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Serpieri R, Franchi F. Resilience of DNA chains to molecular fracture after PCR heating cycles and implications on PCR reliability. Q Rev Biophys 2024; 57:e8. [PMID: 39143895 DOI: 10.1017/s0033583524000064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Soon after its introduction in 1987, polymerase chain reaction (PCR) has become a technique widely employed in diagnostic medical devices and forensic science with the intention of amplifying genetic information. PCR prescribes that each of its cycles must include a heating subprocess at 95 °C or more (denominated DNA denaturation and provided for allowing a claimed orderly separation of the two complementary nucleotides strands), which can produce significant damage to DNA, caused by high-speed collisions with surrounding molecules. Since such disruption should be prevented in order to reliably employ PCR, a study of the mechanics of such loss of structural integrity is herein presented, preceded by a review of the fundamental literature which has elucidated the effects of molecular agitation on DNA fragmentation. The main conclusion of this retrospective survey is that the body of examined theoretical and experimental evidence consistently and redundantly confirms scarce resilience and significant loss of structural integrity when DNA is heated at temperatures above 90 °C, even for 1 minute. Such conclusion contradicts the claimed paradigm of PCR fidelity and raises the concern that, at least for long sequences, if PCR can amplify some information, such amplified information may be unreliable for diagnostic or forensic applications, since it originates from sequences of nucleotides subjected to random fragmentation and reaggregation. Such a low-reliability scenario should be preventively considered in the various fields where DNA amplification methodologies are employed which provide for high-temperature heating under conditions equal to or similar to those prescribed by the PCR protocols reviewed in this study.
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Affiliation(s)
- Roberto Serpieri
- Dipartimento di Architettura e Disegno Industriale, Universita della Campania "Luigi Vanvitelli," Aversa, Italy
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2
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Rolando JC, Melkonian AV, Walt DR. The Present and Future Landscapes of Molecular Diagnostics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:459-474. [PMID: 38360553 DOI: 10.1146/annurev-anchem-061622-015112] [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: 02/17/2024]
Abstract
Nucleic acid testing is the cornerstone of modern molecular diagnostics. This review describes the current status and future directions of molecular diagnostics, focusing on four major techniques: polymerase chain reaction (PCR), next-generation sequencing (NGS), isothermal amplification methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods. We explore the advantages and limitations of each technique, describe how each overlaps with or complements other techniques, and examine current clinical offerings. This review provides a broad perspective into the landscape of molecular diagnostics and highlights potential future directions in this rapidly evolving field.
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Affiliation(s)
- Justin C Rolando
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Arek V Melkonian
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - David R Walt
- 1Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA;
- 2Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
- 3Harvard Medical School, Harvard University, Boston, Massachusetts, USA
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3
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Sondhi P, Adeniji T, Lingden D, Stine KJ. Advances in endotoxin analysis. Adv Clin Chem 2024; 118:1-34. [PMID: 38280803 DOI: 10.1016/bs.acc.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
The outer membrane of gram-negative bacteria is primarily composed of lipopolysaccharide (LPS). In addition to protection, LPS defines the distinct serogroups used to identify bacteria specifically. Furthermore, LPS also act as highly potent stimulators of innate immune cells, a phenomenon essential to understanding pathogen invasion in the body. The complex multi-step process of LPS binding to cells involves several binding partners, including LPS binding protein (LBP), CD14 in both membrane-bound and soluble forms, membrane protein MD-2, and toll-like receptor 4 (TLR4). Once these pathways are activated, pro-inflammatory cytokines are eventually expressed. These binding events are also affected by the presence of monomeric or aggregated LPS. Traditional techniques to detect LPS include the rabbit pyrogen test, the monocyte activation test and Limulus-based tests. Modern approaches are based on protein, antibodies or aptamer binding. Recently, novel techniques including electrochemical methods, HPLC, quartz crystal microbalance (QCM), and molecular imprinting have been developed. These approaches often use nanomaterials such as gold nanoparticles, quantum dots, nanotubes, and magnetic nanoparticles. This chapter reviews current developments in endotoxin detection with a focus on modern novel techniques that use various sensing components, ranging from natural biomolecules to synthetic materials. Highly integrated and miniaturized commercial endotoxin detection devices offer a variety of options as the scientific and technologic revolution proceeds.
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Affiliation(s)
- Palak Sondhi
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States
| | - Taiwo Adeniji
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States
| | - Dhanbir Lingden
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States
| | - Keith J Stine
- Department of Chemistry and Biochemistry, University of Missouri-Saint Louis, Saint Louis, MO, United States.
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4
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Hassan S, Bahar R, Johan MF, Mohamed Hashim EK, Abdullah WZ, Esa E, Abdul Hamid FS, Zulkafli Z. Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia. Diagnostics (Basel) 2023; 13:diagnostics13030373. [PMID: 36766477 PMCID: PMC9914462 DOI: 10.3390/diagnostics13030373] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Thalassemia is one of the most heterogeneous diseases, with more than a thousand mutation types recorded worldwide. Molecular diagnosis of thalassemia by conventional PCR-based DNA analysis is time- and resource-consuming owing to the phenotype variability, disease complexity, and molecular diagnostic test limitations. Moreover, genetic counseling must be backed-up by an extensive diagnosis of the thalassemia-causing phenotype and the possible genetic modifiers. Data coming from advanced molecular techniques such as targeted sequencing by next-generation sequencing (NGS) and third-generation sequencing (TGS) are more appropriate and valuable for DNA analysis of thalassemia. While NGS is superior at variant calling to TGS thanks to its lower error rates, the longer reads nature of the TGS permits haplotype-phasing that is superior for variant discovery on the homologous genes and CNV calling. The emergence of many cutting-edge machine learning-based bioinformatics tools has improved the accuracy of variant and CNV calling. Constant improvement of these sequencing and bioinformatics will enable precise thalassemia detections, especially for the CNV and the homologous HBA and HBG genes. In conclusion, laboratory transiting from conventional DNA analysis to NGS or TGS and following the guidelines towards a single assay will contribute to a better diagnostics approach of thalassemia.
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Affiliation(s)
- Syahzuwan Hassan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | - Rosnah Bahar
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Muhammad Farid Johan
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | | | - Wan Zaidah Abdullah
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ezalia Esa
- Institute for Medical Research, Shah Alam 40170, Malaysia
| | | | - Zefarina Zulkafli
- Department of Hematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
- Correspondence:
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5
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Wang K, Sang B, He L, Guo Y, Geng M, Zheng D, Xu X, Wu W. Construction of dPCR and qPCR integrated system based on commercially available low-cost hardware. Analyst 2022; 147:3494-3503. [PMID: 35772342 DOI: 10.1039/d2an00694d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent quantitative PCR (qPCR) and digital PCR (dPCR) are two mainstream nucleic acid quantification technologies. However, commercial dPCR and qPCR instruments have a low integration, a high price, and a large footprint. To solve these shortcomings, we introduce a compound PCR system with both qPCR and dPCR functions. All the hardware used in this compound PCR system is commercially available and low-cost, and free software was used to realize the absolute quantification of nucleic acids. The compound PCR provides two working modes. In the qPCR mode, thermal cycling is realized by controlling the reciprocating motion of the x axis. The heating rate is 1.25 °C s-1 and the cooling rate is 1.75 °C s-1. We performed amplification experiments of the PGEM-3zf (+)1 gene. The performance level was similar to commercial qPCR instruments. In the dPCR mode, the heating rate is 0.5 °C s-1 and the cooling rate is 0.6 °C s-1. We performed the UPE-Q gene amplification and used the sequential actions of the two-dimensional mechanical sliders to scan the reaction products and used the method of regional statistics and back-inference threshold to get test results. The result we got was 1208 copies per μL-1, which was similar to expectations.
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Affiliation(s)
- Kangning Wang
- Institute of biological and medical engineering, Guangdong Academy of Sciences, China.
| | - Benliang Sang
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Limin He
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Yu Guo
- School of Mechanical and Electrical Engineering, Guangdong University of Technology, China
| | - Mingkun Geng
- Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dezhou Zheng
- College of Applied Physics and Materials, Wuyi University, China
| | - Xiaolong Xu
- School of Biotechnology and Health Sciences, Wuyi University, China
| | - Wenming Wu
- Institute of biological and medical engineering, Guangdong Academy of Sciences, China.
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6
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Somssich M. The Dawn of Plant Molecular Biology: How Three Key Methodologies Paved the Way. Curr Protoc 2022; 2:e417. [PMID: 35441802 DOI: 10.1002/cpz1.417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The adoption of Arabidopsis thaliana in the 1980s as a universal plant model finally enabled researchers to adopt and take full advantage of the molecular biology tools and methods developed in the bacterial and animal fields since the early 1970s. It further brought the plant sciences up to speed with other research fields, which had been employing widely accepted model organisms for decades. In parallel with this major development, the concurrent establishment of the plant transformation methodology and the description of the cauliflower mosaic virus (CaMV) 35S promoter enabled scientists to create robust transgenic plant lines for the first time, thereby providing a valuable tool for studying gene function. The ability to create transgenic plants launched the plant biotechnology sector, with Monsanto and Plant Genetic Systems developing the first herbicide- and pest-tolerant plants, initiating a revolution in the agricultural industry. Here I review the major developments over a less than 10-year span and demonstrate how they complemented each other to trigger a revolution in plant molecular biology and launch an era of unprecedented progress for the whole plant field. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Marc Somssich
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
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Van Gelder RN. Molecular Diagnostics for Ocular Infectious Diseases: LXXVIII Edward Jackson Memorial Lecture. Am J Ophthalmol 2022; 235:300-312. [PMID: 34921773 PMCID: PMC8863649 DOI: 10.1016/j.ajo.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 11/01/2022]
Abstract
PURPOSE To review the use of molecular diagnostic techniques in the management of ocular infectious disease. DESIGN Retrospective review. METHODS A combination of literature review and personal recollections are used. RESULTS Although the broad term molecular diagnostics may encompass techniques to identify pathogens via protein or metabolomic signatures, this review concentrates on detection of pathogen nucleic acid as an indicator of infection. The introduction of the polymerase chain reaction (PCR) in 1985 opened a new era in analysis of nucleic acids. This technique was soon applied to the detection of potential pathogen DNA and RNA, including viruses, bacteria, and parasites in infectious eye disease. Advances in PCR have allowed class-specific diagnostics (ie, pan-bacterial and pan-fungal), quantitation of pathogen DNA, and multiplexed testing. The Human Genome Project in the early 2000s greatly accelerated development of DNA sequencers, ushering in the era of "Next Generation Sequencing" and permitting pathogen-agnostic methods for the detection of potential infectious agents. Most recently, new technologies such as nanopore sequencing have reduced both cost and equipment requirements for whole-genome sequencing; when coupled with real-time sequence analysis methods, these methods offer the promise of true, real-time, point-of-service ocular infectious disease diagnostics. CONCLUSIONS Molecular methods for pathogen detection have greatly advanced the diagnosis of ocular infectious disease. Further methodologic advances will have a direct impact on the management of these conditions.
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Affiliation(s)
- Russell N Van Gelder
- From the Departments of Ophthalmology, Biological Structure, and Laboratory Medicine and Pathology, and Roger and Angie Karalis Johnson Retina Center, University of Washington School of Medicine, Seattle, Washington, USA.
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8
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RT-qPCR Detection of SARS-CoV-2: No Need for a Dedicated Reverse Transcription Step. Int J Mol Sci 2022; 23:ijms23031303. [PMID: 35163227 PMCID: PMC8835954 DOI: 10.3390/ijms23031303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
Abstract
Reverse transcription of RNA coupled to amplification of the resulting cDNA by the polymerase chain reaction (RT-PCR) is one of the principal molecular technologies in use today, with applications across all areas of science and medicine. In its real-time, fluorescence-based usage (RT-qPCR), it has long been a core technology driving the accurate, rapid and sensitive laboratory diagnosis of infectious diseases. However, RT-qPCR protocols have changed little over the past 30 years, with the RT step constituting a significant percentage of the time taken to complete a typical RT-qPCR assay. When applied to research investigations, reverse transcription has been evaluated by criteria such as maximum yield, length of transcription, fidelity, and faithful representation of an RNA pool. Crucially, however, these are of less relevance in a diagnostic RT-PCR test, where speed and sensitivity are the prime RT imperatives, with specificity contributed by the PCR component. We propose a paradigm shift that omits the requirement for a separate high-temperature RT step at the beginning of an RT-qPCR assay. This is achieved by means of an innovative protocol that incorporates suitable reagents with a revised primer and amplicon design and we demonstrate a proof of principle that incorporates the RT step as part of the PCR assay setup at room temperature. Use of this modification as part of a diagnostic assay will of course require additional characterisation, validation and optimisation of the PCR step. Combining this revision with our previous development of fast qPCR protocols allows completion of a 40 cycle RT-qPCR run on a suitable commercial instrument in approximately 15 min. Even faster times, in combination with extreme PCR procedures, can be achieved.
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9
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Danilova VM, Matyshevska OP, Komisarenko SV. Nobel Prize laureate Kary Mullis and the polymerase chain reaction (PCR). UKRAINIAN BIOCHEMICAL JOURNAL 2021. [DOI: 10.15407/ubj93.05.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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10
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Abstract
The most commonly used molecular diagnostic technique is the polymerase chain reaction (PCR). PCR detects a short section of genetic code of interest, a cancer gene, human mRNA or a pathogen's genome. It is used by every specialty in medicine and surgery, with increasing frequency and importance. In this article, the history, steps of the cycle, uses, forms, advantages and disadvantages of PCR are discussed. With the SARS coronavirus-2 pandemic having such an enormous impact on the delivery of elective surgery, decisions to proceed or defer are made by surgeons on a daily basis, based on PCR results. An understanding of these results is provided, what they tell us, what they do not and what other information is required to make these decisions. It is imperative to also look beyond PCR results, seeing the patient within the context of their symptoms, other pathology and imaging results, with the assistance of a medical virologist or microbiologist, in complex cases.
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Affiliation(s)
- Adhyana Mahanama
- is a Senior Clinical Fellow in Medical Virology at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared.,is a Consultant Medical Virologist at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared
| | - Eleri Wilson-Davies
- is a Senior Clinical Fellow in Medical Virology at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared.,is a Consultant Medical Virologist at University Hospital Southampton, Southampton, UK. Conflicts of interest: none declared
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11
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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Mittelberger C, Obkircher L, Oberkofler V, Ianeselli A, Kerschbamer C, Gallmetzer A, Reyes-Dominguez Y, Letschka T, Janik K. Development of a universal endogenous qPCR control for eukaryotic DNA samples. PLANT METHODS 2020; 16:53. [PMID: 32322292 PMCID: PMC7160944 DOI: 10.1186/s13007-020-00597-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Phytoplasma are obligate intracellular plant-pathogenic bacteria that infect a broad range of plant species and are transmitted by different insect species. Quantitative real-time PCR (qPCR) is one of the most commonly used techniques for pathogen detection, especially for pathogens that cannot be cultivated outside their host like phytoplasma. PCR analysis requires the purification of total DNA from the sample and subsequent amplification of pathogen DNA with specific primers. The purified DNA contains mainly host DNA and only a marginal proportion is of phytoplasmal origin. Therefore, detection of phytoplasma DNA in a host DNA background must be sensitive, specific and reliable and is highly dependent on the quality and concentration of the purified DNA. DNA quality and concentration and the presence of PCR-inhibitors therefore have a direct impact on pathogen detection. Thus, it is indispensable for PCR-based diagnostic tests to validate the DNA preparation and DNA integrity before interpreting diagnostic results, especially in case that no pathogen DNA is detected. The use of an internal control allows to evaluate DNA integrity and the detection of PCR-inhibiting substances. Internal controls are generally host-specific or limited to a defined group of related species. A control suitable for the broad range of phytoplasma hosts comprising different insect and plant species is still missing. RESULTS We developed a primer and probe combination that allows amplification of a conserved stretch of the eukaryotic 28S rDNA gene. The developed endogenous qPCR control serves as a DNA quality control and allows the analysis of different eukaryotic host species, including plants, insects, fish, fungi, mammals and human with a single primer/probe set in single- or multiplex assays. CONCLUSIONS Quality and performance control is indispensable for pathogen detection by qPCR. Several plant pathogens are transmitted by insects and have a broad range of host species. The newly developed endogenous control can be used with all so far tested eukaryotic species and since multiplexing is possible, the described primer and probe set can be easily combined with other PCR-based pathogen detection systems.
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Affiliation(s)
- Cecilia Mittelberger
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Lisa Obkircher
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Vicky Oberkofler
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Alan Ianeselli
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Christine Kerschbamer
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Andreas Gallmetzer
- Virology and Diagnostics, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Yazmid Reyes-Dominguez
- Virology and Diagnostics, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Thomas Letschka
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
| | - Katrin Janik
- Applied Genomics and Molecular Biology, Institute for Plant Health, Laimburg Research Centre, Pfatten, Italy
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13
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Feeney O, Cockbain J, Morrison M, Diependaele L, Van Assche K, Sterckx S. Patenting Foundational Technologies: Lessons From CRISPR and Other Core Biotechnologies. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2018; 18:36-48. [PMID: 31159699 DOI: 10.1080/15265161.2018.1531160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 2012, a new and promising gene manipulation technique, CRISPR-Cas9, was announced that seems likely to be a foundational technique in health care and agriculture. However, patents have been granted. As with other technological developments, there are concerns of social justice regarding inequalities in access. Given the technologies' "foundational" nature and societal impact, it is vital for such concerns to be translated into workable recommendations for policymakers and legislators. Colin Farrelly has proposed a moral justification for the use of patents to speed up the arrival of technology by encouraging innovation and investment. While sympathetic to his argument, this article highlights a number of problems. By examining the role of patents in CRISPR and in two previous foundational technologies, we make some recommendations for realistic and workable guidelines for patenting and licensing.
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14
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Gauthier J, Vincent AT, Charette SJ, Derome N. A brief history of bioinformatics. Brief Bioinform 2018; 20:1981-1996. [DOI: 10.1093/bib/bby063] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
AbstractIt is easy for today’s students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. The foundations of bioinformatics were laid in the early 1960s with the application of computational methods to protein sequence analysis (notably, de novo sequence assembly, biological sequence databases and substitution models). Later on, DNA analysis also emerged due to parallel advances in (i) molecular biology methods, which allowed easier manipulation of DNA, as well as its sequencing, and (ii) computer science, which saw the rise of increasingly miniaturized and more powerful computers, as well as novel software better suited to handle bioinformatics tasks. In the 1990s through the 2000s, major improvements in sequencing technology, along with reduced costs, gave rise to an exponential increase of data. The arrival of ‘Big Data’ has laid out new challenges in terms of data mining and management, calling for more expertise from computer science into the field. Coupled with an ever-increasing amount of bioinformatics tools, biological Big Data had (and continues to have) profound implications on the predictive power and reproducibility of bioinformatics results. To overcome this issue, universities are now fully integrating this discipline into the curriculum of biology students. Recent subdisciplines such as synthetic biology, systems biology and whole-cell modeling have emerged from the ever-increasing complementarity between computer science and biology.
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Affiliation(s)
- Jeff Gauthier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030, av. de la Médecine, Québec, Canada
| | - Antony T Vincent
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, 531 boul. des Prairies, Laval, QC, Canada
| | - Steve J Charette
- Centre de Recherche de l'Institut, Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), 2725 Chemin Sainte-Foy, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030, av. de la Médecine, Québec, Canada
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15
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Abstract
Elegance is a prized quality in science that is associated with simplicity and explanatory power. This essay considers the qualities that make a scientific model, experiment, method, or theory "elegant," with a focus on the life sciences. We propose a definition of elegance that includes clarity, cleverness, correctness, explanatory power, parsimony, and beauty. The pursuit of elegance can improve the quality of science, but elegance must be pursued with caution, as the truth is sometimes inelegant.
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16
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Urnov FD. Genome Editing B.C. (Before CRISPR): Lasting Lessons from the “Old Testament”. CRISPR J 2018; 1:34-46. [DOI: 10.1089/crispr.2018.29007.fyu] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Fyodor D. Urnov
- Altius Institute for Biomedical Sciences, Seattle, Washington
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17
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18
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Bustin SA, Wittwer CT. MIQE: A Step Toward More Robust and Reproducible Quantitative PCR. Clin Chem 2017; 63:1537-1538. [PMID: 28606913 DOI: 10.1373/clinchem.2016.268953] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 01/27/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Stephen A Bustin
- Faculty of Medical Science, Anglia Ruskin University, Chelmsford, UK;
| | - Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT
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19
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Collier R, Dasgupta K, Xing YP, Hernandez BT, Shao M, Rohozinski D, Kovak E, Lin J, de Oliveira MLP, Stover E, McCue KF, Harmon FG, Blechl A, Thomson JG, Thilmony R. Accurate measurement of transgene copy number in crop plants using droplet digital PCR. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1014-1025. [PMID: 28231382 DOI: 10.1111/tpj.13517] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/14/2017] [Accepted: 02/15/2017] [Indexed: 05/22/2023]
Abstract
Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species.
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Affiliation(s)
- Ray Collier
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Kasturi Dasgupta
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Yan-Ping Xing
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Bryan Tarape Hernandez
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Min Shao
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Dominica Rohozinski
- Plant Gene Expression Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Emma Kovak
- Plant Gene Expression Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jeanie Lin
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | | | - Ed Stover
- USDA-ARS Subtropical Insects and Horticulture Research Unit, Fort Pierce, FL, 34945, USA
| | - Kent F McCue
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Frank G Harmon
- Plant Gene Expression Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ann Blechl
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - James G Thomson
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Roger Thilmony
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA
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20
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Abstract
In the differential diagnostics of autoimmune-mediated rheumatic diseases, rheumatologists often have to consider infections (e. g. Lyme arthritis) or reactive diseases (e. g. reactive arthritis after urogenital bacterial infections). Furthermore, infections with an atypical presentation or caused by atypical pathogens (opportunistic infections) can complicate the immunosuppressive therapy of autoimmune diseases. For this purpose not only conventional microbiological culture methods but also PCR-based methods are increasingly being applied for the direct detection of pathogens in clinical specimens. The aim of this overview is to present commonly used PCR methods in the clinical practice of rheumatology and to describe their benefits and limitations compared to culture-based detection methods.
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Affiliation(s)
- B Ehrenstein
- Klinik und Poliklinik für Rheumatologie/Klinische Immunologie, Asklepios Klinikum Bad Abbach, 93077, Bad Abbach, Deutschland.
| | - U Reischl
- Institut für Klinische Mikrobiologie und Hygiene, Universitätsklinikum Regensburg (UKR), 93053, Regensburg, Deutschland
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21
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Demain AL, Vandamme EJ, Collins J, Buchholz K. History of Industrial Biotechnology. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Arnold L. Demain
- Drew University; Charles A. Dana Research Institute for Scientists Emeriti (R.I.S.E.); 36, Madison Ave Madison NJ 07940 USA
| | - Erick J. Vandamme
- Ghent University; Department of Biochemical and Microbial Technology; Belgium
| | - John Collins
- Science historian; Leipziger Straße 82A; 38124 Braunschweig Germany
| | - Klaus Buchholz
- Technical University Braunschweig; Institute of Chemical Engineering; Hans-Sommer-Str. 10 38106 Braunschweig Germany
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22
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Barger SW. Gene regulation and genetics in neurochemistry, past to future. J Neurochem 2016; 139 Suppl 2:24-57. [PMID: 27747882 DOI: 10.1111/jnc.13629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/01/2016] [Accepted: 03/30/2016] [Indexed: 12/14/2022]
Abstract
Ask any neuroscientist to name the most profound discoveries in the field in the past 60 years, and at or near the top of the list will be a phenomenon or technique related to genes and their expression. Indeed, our understanding of genetics and gene regulation has ushered in whole new systems of knowledge and new empirical approaches, many of which could not have even been imagined prior to the molecular biology boon of recent decades. Neurochemistry, in the classic sense, intersects with these concepts in the manifestation of neuropeptides, obviously dependent upon the central dogma (the established rules by which DNA sequence is eventually converted into protein primary structure) not only for their conformation but also for their levels and locales of expression. But, expanding these considerations to non-peptide neurotransmitters illustrates how gene regulatory events impact neurochemistry in a much broader sense, extending beyond the neurochemicals that translate electrical signals into chemical ones in the synapse, to also include every aspect of neural development, structure, function, and pathology. From the beginning, the mutability - yet relative stability - of genes and their expression patterns were recognized as potential substrates for some of the most intriguing phenomena in neurobiology - those instances of plasticity required for learning and memory. Near-heretical speculation was offered in the idea that perhaps the very sequence of the genome was altered to encode memories. A fascinating component of the intervening progress includes evidence that the central dogma is not nearly as rigid and consistent as we once thought. And this mutability extends to the potential to manipulate that code for both experimental and clinical purposes. Astonishing progress has been made in the molecular biology of neurochemistry during the 60 years since this journal debuted. Many of the gains in conceptual understanding have been driven by methodological progress, from automated high-throughput sequencing instruments to recombinant-DNA vectors that can convey color-coded genetic modifications in the chromosomes of live adult animals. This review covers the highlights of these advances, both theoretical and technological, along with a brief window into the promising science ahead. This article is part of the 60th Anniversary special issue.
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Affiliation(s)
- Steven W Barger
- Department of Geriatrics, Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA. .,Geriatric Research Education and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, Arkansas, USA.
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23
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Cao L, Cui X, Hu J, Li Z, Choi JR, Yang Q, Lin M, Ying Hui L, Xu F. Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications. Biosens Bioelectron 2016; 90:459-474. [PMID: 27818047 DOI: 10.1016/j.bios.2016.09.082] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/18/2022]
Abstract
Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xingye Cui
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jane Ru Choi
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Qingzhen Yang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Min Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Li Ying Hui
- Foundation of State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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Barciszewska MZ, Perrigue PM, Barciszewski J. tRNA--the golden standard in molecular biology. MOLECULAR BIOSYSTEMS 2016; 12:12-7. [PMID: 26549858 DOI: 10.1039/c5mb00557d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.
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Affiliation(s)
- Mirosława Z Barciszewska
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznań, Poland.
| | - Patrick M Perrigue
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznań, Poland.
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznań, Poland.
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25
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Luchi N, Capretti P, Pazzagli M, Pinzani P. Powerful qPCR assays for the early detection of latent invaders: interdisciplinary approaches in clinical cancer research and plant pathology. Appl Microbiol Biotechnol 2016; 100:5189-204. [PMID: 27112348 DOI: 10.1007/s00253-016-7541-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/07/2016] [Accepted: 04/10/2016] [Indexed: 12/29/2022]
Abstract
Latent invaders represent the first step of disease before symptoms occur in the host. Based on recent findings, tumors are considered to be ecosystems in which cancer cells act as invasive species that interact with the native host cell species. Analogously, in plants latent fungal pathogens coevolve within symptomless host tissues. For these reasons, similar detection approaches can be used for an early diagnosis of the invasion process in both plants and humans to prevent or reduce the spread of the disease. Molecular tools based on the evaluation of nucleic acids have been developed for the specific, rapid, and early detection of human diseases. During the last decades, these techniques to assess and quantify the proliferation of latent invaders in host cells have been transferred from the medical field to different areas of scientific research, such as plant pathology. An improvement in molecular biology protocols (especially referring to qPCR assays) specifically designed and optimized for detection in host plants is therefore advisable. This work is a cross-disciplinary review discussing the use of a methodological approach that is employed within both medical and plant sciences. It provides an overview of the principal qPCR tools for the detection of latent invaders, focusing on comparisons between clinical cancer research and plant pathology, and recent advances in the early detection of latent invaders to improve prevention and control strategies.
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Affiliation(s)
- Nicola Luchi
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
| | - Paolo Capretti
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
- Department of Agri-Food Productions and Environmental Sciences (DiSPAA), University of Florence, Piazzale delle Cascine 28, Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy.
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Abstract
On rare occasions in the history of science, remarkable discoveries transform human society and forever alter mankind’s view of the world. Examples of such discoveries include the heliocentric theory, Newtonian physics, the germ theory of disease, quantum theory, plate tectonics and the discovery that DNA carries genetic information. The science philosopher Thomas Kuhn famously described science as long periods of normality punctuated by times of crisis, when anomalous observations culminate in revolutionary changes that replace one paradigm with another. This essay examines several transformative discoveries in the light of Kuhn’s formulation. We find that each scientific revolution is unique, with disparate origins that may include puzzle solving, serendipity, inspiration, or a convergence of disparate observations. The causes of revolutionary science are varied and lack an obvious common structure. Moreover, it can be difficult to draw a clear distinction between so-called normal and revolutionary science. Revolutionary discoveries often emerge from basic science and are critically dependent on nonrevolutionary research. Revolutionary discoveries may be conceptual or technological in nature, lead to the creation of new fields, and have a lasting impact on many fields in addition to the field from which they emerge. In contrast to political revolutions, scientific revolutions do not necessarily require the destruction of the previous order. For humanity to continue to benefit from revolutionary discoveries, a broad palette of scientific inquiry with a particular emphasis on basic science should be supported.
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Brücher BLDM, Li Y, Schnabel P, Daumer M, Wallace TJ, Kube R, Zilberstein B, Steele S, Voskuil JLA, Jamall IS. Genomics, microRNA, epigenetics, and proteomics for future diagnosis, treatment and monitoring response in upper GI cancers. Clin Transl Med 2016; 5:13. [PMID: 27053248 PMCID: PMC4823224 DOI: 10.1186/s40169-016-0093-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 03/29/2016] [Indexed: 12/15/2022] Open
Abstract
One major objective for our evolving understanding in the treatment of cancers will be to address how a combination of diagnosis and treatment strategies can be used to integrate patient and tumor variables with an outcome-oriented approach. Such an approach, in a multimodal therapy setting, could identify those patients (1) who should undergo a defined treatment (personalized therapy) (2) in whom modifications of the multimodal therapy due to observed responses might lead to an improvement of the response and/or prognosis (individualized therapy), (3) who might not benefit from a particular toxic treatment regimen, and (4) who could be identified early on and thereby be spared the morbidity associated with such treatments. These strategies could lead in the direction of precision medicine and there is hope of integrating translational molecular data to improve cancer classifications. In order to achieve these goals, it is necessary to understand the key issues in different aspects of biotechnology to anticipate future directions of personalized and individualized diagnosis and multimodal treatment strategies. Providing an overview of translational data in cancers proved to be a challenge as different methods and techniques used to obtain molecular data are used and studies are based on different tumor entities with different tumor biology and prognoses as well as vastly different therapeutic approaches. The pros and cons of the available methodologies and the potential response data in genomics, microRNA, epigenetics and proteomics with a focus on upper gastrointestinal cancers are considered herein to allow for an understanding of where these technologies stand with respect to cancer diagnosis, prognosis and treatment.
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Affiliation(s)
- Björn L. D. M. Brücher
- />Theodor-Billroth-Academy®, Munich, Germany
- />Theodor-Billroth-Academy®, Sacramento, CA USA
- />INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Munich, Germany
- />INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Sacramento, CA USA
- />Bon Secours Cancer Institute, Richmond, VA USA
- />Department of Surgery, Carl-Thiem-Klinikum, Cottbus, Germany
| | - Yan Li
- />Proteogenomics Research Institute for Systems Medicine, San Diego, CA USA
| | - Philipp Schnabel
- />Institute of Pathology, University of Homburg Saar, Homburg, Germany
| | - Martin Daumer
- />Theodor-Billroth-Academy®, Munich, Germany
- />Theodor-Billroth-Academy®, Sacramento, CA USA
- />INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Munich, Germany
- />INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Sacramento, CA USA
- />Sylvia Lawry Center for MS Research, Munich, Germany
| | | | - Rainer Kube
- />Department of Surgery, Carl-Thiem-Klinikum, Cottbus, Germany
| | | | - Scott Steele
- />Case Western Reserve University, Cleveland, OH USA
- />Department of Surgery, Madigan Army Medical Center, Tacoma, WA USA
| | | | - Ijaz S. Jamall
- />Theodor-Billroth-Academy®, Munich, Germany
- />Theodor-Billroth-Academy®, Sacramento, CA USA
- />INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Munich, Germany
- />INCORE, International Consortium of Research Excellence of the Theodor-Billroth-Academy®, Sacramento, CA USA
- />Risk-Based Decisions, Inc., Sacramento, CA USA
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28
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Ekstrøm PO, Nakken S, Johansen M, Hovig E. Automated amplicon design suitable for analysis of DNA variants by melting techniques. BMC Res Notes 2015; 8:667. [PMID: 26559640 PMCID: PMC4642734 DOI: 10.1186/s13104-015-1624-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 10/26/2015] [Indexed: 05/28/2023] Open
Abstract
Background The technological development of DNA analysis has had tremendous development in recent years, and the present deep sequencing techniques present unprecedented opportunities for detailed and high-throughput DNA variant detection. Although DNA sequencing has had an exponential decrease in cost per base pair analyzed, focused and target-specific methods are however still much in use for analysis of DNA variants. With increasing capacity in the analytical procedures, an equal demand in automated amplicon and primer design has emerged. Results We have constructed a web-based tool that is able to batch design DNA variant assay suitable for analysis by denaturing gel/capillary electrophoresis and high resolution melting. The tool is developed as a computational workflow that implements one of the most widely used primer design tools, followed by validation of primer specificity, as well as calculation and visualization of the melting properties of the resulting amplicon, with or without an artificial high melting domain attached. The tool will be useful for scientists applying DNA melting techniques in analysis of DNA variations. The tool is freely available at http://meltprimer.ous-research.no/. Conclusion Herein, we demonstrate a novel tool with respect to covering the whole amplicon design workflow necessary for groups that use melting equilibrium techniques to separate DNA variants.
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Affiliation(s)
- Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway.
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway.
| | - Morten Johansen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway.
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello, Oslo, 0310, Norway. .,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hosptal, Nydalen, Oslo, 0424, Norway. .,Department of Informatics, University of Oslo, Blindern, Oslo, 0318, Norway.
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Hodne K, Weltzien FA. Single-Cell Isolation and Gene Analysis: Pitfalls and Possibilities. Int J Mol Sci 2015; 16:26832-49. [PMID: 26569222 PMCID: PMC4661855 DOI: 10.3390/ijms161125996] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/14/2015] [Accepted: 11/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the last two decades single-cell analysis (SCA) has revealed extensive phenotypic differences within homogenous cell populations. These phenotypic differences are reflected in the stochastic nature of gene regulation, which is often masked by qualitatively and quantitatively averaging in whole tissue analyses. The ability to isolate transcripts and investigate how genes are regulated at the single cell level requires highly sensitive and refined methods. This paper reviews different strategies currently used for SCA, including harvesting, reverse transcription, and amplification of the RNA, followed by methods for transcript quantification. The review provides the historical background to SCA, discusses limitations, and current and future possibilities in this exciting field of research.
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Affiliation(s)
- Kjetil Hodne
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences-Campus Adamstuen, 0033 Oslo, Norway.
| | - Finn-Arne Weltzien
- Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences-Campus Adamstuen, 0033 Oslo, Norway.
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31
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Prediction of success for polymerase chain reactions using the Markov maximal order model and support vector machine. J Theor Biol 2015; 369:51-8. [DOI: 10.1016/j.jtbi.2015.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/21/2014] [Accepted: 01/14/2015] [Indexed: 11/18/2022]
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32
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Becker J, Wittmann C. Advanced Biotechnology: Metabolically Engineered Cells for the Bio-Based Production of Chemicals and Fuels, Materials, and Health-Care Products. Angew Chem Int Ed Engl 2015; 54:3328-50. [DOI: 10.1002/anie.201409033] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 12/16/2022]
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33
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Biotechnologie von Morgen: metabolisch optimierte Zellen für die bio-basierte Produktion von Chemikalien und Treibstoffen, Materialien und Gesundheitsprodukten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Witkowski PT, Heinemann P, Klempa B, Krüger DH. Molekulare Identifikation von Hantaviren in neuen Wirten. BIOSPEKTRUM : ZEITSCHRIFT DER GESELLSCHAFT FUR BIOLOGISHE CHEMIE (GBCH) UND DER VEREINIGUNG FUR ALLGEMEINE UND ANGEWANDTE MIKROBIOLOGIE (VAAM) 2015; 21:503-506. [PMID: 32218646 PMCID: PMC7090483 DOI: 10.1007/s12268-015-0609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter T Witkowski
- Institut für Medizinische Virologie, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Helmut-Ruska-Haus Charitéplatz 1, D-10117 Berlin, Germany
| | - Patrick Heinemann
- Institut für Medizinische Virologie, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Helmut-Ruska-Haus Charitéplatz 1, D-10117 Berlin, Germany
| | - Boris Klempa
- Institut für Medizinische Virologie, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Helmut-Ruska-Haus Charitéplatz 1, D-10117 Berlin, Germany
| | - Detlev H Krüger
- Institut für Medizinische Virologie, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Helmut-Ruska-Haus Charitéplatz 1, D-10117 Berlin, Germany
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35
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Abstract
Can we develop technologies to systematically map classical mechanisms throughout the brain, while retaining the flexibility to investigate new mechanisms as they are discovered? We discuss principles of scalable, flexible technologies that could yield comprehensive maps of brain function.
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Affiliation(s)
- Adam H Marblestone
- Synthetic Neurobiology Group, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward S Boyden
- Synthetic Neurobiology Group, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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36
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Yuce M, Kurt H, Mokkapati VRSS, Budak H. Employment of nanomaterials in polymerase chain reaction: insight into the impacts and putative operating mechanisms of nano-additives in PCR. RSC Adv 2014. [DOI: 10.1039/c4ra06144f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The latest developments in the field of nanomaterial-assisted PCR are evaluated with a focus on putative operating mechanisms.
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Affiliation(s)
- Meral Yuce
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul, Turkey
| | - Hasan Kurt
- Sabanci University
- Faculty of Engineering and Natural Sciences
- Istanbul, Turkey
| | | | - Hikmet Budak
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul, Turkey
- Sabanci University
- Faculty of Engineering and Natural Sciences
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37
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Abstract
The examination of organs and tissues macroscopically in order to establish a diagnosis and to select relevant portions for subsequent microscopic examination and special studies is fundamental to the practice of pathology. In the autopsy room, in the surgical pathology laboratory and, very often, in the operating room, gross pathology is the essential, underlying basis of morphologic diagnosis. Diagnoses on the basis of gross examination can be accurately made in as many as 90 % of specimens (Grossman IW, A primer of gross pathology, Charles C Thomas, 1972). In the remaining 10 % the skilled pathologist can be close to the diagnosis or can, at least, construct an accurate differential diagnosis that can provide guidance for subsequent studies. Sadly the numbers of pathologists with skills in macroscopic ("gross") pathology is rapidly declining, with concomitant loss in the quality of gross examinations, lower accuracy and elegance of specimen descriptions, and lack of precision in sample selection for special studies. This clearly impacts the quality of surgical pathology practice and, inevitably, the quality of patient care. The decline of gross pathology is a result of a number of factors, including a marked decrease in the numbers of autopsies which means that there are fewer opportunities for pathologists to hone gross pathology skills and to gain proficiency in handling tissues for appropriate further study. This is compounded by an increasing reliance on pathologists' assistants (PAs) for the handling, description and sampling of gross specimens, by the expanded utilization of biopsies rather than resections prior to initiating therapy and by the reliance on highly sophisticated immunopathology, molecular and genomic methods for diagnosis and even for determination of therapy. Despite these and other changes in medical and pathology practice, careful examination of the gross specimen is still the sine qua non of surgical and autopsy pathology practice.
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Affiliation(s)
- Stephen A Geller
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA, USA,
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39
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Ekstrøm PO, Warren DJ, Thilly WG. Separation principles of cycling temperature capillary electrophoresis. Electrophoresis 2012; 33:1162-8. [PMID: 22539319 DOI: 10.1002/elps.201100550] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
High throughput means to detect and quantify low-frequency mutations (<10(-2) ) in the DNA-coding sequences of human tissues and pathological lesions are required to discover the kinds, numbers, and rates of genetic mutations that (i) confer inherited risk for disease or (ii) arise in somatic tissues as events required for clonal diseases such as cancers and atherosclerotic plaque.While throughput of linear DNA sequencing methods has increased dramatically, such methods are limited by high error rates (>10(-3) ) rendering them unsuitable for the detection of low-frequency risk-conferring mutations among the many neutral mutations carried in the general population or formed in tissue growth and development. In contrast, constant denaturing capillary electrophoresis (CDCE), coupled with high-fidelity PCR, achieved a point mutation detection limit of <10(-5) in exon-sized sequences from human tissue or pooled blood samples. However, increasing CDCE throughput proved difficult due to the need for precise temperature control and the time-consuming optimization steps for each DNA sequence probed. Both of these problems have been solved by the method of cycling temperature capillary electrophoresis (CTCE). The data presented here provide a deeper understanding of the separation principles involved in CTCE and address several elements of a previously presented two-state transport model.
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Affiliation(s)
- Per Olaf Ekstrøm
- Department of Surgical Oncology and Tumor biology, Radiumhospitalet, Oslo University Hospital, Montebello, Oslo, Norway
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40
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Kramer MF, Coen DM. Enzymatic amplification of DNA by PCR: standard procedures and optimization. ACTA ACUST UNITED AC 2012; Chapter 6:Unit6.7. [PMID: 21959762 DOI: 10.1002/0471141755.ph0607s13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR), including procedures to quickly determine conditions for successful amplification of the sequence and primer sets of interest, and to optimize for specificity, sensitivity, and yield. Hot-start methods are described which can greatly improve specificity, sensitivity, and yield. This protocol suggests some relatively inexpensive methods to achieve hot start, and lists several commercial hot-start options which may be more convenient, but of course more expensive. The unit has recently been updated to include new information on reagents to enhance the reaction, better cycling parameters, and innovations in robotics and high-performance thermocyclers.
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Affiliation(s)
- M F Kramer
- Harvard Medical School, Boston, Massachusetts
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41
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Walsh JM, Beuning PJ. Synthetic nucleotides as probes of DNA polymerase specificity. J Nucleic Acids 2012; 2012:530963. [PMID: 22720133 PMCID: PMC3377560 DOI: 10.1155/2012/530963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 03/21/2012] [Indexed: 12/17/2022] Open
Abstract
The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example, Escherichia coli DNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides.
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Affiliation(s)
- Jason M. Walsh
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA
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42
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Abstract
In the biological sciences there have been technological advances that catapult the discipline into golden ages of discovery. For example, the field of microbiology was transformed with the advent of Anton van Leeuwenhoek's microscope, which allowed scientists to visualize prokaryotes for the first time. The development of the polymerase chain reaction (PCR) is one of those innovations that changed the course of molecular science with its impact spanning countless subdisciplines in biology. The theoretical process was outlined by Keppe and coworkers in 1971; however, it was another 14 years until the complete PCR procedure was described and experimentally applied by Kary Mullis while at Cetus Corporation in 1985. Automation and refinement of this technique progressed with the introduction of a thermal stable DNA polymerase from the bacterium Thermus aquaticus, consequently the name Taq DNA polymerase. PCR is a powerful amplification technique that can generate an ample supply of a specific segment of DNA (i.e., an amplicon) from only a small amount of starting material (i.e., DNA template or target sequence). While straightforward and generally trouble-free, there are pitfalls that complicate the reaction producing spurious results. When PCR fails it can lead to many non-specific DNA products of varying sizes that appear as a ladder or smear of bands on agarose gels. Sometimes no products form at all. Another potential problem occurs when mutations are unintentionally introduced in the amplicons, resulting in a heterogeneous population of PCR products. PCR failures can become frustrating unless patience and careful troubleshooting are employed to sort out and solve the problem(s). This protocol outlines the basic principles of PCR, provides a methodology that will result in amplification of most target sequences, and presents strategies for optimizing a reaction. By following this PCR guide, students should be able to: • Set up reactions and thermal cycling conditions for a conventional PCR experiment • Understand the function of various reaction components and their overall effect on a PCR experiment • Design and optimize a PCR experiment for any DNA template • Troubleshoot failed PCR experiments.
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Affiliation(s)
- Todd C Lorenz
- Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA.
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43
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Krokan HE. A life in DNA repair—And beyond. DNA Repair (Amst) 2012; 11:224-35. [DOI: 10.1016/j.dnarep.2011.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Har Gobind Khorana (January 9, 1922–November 9, 2011). DNA Repair (Amst) 2012. [DOI: 10.1016/j.dnarep.2011.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Linko V, Leppiniemi J, Shen B, Niskanen E, Hytönen VP, Toppari JJ. Growth of immobilized DNA by polymerase: bridging nanoelectrodes with individual dsDNA molecules. NANOSCALE 2011; 3:3788-3792. [PMID: 21811739 DOI: 10.1039/c1nr10518c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a method for controlled connection of gold electrodes with dsDNA molecules (locally on a chip) by utilizing polymerase to elongate single-stranded DNA primers attached to the electrodes. Thiol-modified oligonucleotides are directed and immobilized to nanoscale electrodes by means of dielectrophoretic trapping, and extended in a procedure mimicking PCR, finally forming a complete dsDNA molecule bridging the gap between the electrodes. The technique opens up opportunities for building from the bottom-up, for detection and sensing applications, and also for molecular electronics.
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Affiliation(s)
- Veikko Linko
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.
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46
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Kramer MF, Coen DM. Enzymatic amplification of DNA by PCR: standard procedures and optimization. ACTA ACUST UNITED AC 2011; Appendix 3:A.3C.1-14. [PMID: 20972963 DOI: 10.1002/0471140856.txa03cs03] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The polymerase chain reaction (PCR) is used to enzymatically amplify small quantities of specific DNA sequences. The reaction must optimized to specifically amplify the sequences and primers of interest; this includes titration of magnesium chloride and selection of enhancing agents, if appropriate, to minimize nonspecific primer target interactions and maximize the specificity, sensitivity, and yield.
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Affiliation(s)
- M F Kramer
- Harvard Medical School, Boston, Massachusetts, USA
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47
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Abstract
Microarray gene expression profiling has identified gene signatures or "Indicator" genes predictive of outcome in many cancer types including lymphoma, and more recently pancreatic cancer. This has identified novel and powerful diagnostic and prognostic and generically applicable markers, promising more specific diagnosis and treatment, together with improved understanding of pathobiology. There is now an urgent need to translate these signatures to clinical use. However, gene microarrays rely on relatively large amounts of fresh starting tissue obviating measurement of Indicator genes in routine practice, and there is a need for development of another, simple, robust, relatively inexpensive and sensitive method for their translation to clinical use. We have piloted the use of real-time PCR measurement of specific prognostic genes, so called "Indicator" genes, in globally amplified polyA cDNA for this purpose. Poly(A) PCR coordinately amplifies cDNA copies of all polyadenylated mRNAs, thereby generating a PCR product (polyA cDNA) whose composition reflects the relative abundance of all expressed genes in the starting sample. Poly(A) PCR enables global mRNA amplification from picogram amounts of RNA and has been routinely used to analyse expression in small samples including single cells. The poly(A) cDNA pool generated is also indefinitely renewable and as such represents a "molecular block". Real-time PCR measurement, using gene-specific primers and probes, of the expression levels of specific Indicator genes then allows gene signatures to be detected within the poly(A) cDNA, thereby enabling expression profiling of very small amounts of starting material. This chapter details this method as applied to fresh and paraffin embedded tissue and to pancreatic juice. In this chapter, we have concentrated on application of the method to pancreatic cancer, but the generic nature of the method renders it applicable to any cancer type, thereby representing a novel platform for cancer diagnosis across all tumour types.
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48
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Abstract
The development of rapid, accurate, and sensitive diagnostic methods for detecting pathogens is the basis for treating, controlling, and eradicating infectious diseases of veterinary importance. Scientific and technological advancements have revolutionized the field of veterinary diagnostics. Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. The integration of advances in biochemistry, proteomics, engineering, and medicine offers enormous potential for the rapid and accurate diagnosis of viral, microbial, genetic, and metabolic disease. In the future, polymerase chain reaction assays, microarray testing, genomic analysis, and metabolic profiling will be accomplished in a rapid, portable, sensitive, and cost-efficient manner.
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49
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Bustin SA. Why the need for qPCR publication guidelines?—The case for MIQE. Methods 2010; 50:217-26. [DOI: 10.1016/j.ymeth.2009.12.006] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 12/07/2009] [Accepted: 12/11/2009] [Indexed: 12/23/2022] Open
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50
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Ng SK, Lin W, Sachdeva R, Wang DI, Yap MG. Vector fragmentation: Characterizing vector integrity in transfected clones by Southern blotting. Biotechnol Prog 2009; 26:11-20. [DOI: 10.1002/btpr.281] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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