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Price FD, Matyas MN, Gehrke AR, Chen W, Wolin EA, Holton KM, Gibbs RM, Lee A, Singu PS, Sakakeeny JS, Poteracki JM, Goune K, Pfeiffer IT, Boswell SA, Sorger PK, Srivastava M, Pfaff KL, Gussoni E, Buchanan SM, Rubin LL. Organoid culture promotes dedifferentiation of mouse myoblasts into stem cells capable of complete muscle regeneration. Nat Biotechnol 2024:10.1038/s41587-024-02344-7. [PMID: 39261590 DOI: 10.1038/s41587-024-02344-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/27/2024] [Indexed: 09/13/2024]
Abstract
Experimental cell therapies for skeletal muscle conditions have shown little success, primarily because they use committed myogenic progenitors rather than true muscle stem cells, known as satellite cells. Here we present a method to generate in vitro-derived satellite cells (idSCs) from skeletal muscle tissue. When transplanted in small numbers into mouse muscle, mouse idSCs fuse into myofibers, repopulate the satellite cell niche, self-renew, support multiple rounds of muscle regeneration and improve force production on par with freshly isolated satellite cells in damaged skeletal muscle. We compared the epigenomic and transcriptional signatures between idSCs, myoblasts and satellite cells and used these signatures to identify core signaling pathways and genes that confer idSC functionality. Finally, from human muscle biopsies, we successfully generated satellite cell-like cells in vitro. After further development, idSCs may provide a scalable source of cells for the treatment of genetic muscle disorders, trauma-induced muscle damage and age-related muscle weakness.
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Affiliation(s)
- Feodor D Price
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Mark N Matyas
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Andrew R Gehrke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - William Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Erica A Wolin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Kristina M Holton
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca M Gibbs
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Alice Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Pooja S Singu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jeffrey S Sakakeeny
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - James M Poteracki
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kelsey Goune
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Isabella T Pfeiffer
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sarah A Boswell
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kathleen Lindahl Pfaff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Emanuela Gussoni
- Division of Genetics and Genomics and the Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Sean M Buchanan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Mostufa S, Rezaei B, Ciannella S, Yari P, Gómez-Pastora J, He R, Wu K. Advancements and Perspectives in Optical Biosensors. ACS OMEGA 2024; 9:24181-24202. [PMID: 38882113 PMCID: PMC11170745 DOI: 10.1021/acsomega.4c01872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024]
Abstract
Optical biosensors exhibit immense potential, offering extraordinary possibilities for biosensing due to their high sensitivity, reusability, and ultrafast sensing capabilities. This review provides a concise overview of optical biosensors, encompassing various platforms, operational mechanisms, and underlying physics, and it summarizes recent advancements in the field. Special attention is given to plasmonic biosensors and metasurface-based biosensors, emphasizing their significant performance in bioassays and, thus, their increasing attraction in biosensing research, positioning them as excellent candidates for lab-on-chip and point-of-care devices. For plasmonic biosensors, we emphasize surface plasmon resonance (SPR) and its subcategories, along with localized surface plasmon resonance (LSPR) devices and surface enhance Raman spectroscopy (SERS), highlighting their ability to perform diverse bioassays. Additionally, we discuss recently emerged metasurface-based biosensors. Toward the conclusion of this review, we address current challenges, opportunities, and prospects in optical biosensing. Considering the advancements and advantages presented by optical biosensors, it is foreseeable that they will become a robust and widespread platform for early disease diagnostics.
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Affiliation(s)
- Shahriar Mostufa
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Bahareh Rezaei
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Stefano Ciannella
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Parsa Yari
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jenifer Gómez-Pastora
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Rui He
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Kai Wu
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
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3
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Roy SD, Ramasamy S, Obbineni JM. An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review. Virusdisease 2024; 35:357-376. [PMID: 39071869 PMCID: PMC11269559 DOI: 10.1007/s13337-024-00863-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/15/2024] [Indexed: 07/30/2024] Open
Abstract
Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00863-0.
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Affiliation(s)
- Subha Deep Roy
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Jagan M. Obbineni
- School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, Tamil Nadu India
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Kissmann AK, Bolotnikov G, Li R, Müller F, Xing H, Krämer M, Gottschalk KE, Andersson J, Weil T, Rosenau F. IMPATIENT-qPCR: monitoring SELEX success during in vitro aptamer evolution. Appl Microbiol Biotechnol 2024; 108:284. [PMID: 38573322 PMCID: PMC10995058 DOI: 10.1007/s00253-024-13085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Runliu Li
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kay-E Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210, Vienna, Austria
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Boyte ME, Benkowski A, Pane M, Shehata HR. Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques. Front Microbiol 2023; 14:1304621. [PMID: 38192285 PMCID: PMC10773886 DOI: 10.3389/fmicb.2023.1304621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.
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Affiliation(s)
- Marie-Eve Boyte
- NutraPharma Consulting Services Inc., Sainte-Anne-des-Plaines, QC, Canada
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
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Fusco V, Fanelli F, Chieffi D. Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages. Foods 2023; 12:3782. [PMID: 37893675 PMCID: PMC10606304 DOI: 10.3390/foods12203782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.
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Affiliation(s)
- Vincenzina Fusco
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy; (F.F.); (D.C.)
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Genco E, Modena F, Sarcina L, Björkström K, Brunetti C, Caironi M, Caputo M, Demartis VM, Di Franco C, Frusconi G, Haeberle L, Larizza P, Mancini MT, Österbacka R, Reeves W, Scamarcio G, Scandurra C, Wheeler M, Cantatore E, Esposito I, Macchia E, Torricelli F, Viola FA, Torsi L. A Single-Molecule Bioelectronic Portable Array for Early Diagnosis of Pancreatic Cancer Precursors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304102. [PMID: 37452695 DOI: 10.1002/adma.202304102] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
A cohort of 47 patients is screened for pancreatic cancer precursors with a portable 96-well bioelectronic sensing-array for single-molecule assay in cysts fluid and blood plasma, deployable at point-of-care (POC). Pancreatic cancer precursors are mucinous cysts diagnosed with a sensitivity of at most 80% by state-of-the-art cytopathological molecular analyses (e.g., KRASmut DNA). Adding the simultaneous assay of proteins related to malignant transformation (e.g., MUC1 and CD55) is deemed essential to enhance diagnostic accuracy. The bioelectronic array proposed here, based on single-molecule-with-a-large-transistor (SiMoT) technology, can assay both nucleic acids and proteins at the single-molecule limit-of-identification (LOI) (1% of false-positives and false-negatives). It comprises an enzyme-linked immunosorbent assay (ELISA)-like 8 × 12-array organic-electronics disposable cartridge with an electrolyte-gated organic transistor sensor array, and a reusable reader, integrating a custom Si-IC chip, operating via software installed on a USB-connected smart device. The cartridge is complemented by a 3D-printed sensing gate cover plate. KRASmut , MUC1, and CD55 biomarkers either in plasma or cysts-fluid from 5 to 6 patients at a time, are multiplexed at single-molecule LOI in 1.5 h. The pancreatic cancer precursors are classified via a machine-learning analysis resulting in at least 96% diagnostic-sensitivity and 100% diagnostic-specificity. This preliminary study opens the way to POC liquid-biopsy-based early diagnosis of pancreatic-cancer precursors in plasma.
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Affiliation(s)
- Enrico Genco
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Francesco Modena
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milan, 20133, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - Kim Björkström
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Mario Caironi
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Mariapia Caputo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Virginia Maria Demartis
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | | | - Giulia Frusconi
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Lena Haeberle
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Piero Larizza
- Masmec Biomed - Masmec SpA division, Modugno (BA), 70026, Italy
| | | | - Ronald Österbacka
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
| | | | - Gaetano Scamarcio
- CNR IFN, Bari, 70126, Italy
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, 70125, Italy
| | - Cecilia Scandurra
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
| | - May Wheeler
- FlexEnable Technology Ltd, Cambridge, CB4 0FX, UK
| | - Eugenio Cantatore
- Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Irene Esposito
- Institute of Pathology, Heinrich-Heine University and University Hospital of Düsseldorf, 40225, Duesseldorf, Germany
| | - Eleonora Macchia
- The Faculty of Science and Engineering, Åbo Akademi University, Turku, 20500, Finland
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, 70125, Italy
| | - Fabrizio Torricelli
- Dipartimento Ingegneria dell'Informazione, Università degli Studi di Brescia, Brescia, 25123, Italy
| | - Fabrizio Antonio Viola
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, Milan, 20134, Italy
| | - Luisa Torsi
- Dipartimento di Chimica and Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, Bari, 20125, Italy
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Shan H, Chen D, Zhang R, Wang X, Li J, Wang C, Li Y, Huang Y. Relationship between Sugarcane eIF4E Gene and Resistance against Sugarcane Streak Mosaic Virus. PLANTS (BASEL, SWITZERLAND) 2023; 12:2805. [PMID: 37570959 PMCID: PMC10421434 DOI: 10.3390/plants12152805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Sugarcane mosaic disease, mainly caused by Sugarcane streak mosaic virus (SCSMV), has serious adverse effects on the yield and quality of sugarcane. Eukaryotic translation initiation factor 4E (eIF4E) is a natural resistance gene in plants. The eIF4E-mediated natural recessive resistance results from non-synonymous mutations of the eIF4E protein. In this study, two sugarcane varieties, CP94-1100 and ROC22, were selected for analysis of their differences in resistance to SCSMV. Four-base missense mutations in the ORF region of eIF4E resulted in different conserved domains. Therefore, the differences in resistance to SCSMV are due to the inherent differences in eIF4E of the sugarcane varieties. The coding regions of eIF4E included 28 SNP loci and no InDel loci, which were affected by negative selection and were relatively conserved. A total of 11 haploids encoded 11 protein sequences. Prediction of the protein spatial structure revealed three non-synonymous mutation sites for amino acids located in the cap pocket of eIF4E; one of these sites existed only in a resistant material (Yuetang 55), whereas the other site existed only in a susceptible material (ROC22), suggesting that these two sites might be related to the resistance to SCSMV. The results provide a strong basis for further analysis of the functional role of eIF4E in regulating mosaic resistance in sugarcane.
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Affiliation(s)
| | | | | | | | | | | | | | - Yingkun Huang
- Sugarcane Research Institute, Yunnan Academy of Agricultural Science, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (H.S.); (D.C.); (R.Z.); (X.W.); (J.L.); (C.W.); (Y.L.)
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10
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Almuayqil S, Abd El-Ghany S, Shehab A. Multimodality Imaging of COVID-19 Using Fine-Tuned Deep Learning Models. Diagnostics (Basel) 2023; 13:1268. [PMID: 37046486 PMCID: PMC10093688 DOI: 10.3390/diagnostics13071268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
In the face of the COVID-19 pandemic, many studies have been undertaken to provide assistive recommendations to patients to help overcome the burden of the expected shortage in clinicians. Thus, this study focused on diagnosing the COVID-19 virus using a set of fine-tuned deep learning models to overcome the latency in virus checkups. Five recent deep learning algorithms (EfficientB0, VGG-19, DenseNet121, EfficientB7, and MobileNetV2) were utilized to label both CT scan and chest X-ray images as positive or negative for COVID-19. The experimental results showed the superiority of the proposed method compared to state-of-the-art methods in terms of precision, sensitivity, specificity, F1 score, accuracy, and data access time.
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Affiliation(s)
- Saleh Almuayqil
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka 72388, Saudi Arabia; (S.A.); (S.A.E.-G.)
| | - Sameh Abd El-Ghany
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka 72388, Saudi Arabia; (S.A.); (S.A.E.-G.)
- Department of Information Systems, Mansoura University, Mansoura 35516, Egypt
| | - Abdulaziz Shehab
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka 72388, Saudi Arabia; (S.A.); (S.A.E.-G.)
- Department of Information Systems, Mansoura University, Mansoura 35516, Egypt
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11
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Bosco F, Guarnieri L, Nucera S, Scicchitano M, Ruga S, Cardamone A, Maurotti S, Russo C, Coppoletta AR, Macrì R, Bava I, Scarano F, Castagna F, Serra M, Caminiti R, Maiuolo J, Oppedisano F, Ilari S, Lauro F, Giancotti L, Muscoli C, Carresi C, Palma E, Gliozzi M, Musolino V, Mollace V. Pathophysiological Aspects of Muscle Atrophy and Osteopenia Induced by Chronic Constriction Injury (CCI) of the Sciatic Nerve in Rats. Int J Mol Sci 2023; 24:ijms24043765. [PMID: 36835176 PMCID: PMC9962869 DOI: 10.3390/ijms24043765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Skeletal muscle atrophy is a condition characterized by a loss of muscle mass and muscle strength caused by an imbalance between protein synthesis and protein degradation. Muscle atrophy is often associated with a loss of bone mass manifesting as osteoporosis. The aim of this study was to evaluate if chronic constriction injury (CCI) of the sciatic nerve in rats can be a valid model to study muscle atrophy and consequent osteoporosis. Body weight and body composition were assessed weekly. Magnetic resonance imaging (MRI) was performed on day zero before ligation and day 28 before sacrifice. Catabolic markers were assessed via Western blot and Quantitative Real-time PCR. After the sacrifice, a morphological analysis of the gastrocnemius muscle and Micro-Computed Tomography (Micro-CT) on the tibia bone were performed. Rats that underwent CCI had a lower body weight increase on day 28 compared to the naive group of rats (p < 0.001). Increases in lean body mass and fat mass were also significantly lower in the CCI group (p < 0.001). The weight of skeletal muscles was found to be significantly lower in the ipsilateral hindlimb compared to that of contralateral muscles; furthermore, the cross-sectional area of muscle fibers decreased significantly in the ipsilateral gastrocnemius. The CCI of the sciatic nerve induced a statistically significant increase in autophagic and UPS (Ubiquitin Proteasome System) markers and a statistically significant increase in Pax-7 (Paired Box-7) expression. Micro-CT showed a statistically significant decrease in the bone parameters of the ipsilateral tibial bone. Chronic nerve constriction appeared to be a valid model for inducing the condition of muscle atrophy, also causing changes in bone microstructure and leading to osteoporosis. Therefore, sciatic nerve constriction could be a valid approach to study muscle-bone crosstalk and to identify new strategies to prevent osteosarcopenia.
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Affiliation(s)
- Francesca Bosco
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (F.B.); (M.G.)
| | - Lorenza Guarnieri
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Saverio Nucera
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Miriam Scicchitano
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Ruga
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Antonio Cardamone
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Samantha Maurotti
- Department of Medical and Surgical Science, University Magna Grecia, 88100 Catanzaro, Italy
| | - Cristina Russo
- Department of Medical and Surgical Science, University Magna Grecia, 88100 Catanzaro, Italy
| | - Anna Rita Coppoletta
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Roberta Macrì
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Irene Bava
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Federica Scarano
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Fabio Castagna
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Maria Serra
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rosamaria Caminiti
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Jessica Maiuolo
- Laboratory of Pharmaceutical Biology, Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH) Center, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Francesca Oppedisano
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Sara Ilari
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Filomena Lauro
- Henry and Amelia Nasrallah Center for Neuroscience, Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Grand Blvd, St. Louis, MO 63104, USA
| | - Luigi Giancotti
- Henry and Amelia Nasrallah Center for Neuroscience, Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Grand Blvd, St. Louis, MO 63104, USA
| | - Carolina Muscoli
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Cristina Carresi
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Ernesto Palma
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Micaela Gliozzi
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (F.B.); (M.G.)
| | - Vincenzo Musolino
- Laboratory of Pharmaceutical Biology, Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH) Center, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Vincenzo Mollace
- Department of Health Sciences, Institute of Research for Food Safety and Health (IRC-FSH), University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
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12
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Shehata HR, Hassane B, Newmaster SG. Real-time polymerase chain reaction methods for strain specific identification and enumeration of strain Lacticaseibacillus paracasei 8700:2. Front Microbiol 2023; 13:1076631. [PMID: 36741903 PMCID: PMC9889646 DOI: 10.3389/fmicb.2022.1076631] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Reliable and accurate methods for probiotic identification and enumeration, at the strain level plays a major role in confirming product efficacy since probiotic health benefits are strain-specific and dose-dependent. In this study, real-time PCR methods were developed for strain specific identification and enumeration of L. paracasei 8700:2, a probiotic strain that plays a role in fighting the common cold. Methods The assay was designed to target a unique region in L. paracasei 8700:2 genome sequence to achieve strain level specificity. The identification assay was evaluated for specificity and sensitivity. The enumeration viability real-time PCR (v-qPCR) method was first optimized for the viability treatment, then the method was evaluated for efficiency, limit of quantification, precision, and its performance was compared to plate count (PC) and viability droplet digital PCR (v-ddPCR) methods. Results The identification method proved to be strain specific and highly sensitive with a limit of detection of 0.5 pg of DNA. The optimal viability dye (PMAxx) concentration was 50 μM. The method was efficient (> 90% with R 2 values > 0.99), with a linear dynamic range between 6*102 and 6*105 copies. The method was highly precise with a relative standard deviation below 5%. The Pearson correlation coefficient (r) was 0.707 for PC and v-qPCR methods, and 0.922 for v-qPCR and v-ddPCR. Bland-Altman method comparison showed that v-qPCR always gave higher values compared to PC method (relative difference ranging from 119% to 184%) and showed no consistent trend (relative difference ranging from -20% to 22%) when comparing v-qPCR and v-ddPCR methods. Discussion The difference between PC and v-PCR methods can potentially be attributed to the proportion of cells that exist in a viable but non culturable (VBNC) state, which can be count by v-PCR but not with PC. The developed v-qPCR method was confirmed to be strain specific, sensitive, efficient, with low variance, able to count VBNC cells, and has shorter time to results compared to plate count methods. Thus, the identification and enumeration methods developed for L. paracasei 8700:2 will be of great importance to achieve high quality and efficacious probiotic products.
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Affiliation(s)
- Hanan R. Shehata
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Purity-IQ Inc., Guelph, ON, Canada
| | | | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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13
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Costigan R, Stoakes E, Floto RA, Parkhill J, Grant AJ. Development and validation of a CRISPR interference system for gene regulation in Campylobacter jejuni. BMC Microbiol 2022; 22:238. [PMID: 36199015 PMCID: PMC9533551 DOI: 10.1186/s12866-022-02645-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campylobacter spp. are the leading cause of bacterial food-borne illness in humans worldwide, with Campylobacter jejuni responsible for 80% of these infections. There is an urgent need to understand fundamental C. jejuni biology for the development of new strategies to prevent and treat infections. The range of molecular tools available to regulate gene expression in C. jejuni is limited, which in turn constrains our ability to interrogate the function of essential and conditionally essential genes. We have addressed this by developing and utilising a CRISPR-based interference system known as CRISPRi in C. jejuni to control gene expression. To achieve this, a catalytically inactive ("dead") cas9 and sgRNA backbone from the Streptococcus pyogenes CRISPRi system was combined with C. jejuni-derived promoters of predetermined expression activities to develop a CRISPRi-based repression tool in C. jejuni strains M1Cam and 81-176. RESULTS The CRISPRi tool was validated through successful repression of the arylsulphatase-encoding gene astA using a range of sgRNA target sequences spanning the astA gene. The tool was also applied to target astA in an M1Cam CRISPR-Cas9 deletion strain, which showed that the presence of an endogenous CRISPR-Cas9 system did not affect the activity of the CRISPRi-based repression tool. The tool was further validated against the hippicurase-encoding gene hipO. Following this, the flagella genes flgR, flaA, flaB and both flaA and flaB were targeted for CRISPRi-based repression, which resulted in varying levels of motility reduction and flagella phenotypes as determined by phenotypical assays and transmission electron microscopy (TEM). CONCLUSIONS This is the first report of a CRISPRi-based tool in C. jejuni, which will provide a valuable resource to the Campylobacter community.
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Affiliation(s)
- Ruby Costigan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Emily Stoakes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Department of Medicine, MRC-Laboratory of Molecular Biology, Molecular Immunity Unit, University of Cambridge, Cambridge, UK
- University of Cambridge, Centre for AI in Medicine, Cambridge, UK
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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14
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Curtin K, Fike BJ, Binkley B, Godary T, Li P. Recent Advances in Digital Biosensing Technology. BIOSENSORS 2022; 12:bios12090673. [PMID: 36140058 PMCID: PMC9496261 DOI: 10.3390/bios12090673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022]
Abstract
Digital biosensing assays demonstrate remarkable advantages over conventional biosensing systems because of their ability to achieve single-molecule detection and absolute quantification. Unlike traditional low-abundance biomarking screening, digital-based biosensing systems reduce sample volumes significantly to the fL-nL level, which vastly reduces overall reagent consumption, improves reaction time and throughput, and enables high sensitivity and single target detection. This review presents the current technology for compartmentalizing reactions and their applications in detecting proteins and nucleic acids. We also analyze existing challenges and future opportunities associated with digital biosensing and research opportunities for developing integrated digital biosensing systems.
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Affiliation(s)
- Kathrine Curtin
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV 26506, USA
| | - Bethany J. Fike
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Brandi Binkley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Toktam Godary
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
- Correspondence:
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15
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Hsieh SA, Shamsaei D, Eitzmann DR, Anderson JL. Digital Droplet Loop-Mediated Isothermal Amplification Featuring a Molecular Beacon Assay, 3D Printed Droplet Generation, and Smartphone Imaging for Sequence-Specific DNA Detection. Anal Chem 2022; 94:11949-11956. [PMID: 35973866 DOI: 10.1021/acs.analchem.2c02979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleic acid detection is widely used in the amplification and quantitation of nucleic acids from biological samples. While polymerase chain reaction (PCR) enjoys great popularity, expensive thermal cyclers are required for precise temperature control. Loop-mediated isothermal amplification (LAMP) enables highly sensitive, rapid, and low-cost amplification of nucleic acids at constant temperatures. LAMP detection often relies on double-stranded DNA-binding dyes or metal indicators that lack sequence selectivity. Molecular beacons (MBs) are hairpin-shaped oligonucleotide probes whose sequence specificity in LAMP provides the capability of differentiating between single-nucleotide polymorphisms (SNPs). Digital droplet LAMP (ddLAMP) enables a large number of independent LAMP reactions to be performed and provides quantification of target DNA sequences. However, a major challenge with ddLAMP is the requirement of expensive droplet generators to form homogeneous microdroplets. In this study, we demonstrate for the first time that a three-dimensional (3D) printed droplet generation platform can be coupled to a LAMP assay featuring MBs as sequence-specific probes. The low-cost 3D printed droplet generator system was designed, and its customizability was demonstrated in the formation of monodisperse ddLAMP assay-in-oil microdroplets. Additionally, a smartphone-based imaging system is demonstrated to increase accessibility for point-of-care applications. The MB-ddLAMP assay is shown to discriminate between two SNPs at various amplification temperatures to afford a useful platform for sequence-specific, sensitive, and accurate DNA quantification. This work expands the utility of MBs to ddLAMP for quantitative studies in the detection of SNPs and exploits the customizability of 3D printing technologies to optimize the homogeneity, size, and volume of oil-in-water microdroplets.
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Affiliation(s)
- Shu-An Hsieh
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Danial Shamsaei
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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16
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Wang S, Qin A, Chau LY, Fok EWT, Choy MY, Brackman CJ, Siu GKH, Huang CL, Yip SP, Lee TMH. Amine-Functionalized Quantum Dots as a Universal Fluorescent Nanoprobe for a One-Step Loop-Mediated Isothermal Amplification Assay with Single-Copy Sensitivity. ACS APPLIED MATERIALS & INTERFACES 2022; 14:35299-35308. [PMID: 35895859 DOI: 10.1021/acsami.2c02508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) has received considerable attention for decentralized (point-of-care and on-site) nucleic acid testing in view of its simple temperature control (60-65 °C) and short assay time (15-60 min). There remains a challenge in its wide adoption and acceptance due to the limitations of the existing amplification result reporter probes, e.g., photobleaching of organic fluorophore and reduced sensitivity of the pH-sensitive colorimetric dye. Herein, we demonstrate CdSeS/ZnS quantum dots (semiconductor fluorescent nanocrystals with superior photostability than organic fluorophore) with surface modification of cysteamine (amine-QDs) as a new reporter probe for LAMP that enabled single-copy sensitivity (limit of detection of 83 zM; 20 μL reaction volume). For a negative LAMP sample (absence of target sequence), positively charged amine-QDs remained dispersed due to interparticle electrostatic repulsion. While for a positive LAMP sample (presence of target sequence), amine-QDs became precipitated. The characterization data showed that amine-QDs were embedded in magnesium pyrophosphate crystals (generated during positive LAMP), thus leading to their coprecipitation. This amine-QD-based one-step LAMP assay advances the field of QD-based nucleic acid amplification assays in two aspects: (1) compatibility─one-step amplification and detection (versus separation of amplification and detection steps); and (2) universality─the same amine-QDs for different target sequences (versus different oligonucleotide-modified QDs for different target sequences).
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Affiliation(s)
- Shiyao Wang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Ailin Qin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Li Yin Chau
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Eunice W T Fok
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong 000000, China
| | - Mei Yue Choy
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong 000000, China
| | - Christopher J Brackman
- Agriculture, Fisheries and Conservation Department, Government of the Hong Kong Special Administrative Region, Hong Kong 000000, China
| | - Gilman K H Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
| | - Thomas M H Lee
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong 000000, China
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18
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Pallu J, Rabin C, Hui P, Moreira TS, Creste G, Calvet C, Limoges B, Mavré F, Branca M. Exponential amplification by redox cross-catalysis and unmasking of doubly protected molecular probes. Chem Sci 2022; 13:2764-2777. [PMID: 35356676 PMCID: PMC8890127 DOI: 10.1039/d1sc06086d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/10/2022] [Indexed: 11/21/2022] Open
Abstract
The strength of autocatalytic reactions lies in their ability to provide a powerful means of molecular amplification, which can be very useful for improving the analytical performances of a multitude of analytical and bioanalytical methods. However, one of the major difficulties in designing an efficient autocatalytic amplification system is the requirement for reactants that are both highly reactive and chemically stable in order to avoid limitations imposed by undesirable background amplifications. In the present work, we devised a reaction network based on a redox cross-catalysis principle, in which two catalytic loops activate each other. The first loop, catalyzed by H2O2, involves the oxidative deprotection of a naphthylboronate ester probe into a redox-active naphthohydroquinone, which in turn catalyzes the production of H2O2 by redox cycling in the presence of a reducing enzyme/substrate couple. We present here a set of new molecular probes with improved reactivity and stability, resulting in particularly steep sigmoidal kinetic traces and enhanced discrimination between specific and nonspecific responses. This translates into the sensitive detection of H2O2 down to a few nM in less than 10 minutes or a redox cycling compound such as the 2-amino-3-chloro-1,4-naphthoquinone down to 50 pM in less than 30 minutes. The critical reason leading to these remarkably good performances is the extended stability stemming from the double masking of the naphthohydroquinone core by two boronate groups, a counterintuitive strategy if we consider the need for two equivalents of H2O2 for full deprotection. An in-depth study of the mechanism and dynamics of this complex reaction network is conducted in order to better understand, predict and optimize its functioning. From this investigation, the time response as well as detection limit are found to be highly dependent on pH, nature of the buffer, and concentration of the reducing enzyme. Reduction of the non-specific background in autocatalytic molecular amplifications by a double masking strategy.![]()
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Affiliation(s)
- Justine Pallu
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Charlie Rabin
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Pan Hui
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Thamires S Moreira
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Geordie Creste
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Corentin Calvet
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
| | - Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS F-75013 Paris France
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Ali F, Khan A, Muhammad SA, Hassan SSU. Quantitative Real-Time Analysis of Differentially Expressed Genes in Peripheral Blood Samples of Hypertension Patients. Genes (Basel) 2022; 13:genes13020187. [PMID: 35205232 PMCID: PMC8872078 DOI: 10.3390/genes13020187] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Hypertension (HTN) is considered one of the most important and well-established reasons for cardiovascular abnormalities, strokes, and premature mortality globally. This study was designed to explore possible differentially expressed genes (DEGs) that contribute to the pathophysiology of hypertension. To identify the DEGs of HTN, we investigated 22 publicly available cDNA Affymetrix datasets using an integrated system-level framework. Gene Ontology (GO), pathway enrichment, and transcriptional factors were analyzed to reveal biological information. From 50 DEGs, we ranked 7 hypertension-related genes (p-value < 0.05): ADM, ANGPTL4, USP8, EDN, NFIL3, MSR1, and CEBPD. The enriched terms revealed significant functional roles of HIF-1-α transcription; endothelin; GPCR-binding ligand; and signaling pathways of EGF, PIk3, and ARF6. SP1 (66.7%), KLF7 (33.3%), and STAT1 (16.7%) are transcriptional factors associated with the regulatory mechanism. The expression profiles of these DEGs as verified by qPCR showed 3-times higher fold changes (2−ΔΔCt) in ADM, ANGPTL4, USP8, and EDN1 genes compared to control, while CEBPD, MSR1 and NFIL3 were downregulated. The aberrant expression of these genes is associated with the pathophysiological development and cardiovascular abnormalities. This study will help to modulate the therapeutic strategies of hypertension.
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Affiliation(s)
- Fawad Ali
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad 44000, Pakistan; (F.A.); (A.K.)
- Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Arifullah Khan
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Islamabad 44000, Pakistan; (F.A.); (A.K.)
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan 60800, Pakistan
- Correspondence: (S.A.M.); (S.S.u.H.)
| | - Syed Shams ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: (S.A.M.); (S.S.u.H.)
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20
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Shehata HR, Kiefer A, Morovic W, Newmaster SG. Locked Nucleic Acid Hydrolysis Probes for the Specific Identification of Probiotic Strains Bifidobacterium animalis subsp. lactis DSM 15954 and Bi-07™. Front Microbiol 2022; 12:801795. [PMID: 35003031 PMCID: PMC8733699 DOI: 10.3389/fmicb.2021.801795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Probiotic health benefits are now well-recognized to be strain specific. Probiotic strain characterization and identification is thus important in clinical research and in the probiotic industry. This is becoming especially important with reports of probiotic products failing to meet the declared strain content, potentially compromising their efficacy. Availability of reliable identification methods is essential for strain authentication during discovery, evaluation and commercialization of a probiotic strain. This study aims to develop identification methods for strains Bifidobacterium animalis subsp. lactis DSM 15954 and Bi-07 (Bi-07™) based on real-time PCR, targeting single nucleotide polymorphisms (SNPs). The SNPs were targeted by PCR assays with locked nucleic acid (LNA) probes, which is a novel application in probiotic identification. The assays were then validated following the guidelines for validating qualitative real-time PCR assays. Each assay was evaluated for specificity against 22 non-target strains including closely related Bifidobacterium animalis subsp. lactis strains and were found to achieve 100% true positive and 0% false positive rates. To determine reaction sensitivity and efficiency, three standard curves were established for each strain. Reaction efficiency values were 86, 91, and 90% (R square values > 0.99), and 87, 84, and 86% (R square values > 0.98) for B. animalis subsp. lactis DSM 15954 and Bi-07 assays, respectively. The limit of detection (LOD) was 5.0 picograms and 0.5 picograms of DNA for DSM 15954 and Bi-07 assays, respectively. Each assay was evaluated for accuracy using five samples tested at three different DNA concentrations and both assays proved to be highly repeatable and reproducible. Standard deviation of Cq values between two replicates was always below 1.38 and below 1.68 for DSM 15954 and Bi-07 assays, respectively. The assays proved to be applicable to mono-strain and multi-strain samples as well as for samples in various matrices of foods or dietary supplement ingredients. Overall, the methods demonstrated high specificity, sensitivity, efficiency and precision and broad applicability to sample, matrix and machine types. These methods facilitate strain level identification of the highly monophyletic strains B. animalis subsp. lactis DSM 15954 and Bi-07 to ensure probiotic efficacy and provide a strategy to identify other closely related probiotics organisms.
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Affiliation(s)
- Hanan R Shehata
- Natural Health Product Research Alliance, College of Biological Science, University of Guelph, Guelph, ON, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Anthony Kiefer
- IFF Health & Biosciences, International Flavors and Fragrances, Inc., Madison, WI, United States
| | - Wesley Morovic
- IFF Health & Biosciences, International Flavors and Fragrances, Inc., Madison, WI, United States
| | - Steven G Newmaster
- Natural Health Product Research Alliance, College of Biological Science, University of Guelph, Guelph, ON, Canada
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21
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FUJIMOTO M, KITAMURA H. Application of the colorimetric loop-mediated isothermal amplification (LAMP) technique for genotyping <i>Cre</i>-driver mice. J Vet Med Sci 2022; 84:507-510. [PMID: 35228407 PMCID: PMC9096032 DOI: 10.1292/jvms.21-0658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The Cre-loxP system is widely used to investigate the cell-type specific
roles of genes of interest. Cre-driver mice are required for cell-type
specific knockout during the Cre-loxP reaction. To maintain
Cre-driver mouse strains, Polymerase chain reaction (PCR)-oriented
genotyping targeting the Cre gene cassette is usually conducted. In this
study, we instead applied a colorimetric loop-mediated isothermal amplification (LAMP)
method for Cre-genotyping. Among four sets of primers designed by the
in silico program, one set effectively amplified the
Cre cassette of three Cre-driver strains, but not of
C57BL/6 mice. This LAMP-oriented method reduces assay time by less than half compared to
the PCR-based method, and can be carried out using a conventional isothermal incubator.
Applying this LAMP method may accelerate genotyping of Cre-driver
mice.
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Affiliation(s)
- Masaki FUJIMOTO
- Laboratory of Radiation Biology, Faculty of Veterinary Medicine, Hokkaido University
| | - Hiroshi KITAMURA
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, School of Veterinary Medicine, Rakuno Gakuen University
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22
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Culjkovic-Kraljacic B, Borden KLB. Subcellular Fractionation Suitable for Studies of RNA and Protein Trafficking. Methods Mol Biol 2022; 2502:91-104. [PMID: 35412233 DOI: 10.1007/978-1-0716-2337-4_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The nuclear pore complex is the major conduit for trafficking between the nucleus and cytoplasm. Nuclear import and export of both proteins and RNAs represent important functional steps for many biological processes. One of the major means to study NPC activity and the nuclear and cytoplasmic distribution of proteins and RNAs is through biochemical fractionation. Here, we describe detailed methods to generate high quality nuclear and cytoplasmic fractions simultaneously capturing RNA and proteins which can be used subsequently for a wide array of biochemical characterizations including proteomics and next generation sequencings.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, Institute of Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
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23
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Zhang Y, Li H, Shang S, Meng S, Lin T, Zhang Y, Liu H. Evaluation validation of a qPCR curve analysis method and conventional approaches. BMC Genomics 2021; 22:680. [PMID: 34789146 PMCID: PMC8596907 DOI: 10.1186/s12864-021-07986-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Reverse Transcription quantitative polymerase chain reaction (RT-qPCR) is a sensitive and reliable method for mRNA quantification and rapid analysis of gene expression from a large number of starting templates. It is based on the statistical significance of the beginning of exponential phase in real-time PCR kinetics, reflecting quantitative cycle of the initial target quantity and the efficiency of the PCR reaction (the fold increase of product per cycle). RESULTS We used the large clinical biomarker dataset and 94-replicates-4-dilutions set which was published previously as research tools, then proposed a new qPCR curve analysis method--CqMAN, to determine the position of quantitative cycle as well as the efficiency of the PCR reaction and applied in the calculations. To verify algorithm performance, 20 genes from biomarker and partial data with concentration gradients from 94-replicates-4-dilutions set of MYCN gene were used to compare our method with various publicly available methods and established a suitable evaluation index system. CONCLUSIONS The results show that CqMAN method is comparable to other methods and can be a feasible method which applied to our self-developed qPCR data processing and analysis software, providing a simple tool for qPCR analysis.
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Affiliation(s)
- Yashu Zhang
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Hongping Li
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China.
| | - Shucheng Shang
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Shuoyu Meng
- Department of Information Science and Engineering, Ocean University of China, Qingdao, China
| | - Ting Lin
- Apexbio Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Yanhui Zhang
- Apexbio Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Haixing Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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24
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Cui H, de Jong MC, Beerens N, van Oers MM, Teng Q, Li L, Li X, Liu Q, Li Z. Vaccination with inactivated virus against low pathogenic avian influenza subtype H9N2 does not prevent virus transmission in chickens. J Virus Erad 2021; 7:100055. [PMID: 34621531 PMCID: PMC8481976 DOI: 10.1016/j.jve.2021.100055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 11/06/2022] Open
Abstract
H9N2 subtype avian influenza has spread dramatically in China ever since first reported in the 1990s. A national vaccination program for poultry was initiated in 1998. Field isolation data show that the widely used inactivated H9N2 vaccine does not provide effective control of the transmission of this low pathogenic avian influenza (LPAI) virus in poultry. Current research has focused on two reasons: (i) insufficient immune response triggered by the vaccination with the inactivated virus, (ii) the occurrence of escape mutants selected by vaccine-induced immune pressure. However, the lack of effectivity of the inactivated virus vaccine to sufficiently reduce transmission has been noticed. We mimicked the natural infection and transmission process of the H9N2 virus in vaccinated and non-vaccinated chickens. A statistical model was used to estimate the transmission rate parameters among vaccinated chickens, varying in serum hemagglutinin inhibition titers (HIT) and non-vaccinated chickens. We demonstrate, for the first time, that the transmission is not sufficiently reduced by the H9N2 vaccine, even when vaccinated chickens have an IgG serum titer (HIT>23), which is considered protective for vaccination against homologous highly pathogenic avian influenza (HPAI) virus. Our study does, on the other hand, cast new light on virus transmission and immune escape of LPAI H9N2 virus in vaccinated chickens populations, and shows that new mitigation strategies against LPAI viruses in poultry are needed.
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Affiliation(s)
- Hongrui Cui
- Shanghai Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Shanghai, China.,Quantitative Veterinary Epidemiology, Animal Sciences Group, Wageningen University & Research, the Netherlands
| | - Mart Cm de Jong
- Quantitative Veterinary Epidemiology, Animal Sciences Group, Wageningen University & Research, the Netherlands
| | - Nancy Beerens
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, the Netherlands
| | - Monique M van Oers
- Laboratory of Virology, Plant Science Group, Wageningen University & Research, the Netherlands
| | - Qiaoyang Teng
- Shanghai Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Shanghai, China
| | - Luzhao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Shanghai, China
| | - Xuesong Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Shanghai, China
| | - Qinfang Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Shanghai, China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Shanghai, China
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25
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Branca M, Calvet C, Limoges B, Mavré F. Specific Versus Non-specific Response in Exponential Molecular Amplification from Cross-Catalysis: Modeling the Influence of Background Amplifications on the Analytical Performances. Chemphyschem 2021; 22:1611-1621. [PMID: 34038617 DOI: 10.1002/cphc.202100342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/25/2021] [Indexed: 11/05/2022]
Abstract
Molecule based signal amplifications relying on an autocatalytic process may represent an ideal strategy for the development of ultrasensitive analytical or bioanalytical assays, the main reason being the exponential nature of the amplification. However, to take full advantage of such amplification rates, high stability of the starting co-reactants is required in order to avoid any undesirable background amplification. Here, on the basis of a simple kinetic model of cross-catalysis including a certain degree of intrinsic instability of co-reactants, we highlight the key parameters governing the analytical response of the system and discuss the analytical performances that are expected from a given kinetic set. In particular, we show how the detection limit is directly related to the relative instability of reactants within each catalytic loop. The model is validated with an experimental dataset and is intended to serve as a guide in the design and optimization of autocatalytic molecular-based amplification systems with improved analytical performances.
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Affiliation(s)
- Mathieu Branca
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Corentin Calvet
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - Benoît Limoges
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
| | - François Mavré
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, UMR 7591, CNRS, 75013, Paris, France
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26
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Mariconti M, Morel M, Baigl D, Rudiuk S. Enzymatically Active DNA-Protein Nanogels with Tunable Cross-Linking Density. Biomacromolecules 2021; 22:3431-3439. [PMID: 34260203 DOI: 10.1021/acs.biomac.1c00501] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hybrid DNA-protein nanogels represent potential protein vectors and enzymatic nanoreactors for modern biotechnology. Here, we describe a new, easy, and robust method for preparation of tunable DNA-protein nanogels with controllable size and density. For this purpose, polymerase chain reaction is used to prepare highly biotinylated DNA as a soft biopolymeric backbone, which can be efficiently cross-linked via streptavidin-biotin binding. This approach enables us to control both the density and size of the resulting nanogels not only by adjusting the amount of the cross-linking streptavidin but also by using different rates of DNA biotinylation. This gives DNA-streptavidin nanogels with the size ranging from 80 nm, for the most compact state, to up to 200 nm. Furthermore, using streptavidin-enzyme conjugates allows the straightforward one-pot incorporation of enzymes during the preparation of the nanogels. Monoenzymatic and multienzymatic nanogels have been obtained in this manner, and their catalytic activities have been characterized. All tested enzymes (alkaline phosphatase (AP), horseradish peroxidase (HRP), and β-galactosidase (βGal)), incorporated individually or in a coupled manner (glucose oxidase (GOx)-HRP cascade), were shown to remain functional. The activities of AP and βGal were unchanged while that of HRP was slightly improved inside the nanogels. We demonstrate that, for HRP, it is not the DNA-to-enzyme ratio but the physical density of the functionalized DNA nanogels that is responsible for the improvement of its enzymatic activity.
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Affiliation(s)
- Marina Mariconti
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
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27
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Schneider ACR, de Moura AC, Carvalho FB, Alves T, Meurer F, Porawski M, da Silveira TR. Effect of Melatonin on the Reduction of Hepatic Steatosis and Intestinal Leptin Expression in Zebrafish Exposed to Fructose. Zebrafish 2021; 18:184-189. [PMID: 33983041 DOI: 10.1089/zeb.2020.1910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Melatonin is a hormone related to circadian rhythms and has potential clinical applications. Our objectives were to verify the effect of melatonin on the liver of zebrafish exposed to fructose and evaluate the expression of appetite-related genes (leptin, ghrelin, and melanocortin receptor 4 [MC4R]). Animals were divided into three groups: control (CG, n = 25), fructose (FG, n = 25), and fructose+melatonin (FMG, n = 25). The study was carried out in 8 weeks. FG and FMG were exposed to 2% fructose and FMG treated with 1 μM of melatonin. Histological liver studies and gene expression analyses of Leptin, Ghrelin, and MC4R (liver and intestines) were performed. FG developed hepatic steatosis, which did not occur with CG and FMG. Genetic expression of hepatic leptin and MC4R did not show significant difference among the groups. Animals exposed to fructose (FG) presented an increased expression of intestinal leptin compared to those administered with melatonin. Animals exposed to fructose gained weight and developed an important hepatic steatosis, but melatonin reduced significantly the hepatic damage. Intestinal leptin showed increased expression in the group exposed to fructose.
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Affiliation(s)
- Ana Claudia Reis Schneider
- Programa de Pós-Graduação em Pediatria, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Carolina de Moura
- Laboratório de Fisiologia Comportamental e Metabólica, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiano Barbosa Carvalho
- Laboratório de Pesquisa em Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Thiago Alves
- Grupo de Pesquisa Experimental em Zebrafish/Biotério, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabio Meurer
- Campus Avançado de Jandaia do Sul, Universidade Federal do Paraná, Jandaia do Sul, Rio Grande do Sul, Brazil
| | - Marilene Porawski
- Programa de Pós-graduação em Hepatologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Themis Reverbel da Silveira
- Programa de Pós-Graduação em Pediatria, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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28
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Ma J, Hu X, Dai B, Wang Q, Wang H. Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways. PeerJ 2021; 9:e11259. [PMID: 33954053 PMCID: PMC8052978 DOI: 10.7717/peerj.11259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background Laryngeal squamous cell carcinoma (LSCC) is the second most aggressive head and neck squamous cell carcinoma. Although much work has been done to optimize its treatment, patients with LSCC still have poor prognosis. Therefore, figuring out differentially expressed genes (DEGs) contained in the progression of LSCC and employing them as potential therapeutic targets or biomarkers for LSCC is extremely meaningful. Methods Overlapping DEGs were screened from two standalone Gene Expression Omnibus datasets, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. By applying STRING and Cytoscape, a protein–protein network was built, and module analysis was carried out. The hub genes were selected by maximal clique centrality with the CytoHubba plugin of Cytoscape. UALCAN and GEPIA data were examined to validate the gene expression findings. Moreover, the connection of the hub genes with LSCC patient overall survival was studied employing The Cancer Genome Atlas. Then, western blot, qRT-PCR, CCK-8, wound healing and transwell assays were bring to use for further verify the key genes. Results A total of 235 DEGs were recorded, including 83 upregulated and 152 downregulated genes. A total of nine hub genes that displayed a high degree of connectivity were selected. UALCAN and GEPIA databases verified that these genes were highly expressed in LSCC tissues. High expression of the SPP1, SERPINE1 and Matrix metalloproteinases 1 (MMP1) genes was connected to worse prognosis in patients with LSCC, according to the GEPIA online tool. Western blot and qRT-PCR testify SPP1, SERPINE1 and MMP1 were upregulated in LSCC cells. Inhibition of SPP1, SERPINE1 and MMP1 suppressed cell proliferation, invasion and migration. Conclusion The work here identified effective and reliable diagnostic and prognostic molecular biomarkers by unified bioinformatics analysis and experimental verification, indicating novel and necessary therapeutic targets for LSCC.
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Affiliation(s)
- Jinhua Ma
- Department of Otolaryngology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Xiaodong Hu
- Department of Otolaryngology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Baoqiang Dai
- Department of Otolaryngology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Qiang Wang
- Department of Otolaryngology, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Hongqin Wang
- Department of Otolaryngology, Cangzhou Central Hospital, Cangzhou, Hebei, China
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29
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Disruptors, a new class of oligonucleotide reagents, significantly improved PCR performance on templates containing stable intramolecular secondary structures. Anal Biochem 2021; 624:114169. [PMID: 33766577 DOI: 10.1016/j.ab.2021.114169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/21/2022]
Abstract
Intramolecular secondary structures within templates have been shown to lower PCR performance. Whereas many approaches have been developed to mitigate such impairment on PCR, their effects can vary greatly depending on template sequences. Here we present a novel, universally effective approach to improve PCR performance involving specifically designed oligonucleotides called disruptors. A disruptor contained three functional components, an anchor designed to initiate template binding, an effector to disrupt intramolecular secondary structure, and a 3' blocker to prevent its elongation by DNA polymerase. A functional mechanism for a disruptor to improve PCR efficiency was proposed where anchor first binds to template followed by effector-mediated strand displacement to unwind intramolecular secondary structure. Such a mechanism was consistent with the observation that anchor played a more critical role for disruptor function. As an example of potential disruptor applications, inverted terminal repeat sequences of recombinant adeno-associated virus vectors were successfully amplified in the presence of disruptors despite their well-known reputation as some of the most difficult templates for PCR amplification and Sanger sequencing due to their ultra-stable T-shaped hairpin structures. In stark contrast, both DMSO and betaine, two PCR additives routinely used to facilitate PCR amplification and Sanger sequencing of GC-rich templates, did not demonstrate any improving effect.
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30
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Raza W, Guo J, Qadir MI, Bai B, Muhammad SA. qPCR Analysis Reveals Association of Differential Expression of SRR, NFKB1, and PDE4B Genes With Type 2 Diabetes Mellitus. Front Endocrinol (Lausanne) 2021; 12:774696. [PMID: 35046895 PMCID: PMC8761634 DOI: 10.3389/fendo.2021.774696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is a heterogeneous, metabolic, and chronic condition affecting vast numbers of the world's population. The related variables and T2DM associations have not been fully understood due to their diverse nature. However, functional genomics can facilitate understanding of the disease. This information will be useful in drug design, advanced diagnostic, and prognostic markers. AIM To understand the genetic causes of T2DM, this study was designed to identify the differentially expressed genes (DEGs) of the disease. METHODS We investigated 20 publicly available disease-specific cDNA datasets from Gene Expression Omnibus (GEO) containing several attributes including gene symbols and clone identifiers, GenBank accession numbers, and phenotypic feature coordinates. We analyzed an integrated system-level framework involving Gene Ontology (GO), protein motifs and co-expression analysis, pathway enrichment, and transcriptional factors to reveal the biological information of genes. A co-expression network was studied to highlight the genes that showed a coordinated expression pattern across a group of samples. The DEGs were validated by quantitative PCR (qPCR) to analyze the expression levels of case and control samples (50 each) using glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as the reference gene. RESULTS From the list of 50 DEGs, we ranked three T2DM-related genes (p < 0.05): SRR, NFKB1, and PDE4B. The enriched terms revealed a significant functional role in amino acid metabolism, signal transduction, transmembrane and intracellular transport, and other vital biological functions. DMBX1, TAL1, ZFP161, NFIC (66.7%), and NR1H4 (33.3%) are transcriptional factors associated with the regulatory mechanism. We found substantial enrichment of insulin signaling and other T2DM-related pathways, such as valine, leucine and isoleucine biosynthesis, serine and threonine metabolism, adipocytokine signaling pathway, P13K/Akt pathway, and Hedgehog signaling pathway. The expression profiles of these DEGs verified by qPCR showed a substantial level of twofold change (FC) expression (2-ΔΔCT) in the genes SRR (FC ≤ 0.12), NFKB1 (FC ≤ 1.09), and PDE4B (FC ≤ 0.9) compared to controls (FC ≥ 1.6). The downregulated expression of these genes is associated with pathophysiological development and metabolic disorders. CONCLUSION This study would help to modulate the therapeutic strategies for T2DM and could speed up drug discovery outcomes.
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Affiliation(s)
- Waseem Raza
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Jinlei Guo
- School of Medical Engineering, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Muhammad Imran Qadir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Baogang Bai
- School of Information and Technology, Wenzhou Business College, Wenzhou, China
- Engineering Research Center of Intelligent Medicine, Wenzhou, China
- The 1st School of Medical, School of Information and Engineering, The 1st Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Syed Aun Muhammad, ; Baogang Bai,
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Syed Aun Muhammad, ; Baogang Bai,
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Kučera R, Sčensná A, Miletín M, Zimčík P. The chromatographic behaviour of new double-labelled oligodeoxynucleotide probes containing azaphthalocyanine dye as a quencher with respect to evaluation of their purity. Biomed Chromatogr 2020; 35:e5033. [PMID: 33226652 DOI: 10.1002/bmc.5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/12/2020] [Accepted: 11/19/2020] [Indexed: 11/07/2022]
Abstract
The influence of experimental conditions on chromatographic behaviour of promising oligodeoxynucleotide double-labelled molecular probes containing an azaphthalocyanine macrocycle as a perspective dark quencher was studied. A recently introduced new stationary phase based on styrene-divinylbenzene copolymer was tested. The planar and hydrophobic structure of the azaphthalocyanine is considerably different from those of currently used fluorophores and quenchers. Thus, the most challenging issue was the separation of the double-labelled probe from its main impurity represented by a mono-labelled probe, containing only the azaphthalocyanine macrocycle. The absorbance measurement cannot simply determine this impurity, and its presence fundamentally compromises the biological assay. The commonly used gradient elution was not suitable and isocratic conditions seemed to be more appropriate. The azaphthalocyanine moiety influences the properties of the modified oligodeoxynucleotides substantially, and thus their chromatographic behaviour was determined predominantly by this quencher. Acetonitrile was the preferred organic solvent for the analysis of probes containing the azaphthalocyanine quencher and the effect of ion-pairing reagents was dependent on the probe structure. The temperature seemed to be an effective parameter for fine-tuning of the separation and mass transfer improvement. Generally, our findings could be helpful in method development for purity evaluation of double-labelled oligodeoxynucleotide probes and semipreparative methods.
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Affiliation(s)
- Radim Kučera
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Anna Sčensná
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Miroslav Miletín
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Petr Zimčík
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
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If Artificial In Vitro Microenvironment Can Influence Tumor Drug Resistance Network via Modulation of lncRNA Expression?-Comparative Analysis of Glioblastoma-Derived Cell Culture Models and Initial Tumors In Vivo. Cell Mol Neurobiol 2020; 42:1005-1020. [PMID: 33245508 PMCID: PMC8942942 DOI: 10.1007/s10571-020-00991-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022]
Abstract
The tumor resistance of glioblastoma cells in vivo is thought to be enhanced by their heterogeneity and plasticity, which are extremely difficult to curb in vitro. The external microenvironment shapes the molecular profile of tumor culture models, thus influencing potential therapy response. Our study examines the expression profile of selected lncRNAs involved in tumor resistance network in three different glioblastoma-derived models commonly utilized for testing drug response in vitro. Differential expression analysis revealed significant divergence in lncRNA profile between parental tumors and tumor-derived cell cultures in vitro, including the following particles: MALAT1, CASC2, H19, TUSC7, XIST, RP11-838N2.4, DLX6-AS1, GLIDR, MIR210HG, SOX2-OT. The examined lncRNAs influence the phenomenon of tumor resistance via their downstream target genes through a variety of processes: multi-drug resistance, epithelial-mesenchymal transition, autophagy, cell proliferation and viability, and DNA repair. A comparison of in vivo and in vitro expression identified differences in the levels of potential lncRNA targets, with the highest discrepancies detected for the MDR1, LRP1, BCRP and MRP1 genes. Co-expression analyses confirmed the following interrelations: MALAT1-TYMS, MALAT1-MRP5, H19-ZEB1, CASC2-VIM, CASC2-N-CAD; they additionally suggest the possibility of MALAT1-BCRP, MALAT1-mTOR and TUSC7-PTEN interconnections in glioblastoma. Although our results clearly demonstrate that the artificial ex vivo microenvironment changes the profile of lncRNAs related to tumor resistance, it is difficult to anticipate the final phenotypic effect, since this phenomenon is a complex one that involves a network of molecular interactions underlying a variety of cellular processes.
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Shehata HR, Newmaster SG. A Validated Real-Time PCR Method for the Specific Identification of Probiotic Strain Lactobacillus rhamnosus GG (ATCC 53103). J AOAC Int 2020; 103:1604-1609. [PMID: 33247747 DOI: 10.1093/jaoacint/qsaa063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Strain Lactobacillus rhamnosus GG is one of the best-studied and most widely used probiotic strains, with various health benefits. Because probiotic health benefits and safety are strain specific, the availability of a reliable assay for specific identification of Lactobacillus rhamnosus GG is vital to ensure probiotic efficacy. OBJECTIVE To design and validate a probe-based real-time PCR assay for specific identification of strain Lactobacillus rhamnosus GG. METHOD Rapid Annotation using Subsystem Technology (RAST) was used to find a unique sequence region in the genome of Lactobacillus rhamnosus GG. A probe-based assay was designed and evaluated for specificity, sensitivity, efficiency, repeatability, and reproducibility. RESULTS RAST identified a unique gene coding for a hypothetical protein in the genome of Lactobacillus rhamnosus GG. The assay successfully amplified all 22 target samples and did not amplify any of the 28 non-target strains, achieving 100% true positive and 0% false positive results. The Limit of Detection (LOD) was determined to be 0.001 ng. Reaction efficiency values, from three dilution series, were 96.4%, 93.3%, and 96.8% with R square values of 0.9974, 0.9981, and 0.9998, respectively. Relative standard deviation (RSD, %) of repeatability was below 1% and RSD of reproducibility was below 4%. CONCLUSIONS This Lactobacillus rhamnosus GG specific assay proved to be specific, sensitive, efficient, and reproducible. Since the assay was evaluated on two real-time PCR platforms, including a portable one, the assay can be used for onsite testing throughout the supply chain. HIGHLIGHTS The availability of validated and reliable assays for strain-specific identification plays a vital role in achieving compliance in probiotic products.
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Affiliation(s)
- Hanan R Shehata
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Cui M, Zhang Y. Advancing DNA Steganography with Incorporation of Randomness. Chembiochem 2020; 21:2503-2511. [PMID: 32270906 PMCID: PMC7497043 DOI: 10.1002/cbic.202000149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/08/2020] [Indexed: 11/29/2022]
Abstract
DNA has become a promising candidate as a future data storage medium; this makes DNA steganography indispensable in DNA data security. PCR primers are conventional secret keys in DNA steganography. Brute force testing of different primers will be extremely time consuming, and practically unaffordable when high-throughput sequencing is used. However, the encrypted information can be sequenced and read once the primers are intercepted. A new steganography approach is needed to make the DNA-encoded information safer, if not unhackable. Mixing information-carrying DNA with a partially degenerated DNA library containing single or multiple restriction sites, we have built an additional protective layer that can be removed by desired restriction enzymes as secondary secret keys. As PCR is inevitable for reading DNA-encrypted information, heating will cause reshuffling and generate endonuclease-resistant mismatched duplexes, especially for DNA with high sequence diversity. Consequently, with the incorporation of randomness, DNA steganography possesses both quantum key distribution (QKD)-like function for detecting PCR by an interceptor and a self-destructive property. It is noteworthy that the background noise generated through the protective layer is independent from any sequencing technology including Sanger and high-throughput sequencing. With a DNA ink incorporating the steganography, we have shown that the authenticity of a piece of writing can be confirmed only by authorized persons with knowledge of all embedded keys.
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Affiliation(s)
- Meiying Cui
- B CUBE Center for Molecular BioengineeringTechnische Universität DresdenTatzberg 4101307DresdenGermany
| | - Yixin Zhang
- B CUBE Center for Molecular BioengineeringTechnische Universität DresdenTatzberg 4101307DresdenGermany
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Liu Z, Sun J, Zhao G, Xiong S, Ma Y, Zheng M. Transient stem-loop structure of nucleic acid template may interfere with polymerase chain reaction through endonuclease activity of Taq DNA polymerase. Gene 2020; 764:145095. [PMID: 32866587 DOI: 10.1016/j.gene.2020.145095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
As a standard molecular biology technique, PCR uses DNA polymerase to detect, amplify and manipulate DNA targets. Due to its effect of exponential amplification, PCR can achieve high sensitivity required for detecting targets of low abundance. Therefore, it has become the method of choice for the majority of nucleic acid-based tests. In PCR reactions, DNA templates are first unwound into single strands, followed by a quick temperature drop when transient intramolecular secondary structures may form first within the single-stranded templates due to reaction kinetics. In this study, we showed that the adverse effects of stem-loop structures on PCR performance were directly correlated with their thermal stability. Moreover, fractions of intermediate PCR products of templates with stable stem-loop structures were significantly shorter than those without. It was further demonstrated that when encountering the duplex region of such a structure during the PCR extension step, the endonuclease activity of Taq DNA polymerase mediated by its 5'-3' exonuclease activity could digest template strand, resulting in stem-loop structure unwinding and subsequent completion of replication to produce truncated products. This work thus provided some new mechanistic insights into the complex nature of PCR assays, a frequently encountered but neglected aspect of this widely used technique.
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Affiliation(s)
- Zhaocheng Liu
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Jinli Sun
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guodong Zhao
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210009, China
| | - Shangmin Xiong
- Zhejiang University Kunshan Biotechnology Laboratory, Zhejiang University Kunshan Innovation Institute, Kunshan, Jiangsu 215300, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China.
| | - Yong Ma
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| | - Minxue Zheng
- University of Science and Technology of China, Hefei, Anhui 230027, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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36
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Shehata HR, Ragupathy S, Allen S, Leyer G, Newmaster SG. Real-Time PCR Assays for the Specific Identification of Probiotic Strains Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC (NCIMB 30242). Probiotics Antimicrob Proteins 2020; 13:837-846. [PMID: 32780278 DOI: 10.1007/s12602-020-09695-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The broad spectrum of health benefits attributed to probiotics has contributed to a rapid increase in the value of the probiotic market. Probiotic health benefits can be strain specific. Thus, strain-level identification of probiotic strains is of paramount importance to ensure probiotic efficacy. Both Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC (NCIMB 30242) strains have clinically proven health benefits; however, no assays were developed to enable strain-level identification of either of these strains. The objective of this study is to develop strain-specific PCR-based methods for Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC strains, and to validate these assays according to the guidelines for validating qualitative real-time PCR assays. Using RAST (Rapid Annotation using Subsystem Technology), unique sequence regions were identified in the genome sequences of both strains. Probe-based assays were designed and validated for specificity, sensitivity, efficiency, repeatability, and reproducibility. Both assays were specific to target strain with 100% true positive and 0% false positive rates. Reaction efficiency for both assays was in the range of 90 to 108% with R square values > 0.99. Repeatability and reproducibility were evaluated using five samples at three DNA concentrations each and relative standard deviation was < 4% for repeatability and < 8% for reproducibility. Both of the assays developed and validated in this study for the specific identification of Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC strains are specific, sensitive, and precise. These assays can be applied to evaluate and ensure compliance in probiotic products.
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Affiliation(s)
- Hanan R Shehata
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
| | - Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Shara Allen
- UAS Laboratories, 555 N. 72nd Ave, Wausau, WI, 54401, USA
| | - Gregory Leyer
- UAS Laboratories, 555 N. 72nd Ave, Wausau, WI, 54401, USA
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Lee JE, Mun H, Kim SR, Kim MG, Chang JY, Shim WB. A colorimetric Loop-mediated isothermal amplification (LAMP) assay based on HRP-mimicking molecular beacon for the rapid detection of Vibrio parahaemolyticus. Biosens Bioelectron 2020; 151:111968. [DOI: 10.1016/j.bios.2019.111968] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/21/2019] [Accepted: 12/14/2019] [Indexed: 12/20/2022]
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Geissler M, Brassard D, Clime L, Pilar AVC, Malic L, Daoud J, Barrère V, Luebbert C, Blais BW, Corneau N, Veres T. Centrifugal microfluidic lab-on-a-chip system with automated sample lysis, DNA amplification and microarray hybridization for identification of enterohemorrhagic Escherichia coli culture isolates. Analyst 2020; 145:6831-6845. [DOI: 10.1039/d0an01232g] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Automated workflow that starts with a colony isolate and ends with a fluorescence signal on a DNA microarray.
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Affiliation(s)
- Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Daniel Brassard
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Liviu Clime
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | | | - Burton W. Blais
- Ontario Laboratory Network
- Canadian Food Inspection Agency
- Ottawa
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
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Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, P. R. China
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40
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Mallik I, Fulladolsa AC, Yellareddygari SKR, Bittara FG, Charkowski AO, Gudmestad NC. Detection and Quantification of Spongospora subterranea Sporosori in Soil by Quantitative Real-Time PCR. PLANT DISEASE 2019; 103:3189-3198. [PMID: 31613190 DOI: 10.1094/pdis-05-19-1092-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Powdery scab on potato tubers is caused by the obligate soilborne biotroph Spongospora subterranea and is known to cause substantial losses in potato production. The pathogen also infects roots of susceptible hosts, forming galls which can negatively affect root function. S. subterranea is also the vector of Potato mop-top virus, which causes a tuber necrosis disease that can, depending on temperature and cultivar, render potato tubers unmarketable. In this study, we adapted a published protocol to develop a sensitive and robust quantitative real-time PCR (qPCR) assay using specific primers and probes for detecting and quantifying S. subterranea sporosori in soil types that differ in physical properties, including organic matter content and soil pH. For the first time, an external control was utilized and applied directly to the soil prior to DNA extraction, which facilitated normalization of S. subterranea sporosori soil levels from sample to sample. The duplex qPCR protocol was demonstrated to be highly sensitive, capable of detecting and quantifying as few as 1 sporosorus/g of soil, with consistently high qPCR efficiency and the coefficient of determination (R2) values ranging from 94 to 99% and 0.98 to 0.99, respectively. The protocol was successfully implemented in enumerating S. subterranea sporosori in naturally infested field soil collected from several states and in artificial potting mixes with high organic matter content ranging from 64 to 71%. The qPCR method developed can be useful for potato growers to avoid agricultural soils highly infested with S. subterranea and in the development of risk assessment models in the future that incorporate cultivar susceptibility to powdery scab and soil infestation levels.
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Affiliation(s)
- Ipsita Mallik
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Ana Cristina Fulladolsa
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523
| | | | - Francisco G Bittara
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Amy O Charkowski
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523
| | - Neil C Gudmestad
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
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Rapid Detection of Fetal Mendelian Disorders: Thalassemia and Sickle Cell Syndromes. Methods Mol Biol 2019. [PMID: 30506200 DOI: 10.1007/978-1-4939-8889-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The inherited disorders of hemoglobin synthesis constitute the most common monogenic diseases worldwide. The clinical severity of β-thalassemia major and the sickle cell syndromes targets them as priority genetic diseases for prevention programs, which incorporates population screening to identify heterozygotes, with the option of prenatal diagnosis for carrier couples. Rapid genotype characterization is fundamental in the diagnostic laboratory, especially when offering prenatal diagnosis. The application of real-time PCR provides a means for rapid and potentially high throughput assays, without compromising accuracy. It has several advantages over end-point PCR analysis, including the elimination of post-PCR processing steps and a wide dynamic range of detection with a high degree of sensitivity. Although there are over 200 mutations associated with the β-thalassemia and sickle cell syndromes, the relatively small size of the β-, HBB gene (less than 2000 base-pairs) and the close proximity of most mutations facilitates the design of a minimal number of real-time PCR assays using the LightCycler™ system, which are capable of detecting the majority of most common β-gene mutations world-wide. These assays are highly appropriate for rapid genotyping of parental and fetal DNA samples with respect to β-thalassemia and sickle cell syndromes.
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42
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Chu B, Yang L, Wang C, Gu Y, Yuan K, Wang R, Luo Y, Ma Z. Improved Evaluation of Wheat Cultivars (Lines) on Resistance to Puccinia striiformis f. sp. tritici Using Molecular Disease Index. PLANT DISEASE 2019; 103:1206-1212. [PMID: 30995150 DOI: 10.1094/pdis-07-18-1158-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is one of the most destructive diseases of wheat worldwide. Sichuan Province plays an important role in interregional epidemics in China. Application of host resistance is important in disease management, and efficient approaches to evaluate resistance level are necessary to obtain useful varieties. In this study, 100 wheat cultivars (lines) growing in Sichuan were selected to evaluate their resistance to stripe rust. Field experiments were conducted with a mixture of three P. striiformis f. sp. tritici races for inoculations at seeding and adult stages in the 2014 to 2015 season and the 2016 to 2017 season. Leaf samplings were conducted four times during the latent period at early growth stage of wheat. The sampled leaves were processed to extract DNA. The DNA of both wheat and P. striiformis f. sp. tritici was quantified using real-time quantitative polymerase chain reaction, and the molecular disease index (MDI) was used to evaluate the resistance level. The area under the disease progress curve in terms of disease index (AUDPC-DI) was obtained for each studied cultivar (line) in the fields. Among the 100 studied cultivars (lines), 61% of them showed seedling resistance, and 63 and 65% showed adult resistance in the 2014 to 2015 and 2016 to 2017 seasons, respectively, based on the infection type. High consistency in resistance grouping by cluster analysis as the percentage of the studied cultivar (line) belonging to the same group based on AUDPC-DI data and based on MDI data was obtained. The correlations between AUDPC-DI and MDI from samples collected on 9 and 14 or 15 days after inoculation during the latent period were all significant at P < 0.01. This study provided a new and efficient method for evaluation of varietal resistance to wheat stripe rust.
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Affiliation(s)
- Bingyao Chu
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
| | - Lujia Yang
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
| | - Cuicui Wang
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
| | - Yilin Gu
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
| | - Kai Yuan
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
| | - Rui Wang
- 2 Kaifeng Experimental Station of China Agricultural University, Kaifeng 475004, China
| | - Yong Luo
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
| | - Zhanhong Ma
- 1 Department of Plant Pathology, Ministry of Agriculture and Rural Affairs (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; and
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Witusik-Perkowska M, Zakrzewska M, Jaskolski DJ, Liberski PP, Szemraj J. Artificial microenvironment of in vitro glioblastoma cell cultures changes profile of miRNAs related to tumor drug resistance. Onco Targets Ther 2019; 12:3905-3918. [PMID: 31190889 PMCID: PMC6535444 DOI: 10.2147/ott.s190601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/09/2019] [Indexed: 12/26/2022] Open
Abstract
Purpose: The in vitro environment can influence not only the molecular background of glioblastoma drug-resistance and treatment efficiency, but also the mechanisms and pathways of cell death. Both crucial molecular pathways and the deregulation of miRNAs are thought to participate in tumor therapy-resistance. The aim of our study is to examine the potential influence of ex vivo conditions on the expression of miRNAs engaged in the machinery of tumor-drug resistance, since in vitro models are commonly used for testing new therapeutics. Methods: Glioblastoma-derived cells, cultured under three different sets of conditions, were used as experimental models in vitro. The expression of 84 miRNAs relevant to brain tumorigenesis was evaluated by multi-miRNA profiling for initial tumors and their corresponding cultures. Finally, the expression of selected miRNAs related to temozolomide-resistance (miR-125b, miR-130a, miR-21, miR-221, miR-222, miR-31, miR-149, miR-210, miR-181a) was assessed by real-time PCR for each tumor and neoplastic cells in cultures. Results: Our results demonstrate significant discrepancies in the expression of several miRNAs between tumor cells in vivo and in vitro, with miR-130a, miR-221, miR-31, miR-21, miR-222, miR-210 being the most marked. Also differences were observed between particular models in vitro. The results of computational analysis revealed the interplay between examined miRNAs and their targets involved in processes of glioblastoma chemosensitivity, including the genes relevant to temozolomide response (MGMT, PTEN, MDM2, TP53, BBC3A). Conclusion: The artificial environment may influence the selective proliferation of cell populations carrying specific patterns of miRNAs and/or the phenotype of neoplastic cells (eg differentiation) by the action of molecular events including miRNAs. These phenomena may influence the tumor-responsiveness to particular drugs, disturbing the evaluation of their efficacy in vitro, with unpredictable results caused by the interdependency of molecular pathways.
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Affiliation(s)
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Dariusz J Jaskolski
- Department of Neurosurgery and Neurooncology, Medical University of Lodz, Barlicki University Hospital, Lodz, Poland
| | - Pawel P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
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Pallu J, Rabin C, Creste G, Branca M, Mavré F, Limoges B. Exponential Molecular Amplification by H
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‐Mediated Autocatalytic Deprotection of Boronic Ester Probes to Redox Cyclers. Chemistry 2019; 25:7534-7546. [DOI: 10.1002/chem.201900627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 02/23/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Justine Pallu
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Charlie Rabin
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Geordie Creste
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Mathieu Branca
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - François Mavré
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - Benoît Limoges
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRSUniversité Paris Diderot, Sorbonne Paris Cité 15, rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
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A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules. Biosens Bioelectron 2018; 127:108-117. [PMID: 30594890 DOI: 10.1016/j.bios.2018.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023]
Abstract
Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photoisomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.
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Shoute LCT, Loppnow GR. Characterization of the binding interactions between EvaGreen dye and dsDNA. Phys Chem Chem Phys 2018; 20:4772-4780. [PMID: 29380825 DOI: 10.1039/c7cp06058k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Understanding the dsDNA·EG binding interaction is important because the EvaGreen (EG) dye is increasingly used in real-time quantitative polymerase chain reaction, high resolution melting analysis, and routine quantification of DNA. In this work, a binding isotherm for the interactions of EG with duplex DNA (poly-dA17·poly-dT17) has been determined from the absorption and fluorescence spectra of the EG and dsDNA·EG complex. The isotherm has a sigmoidal shape and can be modeled with the Hill equation, indicating positive cooperativity for the binding interaction. A Scatchard plot of the binding data yields a concave-down curve in agreement with the Hill analysis of the binding isotherm for a positive cooperative binding interaction. Analysis of the Scatchard plot with the modified McGhee and von Hippel model for a finite one-dimensional homogeneous lattice and nonspecific binding of ligands to duplex DNA yields the intrinsic binding constant, the number of lattice sites occluded by a bound ligand, and the cooperativity parameter of 3.6 × 105 M-1, 4.0, and 8.1, respectively. The occluded site size of 4 indicates that moieties of the EG intercalate into the adjacent base pairs of the duplex DNA with a gap of 1 intercalation site between EG binding sites, as expected for a bifunctional molecule. Interestingly, at high [EG]/[base pair], the intercalation is disrupted. A model is proposed based on the fluorescence spectrum where the formation of anti-parallel stacked chains of EGs bound externally to the duplex DNA occur at these high ratios.
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Affiliation(s)
- L C T Shoute
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
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Chowdhury G, Stine OC, Rajendran K, Mukhopadhyay AK, Okamoto K, Ramamurthy T. Detection of Uncommon Enteric Bacterial Pathogens from Acute Diarrheal Specimens Using SYBR-Green Real Time PCR. Jpn J Infect Dis 2018; 72:88-93. [PMID: 30381678 DOI: 10.7883/yoken.jjid.2018.142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Acute diarrheal disease is a major health problem, and the second most common cause of death in children under 5 years of age. Conventional diagnostic methods are laborious, time consuming, and occasionally inaccurate. We used SYBR-Green real-time PCR for the detection of 10 uncommon bacterial pathogens using fecal specimens from acute diarrheal patients. In the SYBR-Green real-time PCR assay, the products formed were identified based on a melting point temperature curve analysis, and the assay was validated with the respective reference strain. In a retrospective study, we tested 1,184 stool specimens previously examined using conventional culture methods. Enterotoxigenic Bacteriodes fragilis was detected in 6.7% of the samples followed by enterotoxigenic Bacillus cereus (5.1%), Clostridium perfringens (3.9%), and Aeromonas hydrophila (3.8%). In the prospective study, A. hydrophila, Staphylococcus aureus, and C. perfringens were predominantly detected in 11 > 5 years of age, using real-time PCR. The real-time PCR assay is comprehensive, rapid, accurate, and well suited for surveillance or diagnostic purposes to detect uncommon bacterial pathogens, and should be useful in initiating appropriate care and thereby reducing patient risk.
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Affiliation(s)
- Goutam Chowdhury
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases
| | - Oscar C Stine
- Department of Epidemiology and Public Health, University of Maryland
| | - Krishnan Rajendran
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases
| | | | - Keinosuke Okamoto
- Research Center of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases
| | - Thandavarayan Ramamurthy
- Department of Bacteriology, National Institute of Cholera and Enteric Diseases.,Translational Health Science and Technology Institute
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The Streptococcus pyogenes fibronectin/tenascin-binding protein PrtF.2 contributes to virulence in an influenza superinfection. Sci Rep 2018; 8:12126. [PMID: 30108238 PMCID: PMC6092322 DOI: 10.1038/s41598-018-29714-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/13/2018] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV) and Streptococcus pyogenes (the group A Streptococcus; GAS) are important contributors to viral-bacterial superinfections, which result from incompletely defined mechanisms. We identified changes in gene expression following IAV infection of A549 cells. Changes included an increase in transcripts encoding proteins with fibronectin-type III (FnIII) domains, such as fibronectin (Fn), tenascin N (TNN), and tenascin C (TNC). We tested the idea that increased expression of TNC may affect the outcome of an IAV-GAS superinfection. To do so, we created a GAS strain that lacked the Fn-binding protein PrtF.2. We found that the wild-type GAS strain, but not the mutant, co-localized with TNC and bound to purified TNC. In addition, adherence of the wild-type strain to IAV-infected A549 cells was greater compared to the prtF.2 mutant. The wild-type strain was also more abundant in the lungs of mice 24 hours after superinfection compared to the mutant strain. Finally, all mice infected with IAV and the prtF.2 mutant strain survived superinfection compared to only 42% infected with IAV and the parental GAS strain, indicating that PrtF.2 contributes to virulence in a murine model of IAV-GAS superinfection.
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Pan S, Li S, Hu Y, Zhang H, Liu Y, Jiang H, Fang M, Li Z, Xu K, Zhang H, Lin Z, Xiao J. Resveratrol post-treatment protects against neonatal brain injury after hypoxia-ischemia. Oncotarget 2018; 7:79247-79261. [PMID: 27811363 PMCID: PMC5346711 DOI: 10.18632/oncotarget.13018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/19/2016] [Indexed: 11/25/2022] Open
Abstract
Neonatal hypoxic-ischemic brain injury is a devastating disease with limited treatment options. Preventive treatment with resveratrol has indicated to be well tolerated and has lower toxicity in both experimental models and human patients. However, whether resveratrol administration post-hypoxic-ischemic protects against neonatal hypoxic-ischemic injury is not known. Here we reported that post-treatment with resveratrol significantly reduced brain damage at 7-day after the injury. We found that resveratrol reduced the expression levels of key inflammatory factors at the mRNA and protein levels, and at least partially via inhibiting microglia activation. Moreover, resveratrol exerted an anti-apoptotic effect, as assessed by TUNEL staining, and altered the expression of the apoptosis-related genes Bax, Bcl-2 and caspase3. Our data indicate that post-treatment with resveratrol protects against neonatal hypoxic-ischemic brain injury and suggest a promising therapeutic strategy to this disease.
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Affiliation(s)
- Shulin Pan
- Department of Neonatology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Songlin Li
- The Institute of Life Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yingying Hu
- Department of Neonatology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Hao Zhang
- Department of Neonatology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Yanlong Liu
- The School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Huai Jiang
- Department of Neonatology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Mingchu Fang
- Department of Neonatology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Zhengmao Li
- The School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Kebin Xu
- The School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Hongyu Zhang
- The School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
| | - Zhenlang Lin
- Department of Neonatology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Jian Xiao
- The School of Pharmacy, Wenzhou Medical University, Wenzhou 325035, China
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Gaudreault C, Salvas J, Sirois J. Savitzky-Golay smoothing and differentiation for polymerase chain reaction quantification. Biochem Cell Biol 2017; 96:380-389. [PMID: 29190123 DOI: 10.1139/bcb-2016-0194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In quantitative PCR (qPCR), replicates can minimize the impact of intra-assay variation; however, inter-assay variations must be minimized to obtain a robust quantification method. The method proposed in this study uses Savitzky-Golay smoothing and differentiation (SGSD) to identify a derivative-maximum-based cycle of quantification. It does not rely on curve modeling, as is the case with many existing techniques. PCR fluorescence data sets challenged for inter-assay variations (different thermocycler units, different reagents batches, different operators, different standard curves, and different labs) were used for the evaluation. The algorithm was compared with a four-parameter logistic model (4PLM) method, the Cy0 method, and the threshold method. The SGSD method compared favourably with all methods in terms of inter-assay variation. SGSD was statistically different from the 4PLM (P = 0.03), Cy0 (P = 0.05), and threshold (P = 0.004) methods on relative error comparison basis. For intra-assay variations, SGSD outperformed the threshold method (P = 0.005) and equalled the 4PLM and Cy0 methods (P > 0.05) on relative error basis. Our results demonstrate that the SGSD method could potentially be an alternative to sigmoid modeling based methods (4PLM and Cy0) when PCR data are challenged for inter-assay variations.
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Affiliation(s)
- Charles Gaudreault
- a Université de Sherbrooke, Engineering Faculty, 2500 boul. de l'université, QC J1K 2R1, Canada
| | - Joanny Salvas
- b Process Analytical Science Group, Pfizer Montréal, 1025 boul. Marcel-Laurin, Montréal, QC H4R 1J6, Canada
| | - Joël Sirois
- a Université de Sherbrooke, Engineering Faculty, 2500 boul. de l'université, QC J1K 2R1, Canada
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