Journal articles on the topic 'Molecular probes Diagnostic use'
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Courtney, Samantha, Zachary Stromberg, Adán Myers y Gutiérrez, Daniel Jacobsen, Loreen Stromberg, Kiersten Lenz, James Theiler, et al. "Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA." Biosensors 11, no. 10 (September 30, 2021): 367. http://dx.doi.org/10.3390/bios11100367.
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Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention’s (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC’s probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.
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Betson, Mark, Nigel Allanson, and Philip Wainwright. "A review of methods to synthesise 4′-substituted nucleosides." Org. Biomol. Chem. 12, no. 46 (2014): 9291–306. http://dx.doi.org/10.1039/c4ob01449a.
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Ma, Ying-Yu, Ke-Tao Jin, Shi-Bing Wang, Hui-Ju Wang, Xiang-Min Tong, Dong-Sheng Huang, and Xiao-Zhou Mou. "Molecular Imaging of Cancer with Nanoparticle-Based Theranostic Probes." Contrast Media & Molecular Imaging 2017 (2017): 1–11. http://dx.doi.org/10.1155/2017/1026270.
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Although advancements in medical technology supporting cancer diagnosis and treatment have improved survival, these technologies still have limitations. Recently, the application of noninvasive imaging for cancer diagnosis and therapy has become an indispensable component in clinical practice. However, current imaging contrasts and tracers, which are in widespread clinical use, have their intrinsic limitations and disadvantages. Nanotechnologies, which have improved in vivo detection and enhanced targeting efficiency for cancer, may overcome some of the limitations of cancer diagnosis and therapy. Theranostic nanoparticles have great potential as a therapeutic model, which possesses the ability of their nanoplatforms to load targeted molecule for both imaging and therapeutic functions. The resulting nanosystem will likely be critical with the growth of personalized medicine because of their diagnostic potential, effectiveness as a drug delivery vehicle, and ability to oversee patient response to therapy. In this review, we discuss the achievements of modern nanoparticles with the goal of accurate tumor imaging and effective treatment and discuss the future prospects.
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Sguizzato, Maddalena, Petra Martini, Lorenza Marvelli, Walter Pula, Markus Drechsler, Martina Capozza, Enzo Terreno, et al. "Synthetic and Nanotechnological Approaches for a Diagnostic Use of Manganese." Molecules 27, no. 10 (May 13, 2022): 3124. http://dx.doi.org/10.3390/molecules27103124.
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The development of multimodal imaging techniques such as positron emission tomography (PET) and magnetic resonance imaging (MRI) allows the contemporary obtaining of metabolic and morphological information. To fully exploit the complementarity of the two imaging modalities, the design of probes displaying radioactive and magnetic properties at the same time could be very beneficial. In this regard, transition metals offer appealing options, with manganese representing an ideal candidate. As nanosized imaging probes have demonstrated great value for designing advanced diagnostic/theranostic procedures, this work focuses on the potential of liposomal formulations loaded with a new synthesized paramagnetic Mn(II) chelates. Negatively charged liposomes were produced by thin-layer hydration method and extrusion. The obtained formulations were characterized in terms of size, surface charge, efficiency of encapsulation, stability over time, relaxivity, effective magnetic moment, and in vitro antiproliferative effect on human cells by means of the MTT assay. The negatively charged paramagnetic liposomes were monodisperse, with an average hydrodynamic diameter not exceeding 200 nm, and they displayed good stability and no cytotoxicity. As determined by optical emission spectroscopy, manganese complexes are loaded almost completely on liposomes maintaining their paramagnetic properties.
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Rangasamy, Geronimo, Ortín, Coderch, Zapico, Ramos, and de Pascual-Teresa. "Molecular Imaging Probes Based on Matrix Metalloproteinase Inhibitors (MMPIs)." Molecules 24, no. 16 (August 16, 2019): 2982. http://dx.doi.org/10.3390/molecules24162982.
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Matrix metalloproteinases (MMPs) are a family of zinc- and calcium-dependent endopeptidases which are secreted or anchored in the cell membrane and are capable of degrading the multiple components of the extracellular matrix (ECM). MMPs are frequently overexpressed or highly activated in numerous human diseases. Owing to the important role of MMPs in human diseases, many MMP inhibitors (MMPIs) have been developed as novel therapeutics, and some of them have entered clinical trials. However, so far, only one MMPI (doxycycline) has been approved by the FDA. Therefore, the evaluation of the activity of a specific subset of MMPs in human diseases using clinically relevant imaging techniques would be a powerful tool for the early diagnosis and assessment of the efficacy of therapy. In recent years, numerous MMPIs labeled imaging agents have emerged. This article begins by providing an overview of the MMP subfamily and its structure and function. The latest advances in the design of subtype selective MMPIs and their biological evaluation are then summarized. Subsequently, the potential use of MMPI-labeled diagnostic agents in clinical imaging techniques are discussed, including positron emission tomography (PET), single-photon emission computed tomography (SPECT) and optical imaging (OI). Finally, this article concludes with future perspectives and clinical utility.
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M S, Kumar. "Snake Venom Toxins: Clinical use and as Diagnostic Agents." Shanlax International Journal of Arts, Science and Humanities 8, S1-Feb (February 6, 2021): 1–5. http://dx.doi.org/10.34293/sijash.v8is1-feb.3923.
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Snakes are fascinating creatures and were inhabitants of this world well before the earth was populated by ancient humans. Snakes with a lethal secretion known as venom were endowed by nature. Snake venom is a very poisonous mixture consisting of a number of molecules such as carbohydrates, nucleosides, amino acids, lipids, proteins and peptides, making it a cocktail of diversified molecules. Snake envenomation is responsible for the disruption in the envenomed victim’s fundamental physiological processes contributing to serious health problems. Millions of snakebites are recorded annually, and due to snake venom poisoning, a significant number of individuals are injured and die. However, through technical developments, many fatal snake venom toxins have found potential applications as diagnostic agents, medicinal agents, or drug leads. From the development of Captopril, the first drug derived from Bothrops jarararaca’s bradykinin potentiating peptide, to the disintegrins that have potent activity against some forms of cancers. Therefore, components of snake venom have shown tremendous potential for the development of lead compounds for new drugs. Complementary tools and techniques are currently being used to isolate and characterize peptides and to study their potential uses as molecular probes and templates for drug development and design investigation models.
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Neveling, Kornelia, Arjen R. Mensenkamp, Ronny Derks, Michael Kwint, Hicham Ouchene, Marloes Steehouwer, Bart van Lier, et al. "BRCA Testing by Single-Molecule Molecular Inversion Probes." Clinical Chemistry 63, no. 2 (February 1, 2017): 503–12. http://dx.doi.org/10.1373/clinchem.2016.263897.
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Abstract BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10–15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.
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Fuller, Skylar L., Elizabeth A. Savory, Alexandra J. Weisberg, Jessica Z. Buser, Michael I. Gordon, Melodie L. Putnam, and Jeff H. Chang. "Isothermal Amplification and Lateral-Flow Assay for Detecting Crown-Gall-Causing Agrobacterium spp." Phytopathology® 107, no. 9 (September 2017): 1062–68. http://dx.doi.org/10.1094/phyto-04-17-0144-r.
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Agrobacterium is a genus of soilborne gram-negative bacteria. Members carrying oncogenic plasmids can cause crown gall disease, which has significant economic costs, especially for the orchard and nursery industries. Early and rapid detection of pathogenic Agrobacterium spp. is key to the management of crown gall disease. To this end, we designed oligonucleotide primers and probes to target virD2 for use in a molecular diagnostic tool that relies on isothermal amplification and lateral-flow-based detection. The oligonucleotide tools were tested in the assay and evaluated for detection limit and specificity in detecting alleles of virD2. One set of primers that successfully amplified virD2 when used with an isothermal recombinase was selected. Both tested probes had detection limits in picogram amounts of DNA. Probe 1 could detect all tested pathogenic isolates that represented most of the diversity of virD2. Finally, the coupling of lateral-flow detection to the use of these oligonucleotide primers in isothermal amplification helped to reduce the onerousness of the process, and alleviated reliance on specialized tools necessary for molecular diagnostics. The assay is an advancement for the rapid molecular detection of pathogenic Agrobacterium spp.
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Bentivoglio, Valeria, Michela Varani, Chiara Lauri, Danilo Ranieri, and Alberto Signore. "Methods for Radiolabelling Nanoparticles: PET Use (Part 2)." Biomolecules 12, no. 10 (October 20, 2022): 1517. http://dx.doi.org/10.3390/biom12101517.
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The use of radiolabelled nanoparticles (NPs) is a promising nuclear medicine tool for diagnostic and therapeutic purposes. Thanks to the heterogeneity of their material (organic or inorganic) and their unique physical and chemical characteristics, they are highly versatile for their use in several medical applications. In particular, they have shown interesting results as radiolabelled probes for positron emission tomography (PET) imaging. The high variability of NP types and the possibility to use several isotopes in the radiolabelling process implies different radiolabelling methods that have been applied over the previous years. In this review, we compare and summarize the different methods for NP radiolabelling with the most frequently used PET isotopes.
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Zenteno-Cuevas, Roberto, Betzaida Cuevas-Cordoba, Antonio Enciso, Leonor Enciso, and Aremy Cuellar. "Assessing the utility of three TaqMan probes for the diagnosis of tuberculosis and resistance to rifampin and isoniazid in Veracruz, México." Canadian Journal of Microbiology 58, no. 3 (March 2012): 318–25. http://dx.doi.org/10.1139/w11-127.
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Mutations at codons 526 and 531 in the rpoB gene and at 315 in the katG gene are considered diagnostic markers for resistance to rifampin and isoniazid in tuberculosis. The aim of this study was to design and evaluate three TaqMan probes for the identification of these mutations in 138 respiratory samples positive for acid-fast bacilli, and 32 clinical isolates from a region with considerable levels of drug resistance. The specificities of the probes for the diagnosis of resistance to both drugs were 100%; however, the sensitivities were calculated to be 50% for isoniazid and 56% for rifampin. DNA sequencing of rpoB and katG; and the spoligotyping assay of the clinical isolates, confirmed the diversity of the mutations and the presence of 11 spoligotypes with a shared international type and eight unique spoligotypes. Analysis of the respiratory samples identified 22 (16%) as drug-resistant and 4 (3%) as multidrug-resistant tuberculosis. The diagnostic value of the TaqMan probes was compromised by the diversity of mutations found in the clinical isolates. This highlights the need for better understanding of the molecular mechanisms responsible for drug resistance prior to the use of molecular probes, especially in regions with significant levels of drug-resistant tuberculosis.
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BOYES, STEPHEN G., MISTY D. ROWE, NATALIE J. SERKOVA, FERNANDO J. KIM, JAMES R. LAMBERT, and PRIYA N. WERAHERA. "POLYMER-MODIFIED GADOLINIUM NANOPARTICLES FOR TARGETED MAGNETIC RESONANCE IMAGING AND THERAPY." Nano LIFE 01, no. 03n04 (September 2010): 263–75. http://dx.doi.org/10.1142/s1793984410000250.
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Functional imaging is a novel area in radiological sciences and allows for the non-invasive assessment and visualization of specific targets such as gene and protein expression, metabolic rates, and drug delivery in intact living subjects. As such, the field of molecular imaging has been defined as the non-invasive, quantitative, and repetitive imaging of biomolecules and biological processes in living organisms. For example, cancer cells may be genetically altered to attract molecules that alter the magnetic susceptibility, thereby permitting their identification by magnetic resonance imaging. These contrast agents and/or molecular reporters are seen as essential to the task of molecular medicine to increase both sensitivity and specificity of imaging. Therefore, there are five general principles which need to be fulfilled in order to conduct a successful in vivo molecular imaging study: (1) selection of appropriate cellular and subcellular targets; (2) development of suitable in vivo affinity ligands (molecular probes); (3) delivery of these probes to the target organ; (4) amplification strategies able to detect minimal target concentrations; and (5) development of imaging systems with high resolution. Although there has been a wide range of routes taken to incorporate both imaging agents and a disease-targeting moiety into diagnostic devices, arguably the most interesting of these routes employs the use of nanoparticles. Nanoscale diagnostic systems that incorporate molecular targeting agents and diagnostic imaging capabilities are emerging as the next-generation imaging agents and have the potential to dramatically improve the outcome of the imaging, diagnosis, and treatment of a wide range of diseases. The present review addresses chemical aspects in development of molecular probes based upon gadolinium nanoparticles and their potential role in translational clinical imaging and therapy.
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Bone, Bradley, Barbara Seredick, and Mike Olszowy. "Reactive oxygen probes - a broad range of colors with easier labeling and compatibility with fixation: novel CellROX® reagents from Molecular Probes® (P3295)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 211.5. http://dx.doi.org/10.4049/jimmunol.190.supp.211.5.
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Abstract A natural consequence of aerobic respiration is the generation of highly toxic radicals called reactive oxygen species (ROS). ROS have been implicated in various human pathologies. Although fluorogenic probes such as Aminophenyl fluorescein (APF) and hydroxyphenyl fluorescein (HPF), and 2',7'-dichlorodihydrofluorescein diacetate (H2DCFDA) have been widely used to detect ROS using flow cytometry and imaging platforms, all are excitable by the 488nm laser and emit in the fluorescein channel, and require that labeling occur in a protein-free buffer. In contrast, the novel CellROX® ROS detection reagents from Molecular Probes® offer increased flexibility for multiplex experiments, with fluorescence emission in the fluorescein, PE, or APC channels for CellROX® Green, Orange, and Deep Red. In addition, the CellROX® reagents offer increased ease of use with the ability to label cells in complete growth media, have increased photostability as compared to H2DCFDA, and are compatible with fixation (CellROX® Green and Deep Red). The CellROX® ROS detection reagents are bright and stable ROS sensors that offer significant advantages over existing ROS sensors because they are compatible with labeling in different media and can be used with fixatives. For Research Use Only. Not for use in diagnostic procedures.
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Oyarzún, María Paz, Andreas Tapia-Arellano, Pablo Cabrera, Pedro Jara-Guajardo, and Marcelo J. Kogan. "Plasmonic Nanoparticles as Optical Sensing Probes for the Detection of Alzheimer’s Disease." Sensors 21, no. 6 (March 16, 2021): 2067. http://dx.doi.org/10.3390/s21062067.
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Alzheimer’s disease (AD), considered a common type of dementia, is mainly characterized by a progressive loss of memory and cognitive functions. Although its cause is multifactorial, it has been associated with the accumulation of toxic aggregates of the amyloid-β peptide (Aβ) and neurofibrillary tangles (NFTs) of tau protein. At present, the development of highly sensitive, high cost-effective, and non-invasive diagnostic tools for AD remains a challenge. In the last decades, nanomaterials have emerged as an interesting and useful tool in nanomedicine for diagnostics and therapy. In particular, plasmonic nanoparticles are well-known to display unique optical properties derived from their localized surface plasmon resonance (LSPR), allowing their use as transducers in various sensing configurations and enhancing detection sensitivity. Herein, this review focuses on current advances in in vitro sensing techniques such as Surface-enhanced Raman scattering (SERS), Surface-enhanced fluorescence (SEF), colorimetric, and LSPR using plasmonic nanoparticles for improving the sensitivity in the detection of main biomarkers related to AD in body fluids. Additionally, we refer to the use of plasmonic nanoparticles for in vivo imaging studies in AD.
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Pandey, Shashank, Gaurav Malviya, and Magdalena Chottova Dvorakova. "Role of Peptides in Diagnostics." International Journal of Molecular Sciences 22, no. 16 (August 17, 2021): 8828. http://dx.doi.org/10.3390/ijms22168828.
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The specificity of a diagnostic assay depends upon the purity of the biomolecules used as a probe. To get specific and accurate information of a disease, the use of synthetic peptides in diagnostics have increased in the last few decades, because of their high purity profile and ability to get modified chemically. The discovered peptide probes are used either in imaging diagnostics or in non-imaging diagnostics. In non-imaging diagnostics, techniques such as Enzyme-Linked Immunosorbent Assay (ELISA), lateral flow devices (i.e., point-of-care testing), or microarray or LC-MS/MS are used for direct analysis of biofluids. Among all, peptide-based ELISA is considered to be the most preferred technology platform. Similarly, peptides can also be used as probes for imaging techniques, such as single-photon emission computed tomography (SPECT) and positron emission tomography (PET). The role of radiolabeled peptides, such as somatostatin receptors, interleukin 2 receptor, prostate specific membrane antigen, αβ3 integrin receptor, gastrin-releasing peptide, chemokine receptor 4, and urokinase-type plasminogen receptor, are well established tools for targeted molecular imaging ortumor receptor imaging. Low molecular weight peptides allow a rapid clearance from the blood and result in favorable target-to-non-target ratios. It also displays a good tissue penetration and non-immunogenicity. The only drawback of using peptides is their potential low metabolic stability. In this review article, we have discussed and evaluated the role of peptides in imaging and non-imaging diagnostics. The most popular non-imaging and imaging diagnostic platforms are discussed, categorized, and ranked, as per their scientific contribution on PUBMED. Moreover, the applicability of peptide-based diagnostics in deadly diseases, mainly COVID-19 and cancer, is also discussed in detail.
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Tang, Zhiwen, Parag Parekh, Pete Turner, Richard W. Moyer, and Weihong Tan. "Generating Aptamers for Recognition of Virus-Infected Cells." Clinical Chemistry 55, no. 4 (April 1, 2009): 813–22. http://dx.doi.org/10.1373/clinchem.2008.113514.
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Abstract Background: The development of molecular probes capable of recognizing virus-infected cells is essential to meet the serious clinical, therapeutic, and national-security challenges confronting virology today. We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. Methods: To create aptamer probes capable of recognizing virus-infected cells, we used cell-SELEX (systematic evolution of ligands via exponential enrichment), which uses intact infected live cells as targets for aptamer selection. In this study, vaccinia virus–infected and –uninfected lung cancer A549 cells were chosen to develop our model probes. Results: A panel of aptamers has been evolved by means of the infected cell–SELEX procedure. The results demonstrate that the aptamers bind selectively to vaccinia virus–infected A549 cells with apparent equilibrium dissociation constants in the nanomolar range. In addition, these aptamers can specifically recognize a variety of target infected cell lines. The aptamers’ target is most likely a viral protein located on the cell surface. Conclusions: The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell–SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells.
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Aghazadeh, Amirali, Adam Y. Lin, Mona A. Sheikh, Allen L. Chen, Lisa M. Atkins, Coreen L. Johnson, Joseph F. Petrosino, Rebekah A. Drezek, and Richard G. Baraniuk. "Universal microbial diagnostics using random DNA probes." Science Advances 2, no. 9 (September 2016): e1600025. http://dx.doi.org/10.1126/sciadv.1600025.
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Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal microbial diagnostics (UMD) platform to screen for microbial organisms in an infectious sample, using a small number of random DNA probes that are agnostic to the target DNA sequences. Our platform leverages the theory of sparse signal recovery (compressive sensing) to identify the composition of a microbial sample that potentially contains novel or mutant species. We validated the UMD platform in vitro using five random probes to recover 11 pathogenic bacteria. We further demonstrated in silico that UMD can be generalized to screen for common human pathogens in different taxonomy levels. UMD’s unorthodox sensing approach opens the door to more efficient and universal molecular diagnostics.
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Viti, Serena. "Astrochemistry in external galaxies: how to use molecules as probes of their physical conditions." Proceedings of the International Astronomical Union 11, S315 (August 2015): 17–25. http://dx.doi.org/10.1017/s1743921316007195.
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AbstractIt is now well established that chemistry in external galaxies is rich and complex. In this review I will explore whether one can use molecular emissions to determine their physical conditions. There are several considerations to bear in mind when using molecular emission, and in particular molecular ratios, to determine the densities, temperatures and energetics of a galaxy, which I will briefly summarise here. I will then present an example of a study that uses multiple chemical and radiative transfer analyses in order to tackle the too often neglected ‘degeneracies’ implicit in the interpretation of molecular ratios and show that only via such analyses combined with multi-species and multi-lines high spatial resolution data one can truly make molecules into powerful diagnostics of the evolution and distribution of molecular gas.
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G. Keller, Sascha, Mako Kamiya, and Yasuteru Urano. "Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes." Molecules 25, no. 24 (December 16, 2020): 5964. http://dx.doi.org/10.3390/molecules25245964.
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The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10′. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure–behavior relationship including novel computational approaches.
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Takes, Peter A. "Clinical Laboratory Reagents: The Regulatory Hurdle." Microscopy Today 7, no. 7 (September 1999): 8–9. http://dx.doi.org/10.1017/s1551929500064725.
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Today's clinical laboratory has a diversity of reagents and protocols from which to choose: a variety of clinical chemistry reagents, antibodies, and molecular probes, among others. These materials facilitate serum and urine analysis, histology, hematology, cytology, and a host of additional sensitive and specific assaysRegardless of the application, labs may see an array of labeling statements indicating a reagent's general use: "For Laboratory Use Only" [LUO]; "For Research Use Only" [RUO]; "For Investigational Use Only" [IUO]; "For In Vitro Diagnostic Use" [IVD]; and "Analyte Specific Reagent" [ASR]. These preparations are often employed without realizing the course manufacturer's must follow in order to provide reagents, and the reasons for these designations.
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Yoshimoto, Mitsuyoshi, Hiroaki Kurihara, and Hirofumi Fujii. "Theragnostic Imaging Using Radiolabeled Antibodies and Tyrosine Kinase Inhibitors." Scientific World Journal 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/842101.
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During the past decade, the efficacy of new molecular targeted drugs such as tyrosine kinase inhibitors (TKIs) and monoclonal antibodies has been proven worldwide, and molecular targeted therapies have become the mainstream in cancer therapy. However, clinical use of these new drugs presents unexpected adverse effects or poor therapeutic effects. Therefore, we require diagnostic tools to estimate the target molecule status in cancer tissues and predict therapeutic efficacy and adverse effects. Although immunohistochemical, polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) analyses of biopsy samples are conventional and popular for this diagnostic purpose, molecular imaging modalities such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) are also useful for noninvasive estimation of gene and protein expression and drug pharmacokinetics. In this review, we introduce new radiolabeled TKIs, antibodies, and their clinical application in molecular targeted therapy and discuss the issues of these imaging probes.
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Newby, Rachel, David Rowe, Lindsay Paterson, Maura A. Farquharson, Elaine MacDuff, Amanda Coupe, Juliet Hale, Petra Dildey, and Nick Bown. "Cryptic EWSR1-FLI1 fusions in Ewing sarcoma: potential pitfalls in the diagnostic use of fluorescence in situ hybridization probes." Cancer Genetics and Cytogenetics 200, no. 1 (July 2010): 60–64. http://dx.doi.org/10.1016/j.cancergencyto.2010.03.005.
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Bhadra, Sanchita, Miguel Saldaña, Hannah Han, Grant Hughes, and Andrew Ellington. "Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay." Viruses 10, no. 12 (December 14, 2018): 714. http://dx.doi.org/10.3390/v10120714.
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We have developed a generalizable “smart molecular diagnostic” capable of accurate point-of-care (POC) detection of variable nucleic acid targets. Our isothermal assay relies on multiplex execution of four loop-mediated isothermal amplification reactions, with primers that are degenerate and redundant, thereby increasing the breadth of targets while reducing the probability of amplification failure. An easy-to-read visual answer is computed directly by a multi-input Boolean OR logic gate (gate output is true if either one or more gate inputs is true) signal transducer that uses degenerate strand exchange probes to assess any combination of amplicons. We demonstrate our methodology by using the same assay to detect divergent Asian and African lineages of the evolving Zika virus (ZIKV), while maintaining selectivity against non-target viruses. Direct analysis of biological specimens proved possible, with crudely macerated ZIKV-infected Aedes aegypti mosquitoes being identified with 100% specificity and sensitivity. The ease-of-use with minimal instrumentation, broad programmability, and built-in fail-safe reliability make our smart molecular diagnostic attractive for POC use.
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Gottstein, B. "Molecular and immunological diagnosis of echinococcosis." Clinical Microbiology Reviews 5, no. 3 (July 1992): 248–61. http://dx.doi.org/10.1128/cmr.5.3.248.
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Echinococcosis is an infectious disease of humans caused by the larval (metacestode) stage of the cestode species Echinococcus granulosus (cystic echinococcosis or hydatid disease) or Echinococcus multilocularis (alveolar echinococcosis or alveolar hydatid disease). Clinical manifestations depend primarily on localization and size of hepatic lesions and may include hepatomegaly, obstructive jaundice, or cholangitis. Prognostically, alveolar echinococcosis is considered similar to liver malignancies, including a lethality rate of 90% for untreated cases. Diagnosis is based on imaging techniques coupled with immunodiagnostic procedures. Antibody detection tests for E. multilocularis have markedly improved with the use of affinity-purified Em2 antigen and recombinant antigen II/3-10 in enzyme immunoassays. Antigens of corresponding quality for E. granulosus are still unavailable. The detection of circulating antigens and immune complexes in the sera of patients with cystic echinococcosis, the demonstration of in vitro lymphocyte proliferation in response to stimulation with Echinococcus antigens, and the discrimination of serum immunoglobulin isotype activity to various Echinococcus antigens in both cystic and alveolar echinococcosis have been suggested for diagnostic purposes as well as for monitoring patients after treatment. New diagnostic molecular tools include DNA probes for Southern hybridization tests and polymerase chain reaction for the amplification of E. multilocularis and E. granulosus species-specific DNA fragments.
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Griffith, Christopher C., Alessandra C. Schmitt, James L. Little, and Kelly R. Magliocca. "New Developments in Salivary Gland Pathology: Clinically Useful Ancillary Testing and New Potentially Targetable Molecular Alterations." Archives of Pathology & Laboratory Medicine 141, no. 3 (March 1, 2017): 381–95. http://dx.doi.org/10.5858/arpa.2016-0259-sa.
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Accurate diagnosis of salivary gland tumors can be challenging because of the many diagnostic entities, the sometimes extensive morphologic overlap, and the rarity of most tumor types. Ancillary testing is beginning to ameliorate some of these challenges through access to newer immunohistochemical stains and fluorescence in situ hybridization probes, which can limit differential diagnostic considerations in some cases. These ancillary testing strategies are especially useful in small biopsy samples, including aspiration cytology. Molecular techniques are also expanding our understanding of salivary gland tumor pathology and are helping to identify potential targets that may improve treatment for some of these tumors. Here, we summarize the clinical use of new immunohistochemical markers in our practice and review the current understanding of chromosomal rearrangements in salivary gland tumor pathology, emphasizing the prospects for exploiting molecular alterations in salivary gland tumors for diagnosis and targeted therapy. We find that immunohistochemistry and fluorescence in situ hybridization are powerful tools toward the diagnosis of salivary gland tumors, especially when used in a systematic manner based on morphologic differential-diagnostic considerations. As new targeted therapies emerge, it will become increasingly vital to incorporate appropriate molecular testing into the pathologic evaluation of salivary gland cancers.
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Minaidou, Anna, Stella Tamana, Coralea Stephanou, Maria Xenophontos, Cornelis L. Harteveld, Celeste Bento, Marina Kleanthous, and Petros Kountouris. "A Novel Tool for the Analysis and Detection of Copy Number Variants Associated with Haemoglobinopathies." International Journal of Molecular Sciences 23, no. 24 (December 14, 2022): 15920. http://dx.doi.org/10.3390/ijms232415920.
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Several types of haemoglobinopathies are caused by copy number variants (CNVs). While diagnosis is often based on haematological and biochemical parameters, a definitive diagnosis requires molecular DNA analysis. In some cases, the molecular characterisation of large deletions/duplications is challenging and inconclusive and often requires the use of specific diagnostic procedures, such as multiplex ligation-dependent probe amplification (MLPA). Herein, we collected and comprehensively analysed all known CNVs associated with haemoglobinopathies. The dataset of 291 CNVs was retrieved from the IthaGenes database and was further manually annotated to specify genomic locations, breakpoints and MLPA probes relevant for each CNV. We developed IthaCNVs, a publicly available and easy-to-use online tool that can facilitate the diagnosis of rare and diagnostically challenging haemoglobinopathy cases attributed to CNVs. Importantly, it facilitates the filtering of available entries based on the type of breakpoint information, on specific chromosomal and locus positions, on MLPA probes, and on affected gene(s). IthaCNVs brings together manually curated information about CNV genomic locations, functional effects, and information that can facilitate CNV characterisation through MLPA. It can help laboratory staff and clinicians confirm suspected diagnosis of CNVs based on molecular DNA screening and analysis.
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Wiebe, Leonard I. "Applications of nucleoside-based molecular probes for the in vivo assessment of tumour biochemistry using positron emission tomography (PET)." Brazilian Archives of Biology and Technology 50, no. 3 (May 2007): 445–59. http://dx.doi.org/10.1590/s1516-89132007000300011.
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Positron emission tomography (PET) is a non-invasive nuclear imaging technique. In PET, radiolabelled molecules decay by positron emission. The gamma rays resulting from positron annihilation are detected in coincidence and mapped to produce three dimensional images of radiotracer distribution in the body. Molecular imaging with PET refers to the use of positron-emitting biomolecules that are highly specific substrates for target enzymes, transport proteins or receptor proteins. Molecular imaging with PET produces spatial and temporal maps of the target-related processes. Molecular imaging is an important analytical tool in diagnostic medical imaging, therapy monitoring and the development of new drugs. Molecular imaging has its roots in molecular biology. Originally, molecular biology meant the biology of gene expression, but now molecular biology broadly encompasses the macromolecular biology and biochemistry of proteins, complex carbohydrates and nucleic acids. To date, molecular imaging has focused primarily on proteins, with emphasis on monoclonal antibodies and their derivative forms, small-molecule enzyme substrates and components of cell membranes, including transporters and transmembrane signalling elements. This overview provides an introduction to nucleosides, nucleotides and nucleic acids in the context of molecular imaging.
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Ambur Sankaranarayanan, Ramya, Susanne Kossatz, Wolfgang Weber, Mohsen Beheshti, Agnieszka Morgenroth, and Felix M. Mottaghy. "Advancements in PARP1 Targeted Nuclear Imaging and Theranostic Probes." Journal of Clinical Medicine 9, no. 7 (July 6, 2020): 2130. http://dx.doi.org/10.3390/jcm9072130.
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The central paradigm of novel therapeutic approaches in cancer therapy is identifying and targeting molecular biomarkers. One such target is the nuclear DNA repair enzyme Poly-(ADP ribose) polymerase 1 (PARP1). Sensitivity to PARP inhibition in certain cancers such as gBRCAmut breast and ovarian cancers has led to its exploitation as a target. The overexpression of PARP1 in several types of cancer further evoked interest in its use as an imaging target. While PARP1-targeted inhibitors have fast developed and approved in this past decade, determination of PARP1 expression might help to predict the response to PARP inhibitor treatment. This has the potential of improving prognosis and moving towards tailored therapy options and/or dosages. This review summarizes the recent pre-clinical advancements in imaging and theranostic PARP1 targeted tracers. To assess PARP1 levels, several imaging probes with fluorescent or beta/gamma emitting radionuclides have been proposed and three have advanced to ongoing clinical evaluation. Apart from its diagnostic value in detection of primary tumors as well as metastases, this shall also help in delivering therapeutic radionuclides to PARP1 overexpressing tumors. Henceforth nuclear medicine has now advanced towards conjugating theranostic radionuclides to PARP1 inhibitors. This paves the way for a future of PARP1-targeted theranostics and personalized therapy.
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Bie, Bi-Jie, Xiao-Rui Zhao, Jia-Rui Yan, Xi-Jun Ke, Fan Liu, and Guo-Ping Yan. "Dextran Fluorescent Probes Containing Sulfadiazine and Rhodamine B Groups." Molecules 27, no. 19 (October 10, 2022): 6747. http://dx.doi.org/10.3390/molecules27196747.
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Fluorescent imaging has been expanded, as a non-invasive diagnostic modality for cancers, in recent years. Fluorescent probes in the near-infrared window can provide high sensitivity, resolution, and signal-to-noise ratio, without the use of ionizing radiation. Some fluorescent compounds with low molecular weight, such as rhodamine B (RhB) and indocyanine green (ICG), have been used in fluorescent imaging to improve imaging contrast and sensitivity; however, since these probes are excreted from the body quickly, they possess significant restrictions for imaging. To find a potential solution to this, this work investigated the synthesis and properties of novel macromolecular fluorescent compounds. Herein, water-soluble dextran fluorescent compounds (SD-Dextran-RhB) were prepared by the attachment of RhB and sulfadiazine (SD) derivatives to dextran carrier. These fluorescent compounds were then characterized through IR, 1H NMR, 13C NMR, UV, GPC, and other methods. Assays of their cellular uptake and cell cytotoxicity and fluorescent imaging were also performed. Through this study, it was found that SD-Dextran-RhB is sensitive to acidic conditions and possesses low cell cytotoxicities compared to normal 293 cells and HepG2 and HeLa tumor cells. Moreover, SD-Dextran-RhB demonstrated good fluorescent imaging in HepG2 and HeLa cells. Therefore, SD-Dextran-RhB is suitable to be potentially applied as a probe in the fluorescent imaging of tumors.
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Donahue, Amber C., Adam Abdool, Jay G. Wohlgemuth, and Chen-Hsiung Yeh. "Molecular Characterization of Chromosomal Abnormalities In Myelodysplastic Syndrome and Acute Myeloid Leukemia: Validation of An MLPA Protocol and Analysis Method for Use In a Diagnostic Setting." Blood 116, no. 21 (November 19, 2010): 4849. http://dx.doi.org/10.1182/blood.v116.21.4849.4849.
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Abstract Abstract 4849 Introduction: Current diagnostic screening strategies for copy number variations (CNVs) in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) include fluorescence in situ hybridization (FISH) or karyotyping, both of which are time-consuming, costly, laborious, and lacking in resolution. Multiplex ligation-dependent probe amplification (MLPA) can be used to detect copy number changes in multiple loci simultaneously in a single PCR reaction, and boasts a resolution down to single exons. To adapt MLPA for use in routine clinical diagnostics, we have developed and validated a protocol for automatic data analysis and interpretation of common chromosomal abnormalities in MDS/AML. Patients and Methods: The study used a training set of 45 healthy subjects to establish a normal reference range for each individual probe. Using these ranges we built an automated Excel spreadsheet-based analysis system, which included multiple quality checks, and flagged samples failing these quality controls. Each probe was given a call of “no mutation detected,” “deletion,” or “gain,” based on whether the normalized ratio fell within or outside of the empirically-determined normal range for that probe. We then analyzed over 100 leukemia cases tested by FISH, including both suspected myeloid leukemia samples and suspected chronic lymphocytic leukemia (CLL) samples. Documented chromosomal abnormalities in CLL include 11q-, 17p- (loss of TP53), and trisomy 12, all of which had the potential to be detected by the probes in the MDS MLPA probemix. The greater prevalence of CLL and its associated CNVs provided additional positive controls for the validation of the MDS MLPA probemix and our analysis method. Results: The empirically-determined normal ranges demonstrated that some probes varied widely (3 standard deviation [3SD] normal range of 0.46–1.54), while others were extremely reliable (3SD normal range of 0.84–1.16). The MLPA assay demonstrated excellent overall accuracy (>90%) and specificity (>93%) for both suspected myeloid and CLL samples when compared to FISH. The sensitivity of the MLPA assay is somewhat lower than that of FISH, requiring a probe-dependent 20–40% positivity for a given CNV to be detected. However in several cases, the MDS MLPA assay was able to detect additional lesions too small to be seen by FISH. Conclusions: For MLPA, the total process-to-report time, including data analysis, is 2–3 days, versus the 7–10 days required for FISH analysis. In addition, the MLPA assay is substantially cheaper and considerably less labor-intensive than FISH. Our improved MLPA assay protocol and analysis method provides a clinically robust, multiplexed, high-throughput, high-resolution, and low-cost solution for detection of copy number changes in MDS/AML, and can therefore be used as a first-line screening test in a clinical laboratory. Disclosures: Donahue: Quest Diagnostics Inc.: Employment. Abdool: Quest Diagnostics Inc.: Employment. Wohlgemuth: Quest Diagnostics Inc.: Employment. Yeh: Quest Diagnostics Inc.: Employment.
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Nadasdy, T., C. S. Park, S. C. Peiper, J. E. Wenzl, J. Oates, and F. G. Silva. "Epstein-Barr virus infection-associated renal disease: diagnostic use of molecular hybridization technology in patients with negative serology." Journal of the American Society of Nephrology 2, no. 12 (June 1992): 1734–42. http://dx.doi.org/10.1681/asn.v2121734.
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There are only a few reports of renal disease associated with Epstein-Barr virus (EBV) infection. The diagnosis of EBV infection in these previously reported patients was based primarily on positive serology. Two patients with renal disease who, despite repeatedly negative serologies, were shown by molecular hybridization techniques--in situ hybridization (ISH) and polymerase chain reaction (PCR)--to have EBV infection are reported here. Site-specific molecular probes directed against specific, tandemly repeated EBV genomic regions were used. A synthetic 23-mer terminally biotin-labeled oligonucleotide probe selected from the EBV NotI region was used for ISH. For PCR, oligonucleotide primers were designed from sequences of the highly conserved, long internal direct repeat region of EBV to specifically amplify a 110-base-pair segment. The first patient, a 3-yr-old girl with a 1-yr history of fatigue, fever, splenomegaly, and lymphadenopathy developed hematuria. A renal biopsy revealed widespread glomerular mesangiolysis admixed with segmental mesangial sclerosis; no immune deposits were noted by electron microscopy or immunofluorescence. ISH on paraffin sections of the resected spleen and lymph nodes was positive for EBV. The second patient, a 28-yr-old male renal allograft recipient, received a double dose of OKT3. Seven weeks after transplantation, a renal biopsy revealed a lymphoproliferative disorder. Paraffin sections of the nephrectomy specimen were positive for EBV by both ISH and PCR. It was concluded that (1) EBV cannot be excluded on the basis of multiple negative serologies in some patients, and (2) ISH and PCR may lead to the detection of viral genomic information in renal and nonrenal tissues.
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Shan, Ming, Lei Zhang, Yang Liu, Chunyang Gao, Wenli Kang, Weiwei Yang, Yan He, and Guoqiang Zhang. "DNA Methylation Profiles and Their Diagnostic Utility in BC." Disease Markers 2019 (May 6, 2019): 1–10. http://dx.doi.org/10.1155/2019/6328503.
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Biomarkers, including DNA methylation, have shown a great potential for use in personalized medicine for BC and especially for the diagnosis of BC in developing countries. According to the bisulfite sequencing PCR in twelve specimens (BC and matched normal tissues), nine genetic probes were designed to detect the frequency of methylation of the promoters in a total of 302 paired cases of BC and matched normal breast tissues. Finally, a total of 900 serum samples were used to validate the use of these methylation biomarkers for clinical diagnosis of BC. A high frequency of promoter methylation of SFN, HOXA11, P16, RARβ, PCDHGB7, hMLH1, WNT5a, HOXD13, and RASSF1a was observed in BC tissues. The methylation frequencies of HOXD13 and hMLH1 increased with the progression of BC. The methylation frequencies of HOXD13 and WNT5a were significantly higher in BC. We found that methylation modification-positive samples were most consistently associated with luminal BC. Finally, we confirmed that RASSF1a, P16, and PCDHGB7 displayed a significant sensitivity and specificity as diagnostic biomarkers for BC (P<0.001), and a panel that combined these three genes displayed increased significance (AUC, 0.781; P<0.001). These data suggest that epigenetic markers in serum can potentially be used to diagnose BC. The identification of additional BC-specific methylated genes would improve the sensitivity and specificity of this approach. This study could also indicate that different molecular subtypes of BC are caused by distinct genetic and epigenetic mechanisms.
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Ramsower, Colleen, Tameson Yip, Betty Glinsmann-Gibson, Ryan Robetorye, and Lisa Rimsza. "Clinical Validation of the Lymph3Cx Assay to Distinguish Primary Mediastinal Large B-Cell Lymphoma From Diffuse Large B-Cell Lymphoma." American Journal of Clinical Pathology 152, Supplement_1 (September 11, 2019): S136. http://dx.doi.org/10.1093/ajcp/aqz126.006.
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Abstract Introduction Primary mediastinal large B-cell lymphoma (PMLBCL) is recognized as a distinct lymphoid neoplasm. However, differentiation from diffuse large B-cell lymphoma (DLBCL) can be difficult due to the need for close clinicopathologic correlation and variability in morphology and immunophenotype. In addition, a recent study identified lymphomas that share molecular and morphological features with PMBCL, yet do not involve the mediastinum. Correct classification of PMBCL may impact therapeutic decision making, increasing the demand for more accurate diagnostic methods. Recent research identified a new gene expression signature that robustly differentiated PMLBCL from DLBCL in both training and independent validation cohorts using RNA isolated from routinely available formalin-fixed, paraffin-embedded (FFPE) tissues. Methods This assay, known as the “Lymph3Cx,” utilizes the nCounter platform (NanoString Technologies, Seattle, WA) and consists of probes for 58 target genes (including both discriminatory and housekeeping genes) that can distinguish PMLBCL cases from DLBCL as well as the “cell-of-origin” subtypes of DLBCL. In the current study reported here, the Molecular Diagnostics–Arizona Laboratory (MDAZL) performed a full validation of the Lymph3Cx assay for use in our clinical diagnostic laboratory. Results Assay performance included accuracy (92.9%), precision (100%), analytical sensitivity (100 ng RNA limit of detection), analytical specificity (measures are in place to prevent interfering substances), reproducibility between technologists and technical replicates (100%), specimen stability (18 months for unstained tissue sections), and RNA Isolation Kit Utility (two kits with equal performance) in order to become the first CLIA-certified, CAP-accredited clinical diagnostics laboratory to offer a molecular assay for distinction of PMLBCL from DLBCL. Conclusion The Lymph3Cx assay will be prospectively used for evaluation of Mayo Clinic patients and for use as an integrated biomarker in clinical trials.
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Le Fur, Mariane, Iris Y. Zhou, Onofrio Catalano, and Peter Caravan. "Toward Molecular Imaging of Intestinal Pathology." Inflammatory Bowel Diseases 26, no. 10 (August 14, 2020): 1470–84. http://dx.doi.org/10.1093/ibd/izaa213.
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Abstract Inflammatory bowel disease (IBD) is defined by a chronic relapsing and remitting inflammation of the gastrointestinal tract, with intestinal fibrosis being a major complication. The etiology of IBD remains unknown, but it is thought to arise from a dysregulated and excessive immune response to gut luminal microbes triggered by genetic and environmental factors. To date, IBD has no cure, and treatments are currently directed at relieving symptoms and treating inflammation. The current diagnostic of IBD relies on endoscopy, which is invasive and does not provide information on the presence of extraluminal complications and molecular aspect of the disease. Cross-sectional imaging modalities such as computed tomography enterography (CTE), magnetic resonance enterography (MRE), positron emission tomography (PET), single photon emission computed tomography (SPECT), and hybrid modalities have demonstrated high accuracy for the diagnosis of IBD and can provide both functional and morphological information when combined with the use of molecular imaging probes. This review presents the state-of-the-art imaging techniques and molecular imaging approaches in the field of IBD and points out future directions that could help improve our understanding of IBD pathological processes, along with the development of efficient treatments.
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Kwon, Junyoung, Chandan Narayan, Chonsaeng Kim, Min Jung Han, Meehyein Kim, and Sung Key Jang. "Development of a Subtype-Specific Diagnostic System for Influenza Virus H3N2 Using a Novel Virus-Based Systematic Evolution of Ligands by Exponential Enrichment (Viro-SELEX)." Journal of Biomedical Nanotechnology 15, no. 7 (July 1, 2019): 1609–21. http://dx.doi.org/10.1166/jbn.2019.2789.
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Aptamers are oligonucleotide molecules that bind to specific target molecules generated by systematic evolution of ligands by exponential enrichment (SELEX). Aptamers have high future potential for use in diagnostics and therapeutics as molecular probes that recognize target molecules. To develop aptamers against a target protein using a SELEX process, it is necessary to purify the target protein. Purifying a membrane protein, however, is usually a challenging task. Here, we report a novel approach to developing aptamers against membrane proteins. Surrogate viruses containing target proteins on the surface of an enveloped virus (e.g., baculovirus), instead of purified proteins, were used in a new SELEX process. We designated this new SELEX process as "surrogate virus-based SELEX (viro-SELEX)." Using viro-SELEX, we developed a pair of aptamers that specifically interact with the hemagglutinin protein of influenza subtype H3N2. Using the aptamer pair and a lateral flow assay system, we developed a very sensitive point-of-care diagnostic system for specifically detecting influenza virus subtype H3N2.
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Novis, David A., Richard J. Zarbo, and Paul A. Valenstein. "Diagnostic Uncertainty Expressed in Prostate Needle Biopsies." Archives of Pathology & Laboratory Medicine 123, no. 8 (August 1, 1999): 687–92. http://dx.doi.org/10.5858/1999-123-0687-dueipn.
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Abstract Objective.—To determine the rate of diagnostic uncertainty in rendering diagnoses on prostate needle biopsies and to examine pathology practice variables that influence that rate. Design.—Anatomic pathology departments participating in the College of American Pathologists Q-Probes laboratory quality improvement program retrospectively reviewed their last 50 consecutive prostate needle biopsy diagnoses. For each diagnosis, participants provided information concerning patients' prostate-specific antigen levels; number, locations, and laterality of biopsy specimens; number of tissue levels examined; performance of high-molecular-weight cytokeratin immunoperoxidase staining; and acquisition of consultations from general pathologists or experts in prostate pathology. Characteristics of pathology practices included yearly surgical and prostate needle biopsy caseloads, number of pathologists rendering biopsy diagnoses, use of standard descriptive checklists, access to patients' prostate-specific antigen and digital rectal examination results, percentages of prostate needle biopsies routinely submitted for internal consultations, and presence of departmental experts in prostate pathology. Setting and Participants.—Three hundred thirty-two public and private institutions located in the United States (n = 318), Canada (n = 6), Australia (n = 5), United Kingdom (n = 2), and Guam (n = 1). Main Outcome Measure.—The rate of diagnostic uncertainty in prostate needle biopsy diagnoses. Results.—Participants submitted diagnoses on a total of 15 753 prostate needle biopsy cases, of which 33.4% were adenocarcinoma; 55.5% were benign; 3.9% were carcinoma in situ, prostatic intraepithelial neoplasia, or both; and 7.1% were diagnostically uncertain. The median rate of diagnostic uncertainty was 6%, ranging from 0 at the 10th percentile to 14% at the 90th percentile of all participating laboratories. Performing high-molecular-weight cytokeratin immunoperoxidase staining resolved diagnostic uncertainty in 68% of cases in which it was performed, and obtaining intradepartmental and extradepartmental consultations resolved diagnostic uncertainty in 70% to 87% of cases for which they were obtained. Knowledge of patients' prostate-specific antigen results and examining multiple biopsy cores had marginal effects on the rate of uncertainty. Thoroughness of prostate gland sampling and examination of multiple tissue block levels were not associated with the aggregate rate of diagnostic uncertainty. We found no particular pathology departmental practices or institutional demographic characteristics associated with institutional rates of diagnostic uncertainty. Conclusions.—Use of high-molecular-weight cytokeratin immunoperoxidase staining and obtaining intradepartmental and extradepartmental consultations may be effective in reducing diagnostic uncertainty in prostate biopsies.
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Bilodeau, Guillaume J., Frank N. Martin, Michael D. Coffey, and Cheryl L. Blomquist. "Development of a Multiplex Assay for Genus- and Species-Specific Detection of Phytophthora Based on Differences in Mitochondrial Gene Order." Phytopathology® 104, no. 7 (July 2014): 733–48. http://dx.doi.org/10.1094/phyto-09-13-0263-r.
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A molecular diagnostic assay for Phytophthora spp. that is specific, sensitive, has both genus- and species-specific detection capabilities multiplexed, and can be used to systematically develop markers for detection of a wide range of species would facilitate research and regulatory efforts. To address this need, a marker system was developed based on the high copy sequences of the mitochondrial DNA utilizing gene orders that were highly conserved in the genus Phytophthora but different in the related genus Pythium and plants to reduce the importance of highly controlled annealing temperatures for specificity. An amplification primer pair designed from conserved regions of the atp9 and nad9 genes produced an amplicon of ≈340 bp specific for the Phytophthora spp. tested. The TaqMan probe for the genus-specific Phytophthora test was designed from a conserved portion of the atp9 gene whereas variable intergenic spacer sequences were used for designing the species-specific TaqMan probes. Specific probes were developed for 13 species and the P. citricola species complex. In silico analysis suggests that species-specific probes could be developed for at least 70 additional described and provisional species; the use of locked nucleic acids in TaqMan probes should expand this list. A second locus spanning three tRNAs (trnM-trnP-trnM) was also evaluated for genus-specific detection capabilities. At 206 bp, it was not as useful for systematic development of a broad range of species-specific probes as the larger 340-bp amplicon. All markers were validated against a test panel that included 87 Phytophthora spp., 14 provisional Phytophthora spp., 29 Pythium spp., 1 Phytopythium sp., and 39 plant species. Species-specific probes were validated further against a range of geographically diverse isolates to ensure uniformity of detection at an intraspecific level, as well as with other species having high levels of sequence similarity to ensure specificity. Both diagnostic assays were also validated against 130 environmental samples from a range of hosts. The only limitation observed was that primers for the 340 bp atp9-nad9 locus did not amplify Phytophthora bisheria or P. frigida. The identification of species present in a sample can be determined without the need for culturing by sequencing the genus-specific amplicon and comparing that with a reference sequence database of known Phytophthora spp.
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Porschewski, Peter, Mira A. M. Grättinger, Kerstin Klenzke, Anja Erpenbach, Michael R. Blind, and Frank Schäfer. "Using Aptamers as Capture Reagents in Bead-Based Assay Systems for Diagnostics and Hit Identification." Journal of Biomolecular Screening 11, no. 7 (September 14, 2006): 773–81. http://dx.doi.org/10.1177/1087057106292138.
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Most applications of xMAP™ (Luminex®) bead-based assay technology in diagnostics and drug discovery use immobilized antigens or antibodies. Here the authors describe the development of novel assay systems in which synthetic oligonucleotides that specifically bind and inhibit other biomolecules—so-called aptamers—are directly immobilized on beads. The robustness, specificity, and sensitivity of aptamer-based assays were demonstrated in a test system that detected human α-thrombin in serum samples. xMAP technology was also adapted to competitive screening formats where an aptamer/protein complex was disrupted by a functionally analogous competitor. The results indicate that such assays are excellently suited for diagnostic applications or drug screening, where aptamers serve as competitive binding probes for the identification of small-molecule hits. These methods should be transferable to a large number of applications because specific aptamers can be rapidly generated for almost any protein target.
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Muir, Ryan K., Matteo Guerra, and Matthew M. Bogyo. "Activity-Based Diagnostics: Recent Advances in the Development of Probes for Use with Diverse Detection Modalities." ACS Chemical Biology 17, no. 2 (January 13, 2022): 281–91. http://dx.doi.org/10.1021/acschembio.1c00753.
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Johnston, C. T. "Probing the nanoscale architecture of clay minerals." Clay Minerals 45, no. 3 (September 2010): 245–79. http://dx.doi.org/10.1180/claymin.2010.045.3.245.
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AbstractIn recent years, experimental and theoretical methods have provided new insights into the size, shape, reactivity, and stability of clay minerals. Although diverse and complex, the surface chemistry of all clay minerals is defined spatially on a common scale of nanometres. This review is organized around the nanoscale architecture of clay minerals examined at several different length scales. The first, and perhaps most important, is the length scale associated with Hbonding in clay minerals. Hbonding interactions define the size and shape of 1:1 phyllosilicates and dominate the surface chemistry of many clay minerals. Structural and surface OHgroups contained within and on the surface of clay minerals provide a type of ‘molecular reporter group’ and are sensitive to subtle changes in their local environment. Examples of OH-reporter group studies in clay minerals, and the spatial scales at which they provide diagnostic information, are examined. The second length scale considered here is that associated with clay–water and clay–organic interactions. Inorganic and organic solutes can be used to explore the surface chemistry of clay minerals. Similar to the use of reporter groups, molecular probes have diagnostic properties that are sensitive to changes in their molecular environment. Clay–water interactions occur at a length scale that extends from the size of the H2O molecule (~0.3 nm) to the larger scales associated with clay-swelling (>10 nm). Similarly, clay–organic interactions are also defined, in part, on the basis of their molecular size, in addition to the type of chemical bonding interactions that take place between the organic solute and the clay surface. Examples illustrating the use of clay–water and clay–organic solute interactions as molecular probes are presented. The largest scale to be considered is that of the particles themselves, with scales that approach micrometres. Recent developments in the synthesis and characterization of ultrathin hybrid films of clay minerals provide complementary information about the nature and distribution of active sites on clay minerals, as well as providing new opportunities to exploit the surface chemistry of clay minerals in the design of functional materials.
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Zvara, Ágnes, György Szekeres, Zoltán Janka, János Z. Kelemen, Csongor Cimmer, Miklós Sántha, and László G. Puskás. "Over-Expression of Dopamine D2Receptor and Inwardly Rectifying Potassium Channel Genes in Drug-Naive Schizophrenic Peripheral Blood Lymphocytes as Potential Diagnostic Markers." Disease Markers 21, no. 2 (2005): 61–69. http://dx.doi.org/10.1155/2005/275318.
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Schizophrenia is one of the most common neuropsychiatric disorders affecting nearly 1% of the human population. Current diagnosis of schizophrenia is based on complex clinical symptoms. The use of easily detectable peripheral molecular markers could substantially help the diagnosis of psychiatric disorders. Recent studies showed that peripheral blood lymphocytes (PBL) express subtypes of D1 and D2 subclasses of dopamine receptors. Recently, dopamine receptor D3(DRD3) was found to be over-expressed in schizophrenic PBL and proposed to be a diagnostic and follow-up marker for schizophrenia. In this study we screened PBL of 13 drug-naive/drug-free schizophrenic patients to identify additional markers of schizophrenia. One of the benefits of our study is the use of blood samples of non-medicated, drug-naive patients. This excludes the possibility that changes detected in gene expression levels might be attributed to the medication rather than to the disorder itself. Among others, genes for dopamine receptor D2(DRD2) and the inwardly rectifying potassium channel (Kir2.3) were found to be over-expressed in microarray analysis. Increased mRNA levels were confirmed by quantitative real-time PCR (QRT-PCR) using the SybrGreen method and dual labeled TaqMan probes. The use of both molecular markers allows a more rapid and precise prediction of schizophrenia and might help find the optimal medication for schizophrenic patients.
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Frickmann, Hagen, Wycliffe Omurwa Masanta, and Andreas E. Zautner. "Emerging Rapid Resistance Testing Methods for Clinical Microbiology Laboratories and Their Potential Impact on Patient Management." BioMed Research International 2014 (2014): 1–19. http://dx.doi.org/10.1155/2014/375681.
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Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescencein situhybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory.
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Boschi, Alessandra, Licia Uccelli, and Petra Martini. "A Picture of Modern Tc-99m Radiopharmaceuticals: Production, Chemistry, and Applications in Molecular Imaging." Applied Sciences 9, no. 12 (June 21, 2019): 2526. http://dx.doi.org/10.3390/app9122526.
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Even today, techentium-99m represents the radionuclide of choice for diagnostic radio-imaging applications. Its peculiar physical and chemical properties make it particularly suitable for medical imaging. By the use of molecular probes and perfusion radiotracers, it provides rapid and non-invasive evaluation of the function, physiology, and/or pathology of organs. The versatile chemistry of technetium-99m, due to its multi-oxidation states, and, consequently, the ability to produce a variety of complexes with particular desired characteristics, are the major advantages of this medical radionuclide. The advances in technetium coordination chemistry over the last 20 years, in combination with recent advances in detector technologies and reconstruction algorithms, make SPECT’s spatial resolution comparable to that of PET, allowing 99mTc radiopharmaceuticals to have an important role in nuclear medicine and to be particularly suitable for molecular imaging. In this review the most efficient chemical methods, based on the modern concept of the 99mTc-metal fragment approach, applied to the development of technetium-99m radiopharmaceuticals for molecular imaging, are described. A specific paragraph is dedicated to the development of new 99mTc-based radiopharmaceuticals for prostate cancer.
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Karadimas, Dimitrios, and George Tsekenis. "LATE-PCR for LoC Molecular Diagnostics Devices and Its Application to the Sensitive Detection of SARS-CoV-2." Engineering Proceedings 6, no. 1 (May 17, 2021): 43. http://dx.doi.org/10.3390/i3s2021dresden-10076.
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The emergence of the novel coronavirus, SARS-CoV-2, has highlighted the need for rapid, accurate, and point-of-care diagnostic testing. Lab-on-a-Chip (LoC) devices offer the possibility to run such tests at a low cost, while at the same time permitting the multiplexed detection of several viruses when coupled with microarray detection of the amplified products. Herein, we report the development of a protocol for the qualitative detection of SARS-CoV-2, through the design of appropriate primers that target the evolutionary conserved regions of the virus. The proposed protocol relies on an improved version of asymmetric RT-PCR, the linear-after-the-exponential (LATE)-PCR that uses primers that are deliberately designed for use at unequal concentrations. As a result, LATE-PCR exhibits similar efficiency to symmetric PCR, while promoting accumulation of single-stranded products that can subsequently hybridize to a single-strand DNA probe-spotted microarray. The performance of the developed LATE-PCR protocol was compared to that of symmetric RT-PCR, and validated with the use of artificial viral RNA and nasopharyngeal swab samples from real patients. Furthermore, and in order to illustrate its potential for integration into a biosensor platform, the amplicons were allowed to hybridize with probes that were covalently immobilized onto commercially available functionalized glass, without the need for heat denaturation.
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Karjalainen, Reijo, Leo Rouhiainen, and Hans Söderlund. "Diagnosis of plant viruses by nucleic acid hybridization." Agricultural and Food Science 59, no. 3 (July 1, 1987): 179–91. http://dx.doi.org/10.23986/afsci.72262.
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Nucleic acid hybridization is a powerful technique for the diagnosis of many plant viruses not easily detected by serological techniques. It is particularly effective in the detection of viruses occurring in low amount in plant tissue, viruses that are poor immunogens or contain satellites. Molecular probes with desired specificities can be prepared by recombinant DNA techniques for large scale use. cDNA probes of potato virus X(PVX) RNA were made by molecular cloning, and the clones were 32P labelled by nick translation. Hybridization of cDNA to PVX RNA revealed 1 ng of purified virus in 2 µl spots dried onto nitrocellulose filter. Infected samples of crude leaf extracts were easily detected by hybridization, while probes did not react with healthy leaf samples. Nucleic acid hybridization research aims at replacing radiometric probes with nonradioactive methods involving enzymes which are directly or indirectly coupled to the probe and whose presence is observed with the aid of a colour changing substrate. Hybridization assay formats that can easily be automatized are under development. Sandwich hybridization is a simple test format developed for analyzing unpurified biological material, and it appears to be a powerful tool for microbial diagnostics. Sensitivity can be improved by using detection systems in which the specific activity of the probe is increased. Procedures such as ’polymerase chain reaction’, in which the amount of detectable nucleic acid sequences can be increased, are promising alternatives for increasing sensitivity. It is concluded that even if probe-based assays are in their infancy, they will no doubt develop towards such easy use as have immunological test kits.
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Maglaras, Panagiotis, Ioannis Lilis, Fotini Paliogianni, Vasiliki Bravou, and Despina P. Kalogianni. "A Molecular Lateral Flow Assay for SARS-CoV-2 Quantitative Detection." Biosensors 12, no. 11 (October 26, 2022): 926. http://dx.doi.org/10.3390/bios12110926.
Full textAbstract:
Since the onset of the SARS-CoV-2 pandemic, several COVID-19 detection methods, both commercially available and in the lab, have been developed using different biomolecules as analytes and different detection and sampling methods with high analytical performance. Developing novel COVID-19 detection assays is an exciting research field, as rapid accurate diagnosis is a valuable tool to control the current pandemic, and also because the acquired knowledge can be deployed for facing future infectious outbreaks. We here developed a novel gold-nanoparticle-based nucleic acid lateral flow assay for the rapid, visual, and quantitative detection of SARS-CoV-2. Our method was based on the use of a DNA internal standard (competitor) for quantification and involved RT-PCR, the hybridization of biotinylated PCR products to specific oligonucleotide probes, and detection with a dual lateral flow assay using gold nanoparticles conjugated to an anti-biotin antibody as reporters. The developed test allowed for rapid detection by the naked eye and the simultaneous quantification of SARS-CoV-2 in nasopharyngeal swabs with high specificity, detectability, and repeatability. This novel molecular strip test for COVID-19 detection represents a simple, cost-effective, and accurate rapid test that is very promising to be used as a future diagnostic tool.
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Pham, H. Ph, A. V. Sidorov, A. V. Milovanova, T. P. Antonova, A. N. Lisakov, F. G. Nagieva, G. I. Alatortceva, et al. "New Approach for Diagnostics of VZV Infection by Using Real-Time PCR." Epidemiology and Vaccine Prevention 15, no. 5 (October 20, 2016): 52–58. http://dx.doi.org/10.31631/2073-3046-2016-15-5-52-58.
Full textAbstract:
Clinical picture of diseases caused by VZV in immunocompromised patients is often differed from healthy people and has no visible skin damage. Diagnostics in such cases is difficult but it is important to find out real reason of health deterioration for assignment the treatment. That explains usefulness of molecular methods in diagnostics of VZV-infection. So the goal of this study was checking out usefulness of diagnostics based on detection viral DNA in clinical samples by real-time PCR method. We used pools of peripheral blood samples from sick and healthy patients as clinical materials for analysis and Varilrix vaccine sample as a source of positive control viral DNA. Main methods used here were DNA extraction and real-time PCR in the version of TaqMan probes; amplification reactions were made in triplicates for each sample with standard deviation of threshold cycles less than 1.5%. Amplification results of clinical samples from patients were analyzed by comparison with the results from positive control viral DNA. Final resulting figures were slightly varied and dependent on selected for amplification VZV genome fragment (orf 29 or orf 38), and viral DNA had been detected in 48% of sick patients and only in 4% of practically healthy donors without zoster symptoms. Concluding, we approved the possibility of use real-time PCR as a molecular method for laboratory diagnostics VZV-infection including atypical and subclinical disease forms. One of the advantage of the method described is the possibility of DNA detection straight from blood samples (without extra purification steps such as preparation mononuclear cell fraction from blood samples), therefore this approach can accelerate and simplify diagnostic procedure.
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Ramachandran, Ashwin, Diego A. Huyke, Eesha Sharma, Malaya K. Sahoo, ChunHong Huang, Niaz Banaei, Benjamin A. Pinsky, and Juan G. Santiago. "Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2." Proceedings of the National Academy of Sciences 117, no. 47 (November 4, 2020): 29518–25. http://dx.doi.org/10.1073/pnas.2010254117.
Full textAbstract:
The rapid spread of COVID-19 across the world has revealed major gaps in our ability to respond to new virulent pathogens. Rapid, accurate, and easily configurable molecular diagnostic tests are imperative to prevent global spread of new diseases. CRISPR-based diagnostic approaches are proving to be useful as field-deployable solutions. In one basic form of this assay, the CRISPR–Cas12 enzyme complexes with a synthetic guide RNA (gRNA). This complex becomes activated only when it specifically binds to target DNA and cleaves it. The activated complex thereafter nonspecifically cleaves single-stranded DNA reporter probes labeled with a fluorophore−quencher pair. We discovered that electric field gradients can be used to control and accelerate this CRISPR assay by cofocusing Cas12–gRNA, reporters, and target within a microfluidic chip. We achieve an appropriate electric field gradient using a selective ionic focusing technique known as isotachophoresis (ITP) implemented on a microfluidic chip. Unlike previous CRISPR diagnostic assays, we also use ITP for automated purification of target RNA from raw nasopharyngeal swab samples. We here combine this ITP purification with loop-mediated isothermal amplification and the ITP-enhanced CRISPR assay to achieve detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA (from raw sample to result) in about 35 min for both contrived and clinical nasopharyngeal swab samples. This electric field control enables an alternate modality for a suite of microfluidic CRISPR-based diagnostic assays.
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McKeague, Maureen, and Maria C. DeRosa. "Challenges and Opportunities for Small Molecule Aptamer Development." Journal of Nucleic Acids 2012 (2012): 1–20. http://dx.doi.org/10.1155/2012/748913.
Full textAbstract:
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Duś-Ilnicka, Irena, Elżbieta Krala, Paulina Cholewińska, and Małgorzata Radwan-Oczko. "The Use of Saliva as a Biosample in the Light of COVID-19." Diagnostics 11, no. 10 (September 26, 2021): 1769. http://dx.doi.org/10.3390/diagnostics11101769.
Full textAbstract:
Saliva is easy to collect and a biofluid that is readily available without the need for special equipment for its collection. The collection process, which is non-invasive and inexpensive, leads to obtaining a biomaterial that can serve as a source of information for molecular diagnostics of diseases in general medicine, genetics and dentistry. Unfortunately, many of the salivary methodologies are lacking important parameters to provide for not only the safety of the operator, but also the quality and reproducibility of the research. Since the COVID-19 pandemic, salivary diagnostics demonstrate a great potential for research of SARS-CoV 2. In this review, good practice for unstimulated saliva collection and patient preparation was provided, based on the latest literature and available guidelines. Schemes for saliva collection procedures were presented following an extended literature search. Descriptions of salivary probes/cups, techniques of saliva collection, and the use of specific buffering solutions for the stability of collected samples for SARS-CoV-2 detection were also evaluated.
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Skripka, Artiom, Diego Mendez-Gonzalez, Riccardo Marin, Erving Ximendes, Blanca del Rosal, Daniel Jaque, and Paloma Rodríguez-Sevilla. "Near infrared bioimaging and biosensing with semiconductor and rare-earth nanoparticles: recent developments in multifunctional nanomaterials." Nanoscale Advances 3, no. 22 (2021): 6310–29. http://dx.doi.org/10.1039/d1na00502b.
Full textAbstract:
This review highlights the very recent examples of near infrared contrast agents employed for multivariate diagnostics, multimodal imaging, and theranostic. Considerations on how to further advance these probes towards real-life use are also given.