RA16) and a truncated form, and compared them to trans-RA16 for abilities to target and inhibit NCI-H460 cells. The syn-RA16, preferred for drug development, was by design to difer from trans-RA16 in the extents of RNA modifcations by biotin, which may afect RA16’s anti-tumor efects. We observed aptamer binding to NCI-H460 cells with KD values of 24.75 ± 2.28 nM and 12.14 ± 1.46 nM for syn-RA16 and trans-RA16, respectively. Similar to trans-RA16, syn-RA16 was capable of inhibiting NCI-H460 cell viability in a dose-dependent manner. IC50 values were 118.4 nM (n = 4) for syn-RA16 and 105.7 nM (n = 4) for trans-RA16. Further studies using syn-RA16 demonstrated its internalization into NCI-H460 cells and inhibition of NCI-H460 cell growth. Moreover, in vivo imaging demonstrated the gradual accumulation of both syn-RA16 and trans-RA16 at the grafted tumor site, and qRT-PCR showed high retention of syn-RA16 in tumor tissues. -
An Insight Into Aptamer–Protein Complexes
ISSN: 2514-3247 Aptamers, 2018, Vol 2, 55–63 MINI-REVIEW An insight into aptamer–protein complexes Anastasia A Novoseltseva1,2,*, Elena G Zavyalova1,2, Andrey V Golovin2,3, Alexey M Kopylov1,2 1Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia; 2Apto-Pharm Ltd., Moscow, Russia; 3Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia *Correspondence to: Anastasia Novoseltseva, Email: [email protected], Tel: +749 59393149, Fax: +749 59393181 Received: 04 May 2018 | Revised: 12 July 2018 | Accepted: 23 August 2018 | Published: 24 August 2018 © Copyright The Author(s). This is an open access article, published under the terms of the Creative Commons Attribu- tion Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0). This license permits non-commercial use, distribution and reproduction of this article, provided the original work is appropriately acknowledged, with correct citation details. ABSTRACT A total of forty-five X-ray structures of aptamer–protein complexes have been resolved so far. We uniformly analysed a large dataset using common aptamer parameters such as the type of nucleic acid, aptamer length and presence of chemical modifications, and the various parameters of complexes such as interface area, number of polar contacts and Gibbs free energy change. For the overall aptamer dataset, Gibbs free energy change was found to have no correlation with the interface area or with the number of polar contacts. The elements of the dataset with heterogeneous parameters were clustered, providing a possibility to reveal structure–affinity relationship, SAR. Complexes with DNA aptamers and RNA aptamers had the same charac- teristics.