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Jansson L, Aili Fagerholm S, Börkén E, Hedén Gynnå A, Sidstedt M, Forsberg C, Ansell R, Hedman J, Tillmar A. Assessment of DNA quality for whole genome library preparation. Anal Biochem 2024; 695:115636. [PMID: 39111682 DOI: 10.1016/j.ab.2024.115636] [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] [Received: 03/11/2024] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 08/22/2024]
Abstract
In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.
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Affiliation(s)
- Linda Jansson
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | | | - Emelie Börkén
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Arvid Hedén Gynnå
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden
| | - Maja Sidstedt
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden
| | | | - Ricky Ansell
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Department of Physics, Chemistry and Biology, IFM, Linköping University, Linköping, Sweden
| | - Johannes Hedman
- National Forensic Centre, Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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2
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Martin R, Mullin KE, White NFD, Grimason N, Jehle R, Wilkinson JW, Orozco-terWengel P, Cunningham AA, Maddock ST. Optimising recovery of DNA from minimally invasive sampling methods: Efficacy of buccal swabs, preservation strategy and DNA extraction approaches for amphibian studies. Ecol Evol 2024; 14:e70294. [PMID: 39267688 PMCID: PMC11392594 DOI: 10.1002/ece3.70294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/14/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Studies in evolution, ecology and conservation are increasingly based on genetic and genomic data. With increased focus on molecular approaches, ethical concerns about destructive or more invasive techniques need to be considered, with a push for minimally invasive sampling to be optimised. Buccal swabs have been increasingly used to collect DNA in a number of taxa, including amphibians. However, DNA yield and purity from swabs are often low, limiting its use. In this study, we compare different types of swabs, preservation method and storage, and DNA extraction techniques in three case studies to assess the optimal approach for recovering DNA in anurans. Out of the five different types of swabs that we tested, Isohelix MS-02 and Rapidry swabs generated higher DNA yields than other swabs. When comparing storage buffers, ethanol is a better preservative than a non-alcoholic alternative. Dried samples resulted in similar or better final DNA yields compared to ethanol-fixed samples if kept cool. DNA extraction via a Qiagen™ DNeasy Blood and Tissue Kit and McHale's salting-out extraction method resulted in similar DNA yields but the Qiagen™ kit extracts contained less contamination. We also found that samples have better DNA recovery if they are frozen as soon as possible after collection. We provide recommendations for sample collection and extraction under different conditions, including budgetary considerations, size of individual animal sampled, access to cold storage facilities and DNA extraction methodology. Maximising efficacy of all of these factors for better DNA recovery will allow buccal swabs to be used for genetic and genomic studies in a range of vertebrates.
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Affiliation(s)
- R Martin
- Faculty of Science and Engineering, School of Life Sciences University of Wolverhampton Wolverhampton UK
- School of Science, Engineering and Environment University of Salford Salford UK
- Amphibian and Reptile Conservation Bournemouth UK
| | - K E Mullin
- Cardiff School of Biosciences Cardiff UK
| | - N F D White
- Cardiff School of Biosciences Cardiff UK
- Institute of Zoology, Zoological Society of London London UK
| | - N Grimason
- Faculty of Science and Engineering, School of Life Sciences University of Wolverhampton Wolverhampton UK
| | - R Jehle
- School of Science, Engineering and Environment University of Salford Salford UK
| | | | | | - A A Cunningham
- Institute of Zoology, Zoological Society of London London UK
| | - S T Maddock
- Faculty of Science and Engineering, School of Life Sciences University of Wolverhampton Wolverhampton UK
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Department of Life Sciences The Natural History Museum London UK
- Island Biodiversity and Conservation Centre University of Seychelles Victoria Seychelles
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3
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Pandey A, Momeni O, Pandey P. Quantitative Analysis of Genomic DNA Degradation of E. coli Using Automated Gel Electrophoresis under Various Levels of Microwave Exposure. Gels 2024; 10:242. [PMID: 38667661 PMCID: PMC11049425 DOI: 10.3390/gels10040242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/10/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
The problem that this study addresses is to understand how microwave radiation is able to degrade genomic DNA of E. coli. In addition, a comparative study was made to evaluate the suitability of a high-throughput automated electrophoresis platform for quantifying the DNA degradation under microwave radiation. Overall, this study investigated the genomic DNA degradation of E. coli under microwave radiation using automated gel electrophoresis. To examine the viable organisms and degradation of genomic DNA under microwave exposure, we used three methods: (1) post-microwave exposure, where E. coli was enumerated using modified mTEC agar method using membrane filtration technique; (2) extracted genomic DNA of microwaved sample was quantified using the Qubit method; and (3) automated gel electrophoresis, the TapeStation 4200, was used to examine the bands of extracted DNA of microwaved samples. In addition, to examine the impacts of microwaves, E. coli colonies were isolated from a fecal sample (dairy cow manure), these colonies were grown overnight to prepare fresh E. coli culture, and this culture was exposed to microwave radiation for three durations: (1) 2 min; (2) 5 min; and (3) 8 min. In general, Qubit values (ng/µL) were proportional to the results of automated gel electrophoresis, TapeStation 4200, DNA integrity numbers (DINs). Samples from exposure studies (2 min, 5 min, and 8 min) showed no viable E. coli. Initial E. coli levels (at 0 min microwave exposure) were 5 × 108 CFU/mL, and the E. coli level was reduced to a non-detectable level within 2 min of microwave exposure. The relationships between Qubit and TapeStation measurements was linear, except for when the DNA level was lower than 2 ng/µL. In 8 min of microwave exposure, E. coli DNA integrity was reduced by 61.7%, and DNA concentration was reduced by 81.6%. The overall conclusion of this study is that microwave radiation had a significant impact on the genomic DNA of E. coli, and prolonged exposure of E. coli to microwaves can thus lead to a loss of genomic DNA integrity and DNA concentrations.
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Affiliation(s)
- Aditya Pandey
- Department of Electrical and Computer Engineering, University of California at Davis, Davis, CA 95616, USA; (A.P.); (O.M.)
| | - Omeed Momeni
- Department of Electrical and Computer Engineering, University of California at Davis, Davis, CA 95616, USA; (A.P.); (O.M.)
| | - Pramod Pandey
- Department of Population Health and Reproduction, University of California at Davis, Davis, CA 95616, USA
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Das D, Avssn R, Chittela RK. A phenol-chloroform free method for cfDNA isolation from cell conditioned media: development, optimization and comparative analysis. Anal Biochem 2024; 687:115454. [PMID: 38158107 DOI: 10.1016/j.ab.2023.115454] [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] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The non-invasive invasive nature of cell-free DNA (cfDNA) as diagnostic, prognostic, and theragnostic biomarkers has gained immense popularity in recent years. The clinical utility of cfDNA biomarkers may depend on understanding their origin and biological significance. Apoptosis, necrosis, and/or active release are possible mechanisms of cellular DNA release into the cell-free milieu. In-vitro cell culture models can provide useful insights into cfDNA biology. The yields and quality of cfDNA in the cell conditioned media (CCM) are largely dependent on the extraction method used. Here, we developed a phenol-chloroform-free cfDNA extraction method from CCM and compared it with three others published cfDNA extraction methods and four commercially available kits. Real-Time PCR (qPCR) targeting two different loci and a fluorescence-based Qubit assay were performed to quantify the extracted cfDNA. The absolute concentration of the extracted cfDNA varies with the target used for the qPCR assay; however, the relative trend remains similar for both qPCR assays. The cfDNA yield from CCM provided by the developed method was found to be either higher or comparable to the other methods used. In conclusion, we developed a safe, rapid and cost-effective cfDNA extraction protocol with minimal hands-on time; with no compromise in cfDNA yields.
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Affiliation(s)
- Dhruv Das
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India
| | - Rao Avssn
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Rajani Kant Chittela
- Applied Genomics Section, Bioscience Group, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute (HBNI), Anushaktinagar, Trombay, Mumbai, 400094, India.
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5
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Murakami S, Shinada K, Otsutsumi Y, Komine F, Yuan Y, Nakamura J, Katakura S, Kondo T, Kato T, Yokose T, Saito H. Comparison between next-generation sequencing and multiplex polymerase chain reaction assays for nonsmall-cell lung cancer molecular diagnosis. Cancer Med 2024; 13:e7162. [PMID: 38572952 PMCID: PMC10993699 DOI: 10.1002/cam4.7162] [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: 11/11/2023] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
PURPOSE Genetic mutation detection has become an important step in nonsmall-cell lung cancer (NSCLC) treatment because of the increasing number of drugs that target genomic rearrangements. A multiplex test that can detect multiple gene mutations prior to treatment is thus necessary. Currently, either next-generation sequencing (NGS)-based or polymerase chain reaction (PCR)-based tests are used. We evaluated the performance of the Oncomine Dx Target Test (ODxTT), an NGS-based multiplex biomarker panel test, and the AmoyDx Pan Lung Cancer PCR Panel (AmoyDx PLC panel), a real-time PCR-based multiplex biomarker panel test. MATERIALS AND METHODS Patients with histologically diagnosed NSCLC and a sufficient sample volume to simultaneously perform the AmoyDx PLC panel and ODxTT-M were included in the study. The success and detection rates of both tests were evaluated. RESULTS Biopsies revealed 116 cases of malignancies, 100 of which were NSCLC. Of these, 59 met the inclusion criteria and were eligible for analysis. The success rates were 100% and 98% for AmoyDx PLC panel and ODxTT-M, respectively. Nine driver mutations were detected in 35.9% and 37.3% of AmoyDx PLC and ODxTT-M panels, respectively. EGFR mutations were detected in 14% and 12% of samples using the AmoyDx PLC panel and ODxTT-M, respectively. Of the 58 cases in which both NGS and AmoyDx PLC panels were successful, discordant results were observed in seven cases. These differences were mainly due to different sensitivities of the detection methods used and the gene variants targeted in each test. DISCUSSION The AmoyDx PLC panel, a PCR-based multiplex diagnostic test, exhibits a high success rate. The frequency of the nine genes targeted for treatment detected by the AmoyDx PLC panel was comparable to the frequency of mutations detected by ODxTT-M. Clinicians should understand and use the AmoyDx PLC panel and ODxTT-M with respect to their respective performances and limitations.
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Affiliation(s)
- Shuji Murakami
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Kanako Shinada
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Yuka Otsutsumi
- Department of PathologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | | | - Yuan Yuan
- Riken Genesis Co., Ltd.Shinagawa‐kuTokyoJapan
| | | | - Seigo Katakura
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Tetsuro Kondo
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Terufumi Kato
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Tomoyuki Yokose
- Department of PathologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Haruhiro Saito
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
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Abugattas-Núñez del Prado J, Quintana Reyes A, Leon J, Blume La Torre J, Gutiérrez Loli R, Pinzón Olejua A, Chamorro Chirinos ER, Loza Mauricio FA, Maguiña JL, Rodriguez-Aliaga P, Málaga-Trillo E. Clinical validation of RCSMS: A rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva. PLoS One 2024; 19:e0290466. [PMID: 38527001 PMCID: PMC10962837 DOI: 10.1371/journal.pone.0290466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/08/2023] [Indexed: 03/27/2024] Open
Abstract
Peru's holds the highest COVID death rate per capita worldwide. Key to this outcome is the lack of robust, rapid, and accurate molecular tests to circumvent the elevated costs and logistics of SARS-CoV-2 detection via RT-qPCR. To facilitate massive and timely COVID-19 testing in rural and socioeconomically deprived contexts, we implemented and validated RCSMS, a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva. RCSMS uses the power of CRISPR-Cas technology and lateral flow strips to easily visualize the presence of SARS-CoV-2 even in laboratories with limited equipment. We show that a low-cost thermochemical treatment with TCEP/EDTA is sufficient to inactivate viral particles and cellular nucleases in saliva, eliminating the need to extract viral RNA with commercial kits, as well as the cumbersome nasopharyngeal swab procedure and the requirement of biosafety level 2 laboratories for molecular analyses. Notably, RCSMS performed outstandingly in a clinical validation done with 352 patients from two hospitals in Lima, detecting as low as 50 viral copies per 10 μl reaction in 40 min, with sensitivity and specificity of 96.5% and 99.0%, respectively, relative to RT-qPCR. The negative and positive predicted values obtained from this field validation indicate that RCSMS can be confidently deployed in both high and low prevalence settings. Like other CRISPR-Cas-based biosensors, RCSMS can be easily reprogrammed for the detection of new SARS-CoV-2 variants. We conclude that RCSMS is a fast, efficient and inexpensive alternative to RT-qPCR for expanding COVID-19 testing capacity in Peru and other low- and middle-income countries with precarious healthcare systems.
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Affiliation(s)
| | | | - Julio Leon
- IMS RIKEN Center for Integrative Medical Sciences, Japan
- University of California San Francisco, San Francisco, California, United States of America
| | - Juan Blume La Torre
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Renzo Gutiérrez Loli
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | | | | | - Jorge L. Maguiña
- Instituto de Evaluación de Tecnologías en Salud e Investigación (IETSI), EsSalud, Lima, Perú
| | - Piere Rodriguez-Aliaga
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Edward Málaga-Trillo
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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Cottenet G, Blancpain C, Holzwarth J. A digital PCR approach to assess the purity of oregano. Heliyon 2024; 10:e25985. [PMID: 38420487 PMCID: PMC10900423 DOI: 10.1016/j.heliyon.2024.e25985] [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: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Herbs and spices are food categories known to be at high risk of adulteration. Presence of undeclared foreign plant species has often been reported in oregano and may have a direct impact on its organoleptic quality and potentially the safety of this aromatic herb. A droplet digital PCR approach was developed to assess the purity of oregano by quantifying the DNA copies of oregano versus the total plant DNA copies. Nuclear single-copy genes were selected by targeting the terpene synthase 5 gene from oregano and the plant phosphoenolpyruvate carboxylase 2 gene. The reactions were specific to the Origanum genus and plant materials respectively, whereas trueness and precision data confirmed the reliability of the method to quantify oregano. The applicability of the method was further verified on proficiency test samples before being applied on commercial oregano samples.
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Affiliation(s)
- Geoffrey Cottenet
- Institute of Food Safety & Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland
| | - Carine Blancpain
- Institute of Food Safety & Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland
| | - James Holzwarth
- Institute of Food Safety & Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland
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Zhang Y, Takaki Y, Yoshida-Takashima Y, Hiraoka S, Kurosawa K, Nunoura T, Takai K. A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems. mSystems 2023; 8:e0081723. [PMID: 37843256 PMCID: PMC10734518 DOI: 10.1128/msystems.00817-23] [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: 08/03/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE The elucidation of the molecular basis of virus-host coevolutionary interactions is boosted with state-of-the-art sequencing technologies. However, the sequence-only information is often insufficient to output a conclusive argument without biochemical characterizations. We proposed a 1-day and one-pot approach to confirm the exact function of putative restriction-modification (R-M) genes that presumably mediate microbial coevolution. The experiments mainly focused on a series of putative R-M enzymes from a deep-sea virus and its host bacterium. The results quickly unveiled unambiguous substrate specificities, superior catalytic performance, and unique sequence preferences for two new restriction enzymes (capable of cleaving DNA) and two new methyltransferases (capable of modifying DNA with methyl groups). The reality of the functional R-M system reinforced a model of mutually beneficial interactions with the virus in the deep-sea microbial ecosystem. The cell culture-independent approach also holds great potential for exploring novel and biotechnologically significant R-M enzymes from microbial dark matter.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yukari Yoshida-Takashima
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Hiraoka
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), MRU, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Ken Takai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Rashmi M, Singh T, Rajput NS, Kulshreshtha S. Biodegradation of di-2-ethylhexyl phthalate by Bacillus firmus MP04 strain: parametric optimization using full factorial design. Biodegradation 2023; 34:567-579. [PMID: 37354272 DOI: 10.1007/s10532-023-10043-4] [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] [Received: 05/01/2022] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Di-2-ethylhexyl phthalate (DEHP) is used as a plasticizer in making plastics and released from landfills. This study attempted to degrade DEHP using microbial isolates. Isolates of Bacillus spp. were tested for their efficacy in degrading DEHP. Degradation was assessed using liquid chromatography-mass spectrometry (LC-MS). The most efficient DEHP degradation was achieved by Bacillus firmus MP04, which has been identified as Bacillus firmus MP04. This strain was found to use DEHP as the sole source of carbon without carbon source supplementation. Full factorial design was used to optimize the conditions for DEHP degradation which revealed the suitability of pH 7, 5% salt concentration, 20 to 37 °C temperature, and yeast extract as a nitrogen source. LC-MS elucidated the possible degradation mechanism via benzoic acid formation. However, prolonged incubation formed a typical compound denatonium benzoate due to reactions with other compounds. As maximum degradation was achieved in 4 days, prolonged incubation is not suggested. It can be concluded that new strain Bacillus firmus MP04 is the most efficient strain among all the tested strains for DEHP degradation.
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Affiliation(s)
- Madhavi Rashmi
- Department of Biotechnology, Magadh University, Bodh Gaya, Bihar, India
| | - Tanuja Singh
- Department of Botany, Patliputra University, Patna, Bihar, India
| | - Nitesh Singh Rajput
- Amity School of Engineering and Technology, Amity University Rajasthan, Jaipur, Rajasthan, 303007, India
| | - Shweta Kulshreshtha
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, 303007, India.
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10
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Sun M, Cheng Y, Gao C, Peng H, Wang N, Gu W, Lu D. Construction and characterization of microsatellite markers for the Schistosoma japonicum isolate from a hilly area of China based on whole genome sequencing. Parasitol Res 2023; 122:2737-2748. [PMID: 37710024 DOI: 10.1007/s00436-023-07976-3] [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] [Received: 07/10/2023] [Accepted: 09/10/2023] [Indexed: 09/16/2023]
Abstract
Schistosoma japonicum had once caused the greatest disease burden in China and has still been transmitted in some hilly areas, for example, in Shitai of Anhui province, where rodents are projected to be the main reservoir. This may lead to a critical need of molecular tools with high efficiency in monitoring the dynamic of the rodent-associated S. japonicum, as an appropriate amount of schistosome input can re-establish its life cycle in a place with snails and then result in the re-emergence of schistosomiasis. Therefore, the goal of this study was to develop high polymorphic microsatellites from the whole genome of rodent-associated S. japonicum strain to monitor its transmission dynamic. We sampled the hilly schistosome isolate from Shitai of Anhui in China and sequenced the parasite with the next-generation sequencing technology. The whole genome was assembled with four different approaches. We then developed 71 microsatellite markers at a genome-wide scale throughout two best assembled genomes. Based on their chromosome mapping and the expected length of targeted sequences, we selected 24 markers for the development of multiplex reactions. Two multiplexes composed of 10 loci were finally developed, and their potential was revealed by their successful application on and capturing the genetic diversity of three schistosome populations. The selected 10 markers, each with clear chromosome location and characteristics, will be greatly useful in tracing the dispersal pathways or/and dynamics of the rodent-associated S. japonicum or others in the hilly area of China or elsewhere.
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Affiliation(s)
- Mengtao Sun
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Yuheng Cheng
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Changzhe Gao
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Hanqi Peng
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Ning Wang
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Weiling Gu
- Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, China.
| | - Dabing Lu
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China.
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11
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Molbert N, Ghanavi HR, Johansson T, Mostadius M, Hansson MC. An evaluation of DNA extraction methods on historical and roadkill mammalian specimen. Sci Rep 2023; 13:13080. [PMID: 37567875 PMCID: PMC10421861 DOI: 10.1038/s41598-023-39465-z] [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: 03/16/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.
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Affiliation(s)
- Noëlie Molbert
- Centre for Environmental and Climate Science, Lund University, Ecology Building, 223 62, Lund, Sweden.
| | - Hamid Reza Ghanavi
- Department of Biology, Functional Zoology Unit, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Tomas Johansson
- Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Maria Mostadius
- The Biological Museum, Lund University, Arkivcentrum Syd, Porfyrvägen 20, 22478, Lund, Sweden
| | - Maria C Hansson
- Centre for Environmental and Climate Science, Lund University, Ecology Building, 223 62, Lund, Sweden
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12
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [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: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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13
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López-Sánchez R, Hernández-Oaxaca D, Escobar-Zepeda A, Ramos Cerrillo B, López-Munguía A, Segovia L. Analysing the dynamics of the bacterial community in pozol, a Mexican fermented corn dough. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001355. [PMID: 37410634 PMCID: PMC10433422 DOI: 10.1099/mic.0.001355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023]
Abstract
Pozol is a traditional prehispanic Mexican beverage made from fermented nixtamal dough; it is still part of everyday life in many communities due to its nutritional properties. It is the product of spontaneous fermentation and has a complex microbiota composed primarily of lactic acid bacteria (LAB). Although this is a beverage that has been used for centuries, the microbial processes that participate in this fermented beverage are not well understood. We fermented corn dough to produce pozol and sampled it at four key times to follow the community and metabolic changes (0, 9 24 and 48 h) by shotgun metagenomic sequencing to determine structural changes in the bacterial community, as well as metabolic genes used for substrate fermentation, nutritional properties and product safety. We found a core of 25 abundant genera throughout the 4 key fermentation times, with the genus Streptococcus being the most prevalent throughout fermentation. We also performed an analysis focused on metagenomic assembled genomes (MAGs) to identify species from the most abundant genera. Genes involving starch, plant cell wall (PCW), fructan and sucrose degradation were found throughout fermentation and in MAGs, indicating the metabolic potential of the pozol microbiota to degrade these carbohydrates. Complete metabolic modules responsible for amino acid and vitamin biosynthesis increased considerably during fermentation, and were also found to be abundant in MAG, highlighting the bacterial contribution to the well-known nutritional properties attributed to pozol. Further, clusters of genes containing CAZymes (CGCs) and essential amino acids and vitamins were found in the reconstructed MAGs for abundant species in pozol. The results of this study contribute to our understanding of the metabolic role of micro-organisms in the transformation of corn to produce this traditional beverage and their contribution to the nutritional impact that pozol has had for centuries in the traditional cuisine of southeast Mexico.
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Affiliation(s)
- Rafael López-Sánchez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | - Diana Hernández-Oaxaca
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | | | - Blanca Ramos Cerrillo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | - Agustin López-Munguía
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
| | - Lorenzo Segovia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, CP 62210, Mexico
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14
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Sharafeldin M, Rusling JF. Multiplexed electrochemical assays for clinical applications. CURRENT OPINION IN ELECTROCHEMISTRY 2023; 39:101256. [PMID: 37006828 PMCID: PMC10062004 DOI: 10.1016/j.coelec.2023.101256] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Rapid, accurate diagnoses are central to future efficient healthcare to identify diseases at early stages, avoid unnecessary treatment, and improve outcomes. Electrochemical techniques have been applied in many ways to support clinical applications by enabling the analysis of relevant disease biomarkers in user-friendly, sensitive, low-cost assays. Electrochemistry offers a launchpad for multiplexed biomarker assays that offer more accurate and precise diagnostics compared to single biomarker assays. In this short review, we underpin the importance of multiplexed analyses and provide a universal overview of current electrochemical assay strategies for multiple biomarkers. We highlight relevant examples of electrochemical methods that successfully quantify important disease biomarkers. Finally, we offer a future outlook on possible strategies that can be employed to increase throughput, sensitivity, and specificity of multiplexed electrochemical assays.
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Affiliation(s)
| | - James F. Rusling
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060
- Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136
- Department of Surgery and Neag Cancer Center, Uconn Health, Farmington, CT 06030
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland. H91 TK33
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15
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Carvalho DN, Gelinsky M, Williams DS, Mearns-Spragg A, Reis RL, Silva TH. Marine collagen-chitosan-fucoidan/chondroitin sulfate cryo-biomaterials loaded with primary human cells envisaging cartilage tissue engineering. Int J Biol Macromol 2023; 241:124510. [PMID: 37080412 DOI: 10.1016/j.ijbiomac.2023.124510] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023]
Abstract
Cartilage repair after a trauma or a degenerative disease like osteoarthritis (OA) continues to be a big challenge in current medicine due to the limited self-regenerative capacity of the articular cartilage tissues. To overcome the current limitations, tissue engineering and regenerative medicine (TERM) and adjacent areas have focused their efforts on new therapeutical procedures and materials capable of restoring normal tissue functionalities through polymeric scaffolding and stem cell engineering approaches. For this, the sustainable exploration of marine origin materials has emerged in the last years as a natural alternative to mammal sources, benefiting from their biological properties (e.g., biocompatibility, biodegradability, no toxicity, among others) for the development of several types of scaffolds. In this study, marine collagen(jCOL)-chitosan(sCHT)-fucoidan(aFUC)/chondroitin sulfate(aCS) were cryo-processed (-20 °C, -80 °C, and -196 °C) and a chemical-free crosslinking approach was explored to establish cohesive and stable cryogel materials. The cryogels were intensively characterized to assess their oscillatory behavior, thermal structural stability, thixotropic properties (around 45 % for the best formulations), injectability, and surface structural organization. Additionally, the cryogels demonstrate an interesting microenvironment in in vitro studies using human adipose-derived stem cells (hASCs), supporting their viability and proliferation. In both physic-chemical and in vitro studies, the systems that contain fucoidan in their formulations, i.e., C1 (jCOL, sCHT, aFUC) and C3 (jCOL, sCHT, aFUC, aCS), submitted at -80 °C, are those that demonstrated most promising results for future application in articular cartilage tissues.
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Affiliation(s)
- Duarte Nuno Carvalho
- 3B's Research Group, I3B's - Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Michael Gelinsky
- Centre for Translational Bone, Joint- and Soft Tissue Research, Technische Universität Dresden, Faculty of Medicine and University Hospital, 01307 Dresden, Germany
| | - David S Williams
- Jellagen Limited, Unit G6, Capital Business Park, Parkway, St Mellons, Cardiff CF3 2PY, United Kingdom
| | - Andrew Mearns-Spragg
- Jellagen Limited, Unit G6, Capital Business Park, Parkway, St Mellons, Cardiff CF3 2PY, United Kingdom
| | - Rui L Reis
- 3B's Research Group, I3B's - Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Tiago H Silva
- 3B's Research Group, I3B's - Research Institute on Biomaterials, Biodegradables and Biomimetics of University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, 4805-017 Barco, Guimarães, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
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16
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Lehle S, Emons J, Hack CC, Heindl F, Hein A, Preuß C, Seitz K, Zahn AL, Beckmann MW, Fasching PA, Ruebner M, Huebner H. Evaluation of automated techniques for extraction of circulating cell-free DNA for implementation in standardized high-throughput workflows. Sci Rep 2023; 13:373. [PMID: 36611077 PMCID: PMC9825368 DOI: 10.1038/s41598-022-27216-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023] Open
Abstract
Analysis of circulating cell-free DNA (ccfDNA) is a suitable tool for detecting somatic mutations for the purpose of making decisions on treatment, monitoring treatment response, and predicting survival. High-throughput techniques for ccfDNA extraction are essential to implementing ccfDNA testing in the clinical setting. We set out to compare two automated techniques with regard to hands-on time, ccfDNA output and integrity, and circulating mitochondrial DNA (mtDNA). CcfDNA was isolated using the EZ1&2 ccfDNA field test kit (EZ2 kit, QIAGEN) and the Maxwell RSC ccfDNA plasma kit (Maxwell kit, Promega). DNA was extracted from plasma of 30 breast cancer patients enrolled in the iMODE-B (#325_19B; 12.10.2020) study. Real-time PCR, fluorescence-based detection and automated electrophoresis were used to assess ccfDNA concentrations. The ccfDNA yield was significantly higher when extracted with the EZ2 kit. The EZ2 kit enabled the isolation of a higher proportion of short fragments and a lower proportion of long fragments, resulting in lower DNA integrity. Significantly lower mtDNA quantities were detected in the Maxwell eluate than in the EZ2 eluate. Thus, decisions on which extraction method to use should proceed on the basis of the required input for downstream applications, the anticipated fragment size and minimum hands-on time.
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Affiliation(s)
- Sarah Lehle
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Julius Emons
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Carolin C. Hack
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Felix Heindl
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Alexander Hein
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Caroline Preuß
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Katharina Seitz
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Anna L. Zahn
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Peter A. Fasching
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Matthias Ruebner
- grid.411668.c0000 0000 9935 6525Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054 Erlangen, Germany
| | - Hanna Huebner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstrasse 21-23, 91054, Erlangen, Germany.
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17
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Doleschall M, Darvasi O, Herold Z, Doleschall Z, Nyirő G, Somogyi A, Igaz P, Patócs A. Quantitative PCR from human genomic DNA: The determination of gene copy numbers for congenital adrenal hyperplasia and RCCX copy number variation. PLoS One 2022; 17:e0277299. [PMID: 36454796 PMCID: PMC9714944 DOI: 10.1371/journal.pone.0277299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/25/2022] [Indexed: 12/05/2022] Open
Abstract
Quantitative PCR (qPCR) is used for the determination of gene copy number (GCN). GCNs contribute to human disorders, and characterize copy number variation (CNV). The single laboratory method validations of duplex qPCR assays with hydrolysis probes on CYP21A1P and CYP21A2 genes, residing a CNV (RCCX CNV) and related to congenital adrenal hyperplasia, were performed using 46 human genomic DNA samples. We also performed the verifications on 5 qPCR assays for the genetic elements of RCCX CNV; C4A, C4B, CNV breakpoint, HERV-K(C4) CNV deletion and insertion alleles. Precision of each qPCR assay was under 1.01 CV%. Accuracy (relative error) ranged from 4.96±4.08% to 9.91±8.93%. Accuracy was not tightly linked to precision, but was significantly correlated with the efficiency of normalization using the RPPH1 internal reference gene (Spearman's ρ: 0.793-0.940, p>0.0001), ambiguity (ρ = 0.671, p = 0.029) and misclassification (ρ = 0.769, p = 0.009). A strong genomic matrix effect was observed, and target-singleplex (one target gene in one assay) qPCR was able to appropriately differentiate 2 GCN from 3 GCN at best. The analysis of all GCNs from the 7 qPCR assays using a multiplex approach increased the resolution of differentiation, and produced 98% of GCNs unambiguously, and all of which were in 100% concordance with GCNs measured by Southern blot, MLPA and aCGH. We conclude that the use of an internal (in one assay with the target gene) reference gene, the use of allele-specific primers or probes, and the multiplex approach (in one assay or different assays) are crucial for GCN determination using qPCR or other methods.
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Affiliation(s)
- Márton Doleschall
- Molecular Medicine Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Ottó Darvasi
- Hereditary Tumours Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
| | - Zoltán Herold
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Zoltán Doleschall
- Department of Pathogenetics, National Institute of Oncology, Budapest, Hungary
| | - Gábor Nyirő
- Molecular Medicine Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Anikó Somogyi
- Department of Internal Medicine and Hematology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Hereditary Tumours Research Group, Eotvos Lorand Research Network and Semmelweis University, Budapest, Hungary
- Department of Internal Medicine and Hematology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
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18
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Baig MMFA, Gao X, Farid A, Zia AW, Abbas M, Wu H. Synthesis of stable 2D micro-assemblies of DNA tiles achieved via intrinsic curvatures in the skeleton of DNA duplexes coupled with the flexible support of the twisted side-arms. APPLIED NANOSCIENCE 2022. [DOI: 10.1007/s13204-022-02616-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Le Dortz LL, Rouxel C, Leroy Q, Brosseau N, Boulouis HJ, Haddad N, Lagrée AC, Deshuillers PL. Optimized Lambda Exonuclease Digestion or Purification Using Streptavidin-Coated Beads: Which One Is Best for Successful DNA Aptamer Selection? Methods Protoc 2022; 5:mps5060089. [PMID: 36412811 PMCID: PMC9680285 DOI: 10.3390/mps5060089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 12/14/2022] Open
Abstract
The high failure rate of the in vitro aptamer selection process by SELEX (Systematic Evolution of Ligands by EXponential enrichment) limits the production of these innovative oligonucleotides and, consequently, limits their potential applications. The generation of single-stranded DNA (ssDNA) is a critical step of SELEX, directly affecting the enrichment and the selection of potential binding sequences. The main goal of this study was to confirm the best method for generating ssDNA by comparing the purification of ssDNA, using streptavidin-coated beads, and lambda exonuclease digestion, and by improving ssDNA recovery through protocol improvements. In addition, three techniques for quantifying the ssDNA generated (Qubit vs. NanodropTM vs. gel quantification) were compared, and these demonstrated the accuracy of the gel-based quantification method. Lambda exonuclease digestion was found to be more efficient for ssDNA recovery than purification using streptavidin-coated beads, both quantitatively and qualitatively. In conclusion, this work provides a detailed and rigorous protocol for generating ssDNA, improving the chances of a successful aptamer selection process.
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20
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Lokras A, Chakravarty A, Rades T, Christensen D, Franzyk H, Thakur A, Foged C. Simultaneous quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems. Int J Pharm 2022; 626:122171. [PMID: 36070841 DOI: 10.1016/j.ijpharm.2022.122171] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Robust, sensitive, and versatile analytical methods are essential for quantification of RNA drug cargos loaded into nanoparticle-based delivery systems. However, simultaneous quantification of multiple RNA cargos co-loaded into nanoparticles remains a challenge. Here, we developed and validated the use of ion-pair reversed-phase high-performance liquid chromatography combined with UV detection (IP-RP-HPLC-UV) for simultaneous quantification of single- and double-stranded RNA cargos. Complete extraction of RNA cargo from the nanoparticle carrier was achieved using a phenol:chloroform:isoamyl alcohol mixture. Separations were performed using either a C18 or a PLRP-S column, eluted with 0.1 M triethylammonium acetate (TEAA) solution as ion-pairing reagent (eluent A), and 0.1 M TEAA containing 25 % (v/v) CH3CN as eluent B. These methods were applied to quantify mRNA and polyinosinic:polycytidylic acid co-loaded into lipid-polymer hybrid nanoparticles, and single-stranded oligodeoxynucleotide donors and Alt-R CRISPR single guide RNAs co-loaded into lipid nanoparticles. The developed methods were sensitive (limit of RNA quantification < 60 ng), linear (R2 > 0.997), and accurate (≈ 100 % recovery of RNA spiked in nanoparticles). Hence, the present study may facilitate convenient quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems.
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Affiliation(s)
- Abhijeet Lokras
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Akash Chakravarty
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Thomas Rades
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Dennis Christensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen Ø, Denmark
| | - Aneesh Thakur
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Camilla Foged
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark.
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21
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Performance of Spectrophotometric and Fluorometric DNA Quantification Methods. ANALYTICA 2022. [DOI: 10.3390/analytica3030025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Accurate DNA quantification is a highly important method within molecular biology. Methods widely used to quantify DNA are UV spectrometry and fluorometry. In this research, seven different DNA samples and one blank (MilliQ ultrapure water) were quantified by three analysts using one spectrophotometric (i.e., a NanoDrop instrument) and three fluorometric (i.e., the AccuGreen High Sensitivity kit, the AccuClear Ultra High Sensitivity kit, and the Qubit dsDNA HS Assay kit) methods. An analysis of variance (ANOVA) scheme was used to determine the influence of the analyst, the method, and the combination of analyst and method, on DNA quantification. For most samples, the measured DNA concentration was close to or slightly above the concentration of 10 ng/μL as specified by the supplier. Results obtained by the three analysts were equal. However, it was found that, compared to the fluorometric kits, the used spectrophotometric instrument in the case of fish DNA samples tends to overestimate the DNA concentration. Therefore, if sufficient sample volume is available, a combination of a spectrophotometric and a fluorometric method is recommended for obtaining data on the purity and the dsDNA concentration of a sample.
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22
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The suitability of using spectrophotometry to determine the concentration and purity of DNA extracted from processed food matrices. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104689] [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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23
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Burke D, Pinheiro L, Glover ES, Moon F, Deans Z, Corner A. Between Laboratory Reproducibility of DNA Extraction from Human Blood and Fresh Frozen Tissue. J Mol Diagn 2022; 24:1041-1049. [PMID: 35835375 DOI: 10.1016/j.jmoldx.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/29/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022] Open
Abstract
Standardization of molecular diagnostics is fundamental for effective application of genetic analyses in personalized medicine. The amount of DNA extracted from a specimen can have a significant impact on diagnostic accuracy, especially in cases where the diagnostic variant has a low concentration such as cancer. Blood and tissue samples were supplied to genetic laboratories to assess the reproducibility of extraction methodologies; DNA was extracted using participants' routine procedures and returned to the external quality assessment provider. The amount of DNA was measured by two independent analytical techniques, fluorescence intensity of intercalating dye and digital PCR; DNA quality was evaluated by DNA integrity number scores. The amount of DNA extracted varied widely between and within participants and for different blood volumes, indicating that consistent diagnostic quality is challenging even within a single test center. The median digital PCR-measured amount of DNA was on average six times higher than the intercalating dye measurements obtained in this study, indicating the possibility that the latter quantitative method may significantly underestimate the amount of DNA, thus making it not fit for purpose. Standardization of genetic diagnostic tests will require a significant improvement in the reproducibility of DNA extraction; this could be achieved if suppliers and users of DNA extraction kits validate their extraction methodology using reliable quantitative measurements or reference materials.
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Affiliation(s)
- Daniel Burke
- National Measurement Institute, Australia (NMIA), Lindfield, New South Wales, Australia.
| | - Leonardo Pinheiro
- National Measurement Institute, Australia (NMIA), Lindfield, New South Wales, Australia
| | | | - Fiona Moon
- Genomics Quality Assessment, the Department of Laboratory Medicine, The Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Zandra Deans
- Genomics Quality Assessment, the Department of Laboratory Medicine, The Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Adam Corner
- Bio-Rad Laboratories Ltd., Digital Biology Group, Pleasanton, California
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Cheng Y, Tang Q, Lu Y, Li M, Zhou Y, Wu P, Li J, Pan F, Han X, Chen M, Lu C, Wang X, Wu W, Xia Y. Semen quality and sperm DNA methylation in relation to long-term exposure to air pollution in fertile men: A cross-sectional study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 300:118994. [PMID: 35167929 DOI: 10.1016/j.envpol.2022.118994] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Some studies have examined the association between air pollution and semen quality. While it is less of evidence on the sperm quality after long-term air pollution exposure, especially the co-exposure of different air pollution components. Additionally, the role of DNA methylation in it hasn't been confirmed. This study aimed to investigate whether long-term exposure to air pollution was associated with semen quality, as well as to explore the effect of sperm DNA methylation in such association. From 2014 to 2016, 1607 fertile men were enrolled to evaluate 14 parameters of semen quality. Exposure window was defined as one-year before semen sampling. Multivariable linear regression and weighted quantile sum (WQS) regression model were used to investigate the association between six air pollutants co-exposure and semen quality. Sensitivity analysis regarding at the normal semen quality group was also conducted. Semen samples were randomly selected from 200 participants to detect the genomic 5-methylcytosine (5 mC) and 5-hydroxymethylcytosine (5-hmC) levels in sperm. In the total population, PM10, PM2.5, SO2, and NO2 were negatively associated with sperm total motility (PM10: β = -2.67, P = 0.009; PM2.5: β = -2.86, P = 0.004; SO2: β = -2.32, P = 0.011; NO2: β = -2.21, P = 0.012). Results of the normal semen quality group were consistent with those from the whole population. WQS regression results indicated significant decreasing sperm total motility after the co-exposure of the six air pollutants (β = -1.64, P = 0.003) in whole participants. Wherein, PM10 accounted for largest proportion (43.4%). The 5-hmC level was positively associated with PM10 exposure (β = 0.002, P < 0.001). Long-term exposure to PM10, PM2.5, SO2, and NO2, as well as co-exposure to six air pollutants, reduced semen quality in fertile men. As the most significant contributor of air pollutant, PM10 exposure decreased sperm DNA methylation.
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Affiliation(s)
- Yuting Cheng
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiuqin Tang
- Department of Obstetrics, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiwen Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mei Li
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yijie Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peihao Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jinhui Li
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Feng Pan
- Department of Urology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiumei Han
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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Del Core L, Cesana D, Gallina P, Secanechia YNS, Rudilosso L, Montini E, Wit EC, Calabria A, Grzegorczyk MA. Normalization of clonal diversity in gene therapy studies using shape constrained splines. Sci Rep 2022; 12:3836. [PMID: 35264585 PMCID: PMC8907296 DOI: 10.1038/s41598-022-05837-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/09/2021] [Indexed: 12/27/2022] Open
Abstract
Viral vectors are used to insert genetic material into semirandom genomic positions of hematopoietic stem cells which, after reinfusion into patients, regenerate the entire hematopoietic system. Hematopoietic cells originating from genetically modified stem cells will harbor insertions in specific genomic positions called integration sites, which represent unique genetic marks of clonal identity. Therefore, the analysis of vector integration sites present in the genomic DNA of circulating cells allows to determine the number of clones in the blood ecosystem. Shannon diversity index is adopted to evaluate the heterogeneity of the transduced population of gene corrected cells. However, this measure can be affected by several technical variables such as the DNA amount used and the sequencing depth of the library analyzed and therefore the comparison across samples may be affected by these confounding factors. We developed an advanced spline-regression approach that leverages on confounding effects to provide a normalized entropy index. Our proposed method was first validated and compared with two state of the art approaches in a specifically designed in vitro assay. Subsequently our approach allowed to observe the expected impact of vector genotoxicity on entropy level decay in an in vivo model of hematopoietic stem cell gene therapy based on tumor prone mice.
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Affiliation(s)
- L Del Core
- University of Groningen - Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, Groningen, Netherlands. .,IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy.
| | - D Cesana
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - P Gallina
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - Y N Serina Secanechia
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - L Rudilosso
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - E Montini
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy
| | - E C Wit
- Università della Svizzera italiana - Institute of Computing, Lugano, Switzerland.
| | - A Calabria
- IRCCS Ospedale San Raffaele, San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), Milan, Italy.
| | - M A Grzegorczyk
- University of Groningen - Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, Groningen, Netherlands.
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Porcine Small Intestinal Submucosa (SIS) as a Suitable Scaffold for the Creation of a Tissue-Engineered Urinary Conduit: Decellularization, Biomechanical and Biocompatibility Characterization Using New Approaches. Int J Mol Sci 2022; 23:ijms23052826. [PMID: 35269969 PMCID: PMC8910833 DOI: 10.3390/ijms23052826] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 02/06/2023] Open
Abstract
Bladder cancer (BC) is among the most common malignancies in the world and a relevant cause of cancer mortality. BC is one of the most frequent causes for bladder removal through radical cystectomy, the gold-standard treatment for localized muscle-invasive and some cases of high-risk, non-muscle-invasive bladder cancer. In order to restore urinary functionality, an autologous intestinal segment has to be used to create a urinary diversion. However, several complications are associated with bowel-tract removal, affecting patients' quality of life. The present study project aims to develop a bio-engineered material to simplify this surgical procedure, avoiding related surgical complications and improving patients' quality of life. The main novelty of such a therapeutic approach is the decellularization of a porcine small intestinal submucosa (SIS) conduit to replace the autologous intestinal segment currently used as urinary diversion after radical cystectomy, while avoiding an immune rejection. Here, we performed a preliminary evaluation of this acellular product by developing a novel decellularization process based on an environmentally friendly, mild detergent, i.e., Tergitol, to replace the recently declared toxic Triton X-100. Treatment efficacy was evaluated through histology, DNA, hydroxyproline and elastin quantification, mechanical and insufflation tests, two-photon microscopy, FTIR analysis, and cytocompatibility tests. The optimized decellularization protocol is effective in removing cells, including DNA content, from the porcine SIS, while preserving the integrity of the extracellular matrix despite an increase in stiffness. An effective sterilization protocol was found, and cytocompatibility of treated SIS was demonstrated from day 1 to day 7, during which human fibroblasts were able to increase in number and strongly organize along tissue fibres. Taken together, this in vitro study suggests that SIS is a suitable candidate for use in urinary diversions in place of autologous intestinal segments, considering the optimal results of decellularization and cell proliferation. Further efforts should be undertaken in order to improve SIS conduit patency and impermeability to realize a future viable substitute.
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Transcriptomic Analysis Reveals that Changes in Gene Expression Contribute to Microbacterium sediminis YLB-01 Adaptation at Low Temperature Under High Hydrostatic Pressure. Curr Microbiol 2022; 79:95. [PMID: 35150317 DOI: 10.1007/s00284-022-02786-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/25/2022] [Indexed: 11/03/2022]
Abstract
Microbes living in extreme environments often adopt strategies for survival, however, only a few studies have examined the adaptive mechanism of deep-sea bacteria in in-situ environments. In this study, transcriptomic data of the deep-sea piezotolerant and psychrotolerant actinomycete Microbacterium sediminis YLB-01 under the conditions of NPNT (normal temperature and pressure: 28 °C, 0.1 MPa), HPNT (normal temperature and high pressure: 28 °C, 30 MPa), NPLT (low temperature and atmospheric pressure: 4 °C, 0.1 MPa) and HPLT (low temperature and high pressure: 4 °C, 30 MPa) were examined and compared. Transcriptome results showed that M. sediminis YLB-01 responds to deep-sea low temperature under high-pressure environments by upregulating the ABC transport system, DNA damage repair response, pentose phosphate pathway, amino acid metabolism and fatty acid metabolism, while down-regulating division, oxidative phosphorylation, the TCA cycle, pyruvate metabolism, ion transport and peptidoglycan biosynthesis. Seven key genes specifically expressed under HPLT conditions were screened, and these genes are present in many strains that are tolerant to low temperatures and high pressures. This study provides transcription level insights into the tolerance mechanisms of M. sediminis YLB-01 in a simulated deep-sea in situ environment.
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Menacho-Melgar R, Lynch MD. Measuring Oligonucleotide Hydrolysis in Cellular Lysates via Viscosity Measurements. Bio Protoc 2022; 12:e4304. [PMID: 35127994 PMCID: PMC8799667 DOI: 10.21769/bioprotoc.4304] [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: 09/17/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/01/2023] Open
Abstract
Cell lysis, a process that releases host oligonucleotides, is required in many biotechnological applications. However, intact oligonucleotides in crude cellular lysates increase the viscosity of lysates, which complicates downstream processes and routine laboratory workflows. To address this, nucleases that hydrolyze the intact oligonucleotides are commonly added, either as purified enzymes or co-expressed in genetically engineered bacterial strains. To measure oligonucleotide hydrolysis, common DNA quantification methods, such as qPCR or fluorescence-based, require expensive reagents and equipment, and cannot distinguish different-sized DNA fragments. Here, we outline a simple alternative method for measuring DNA/RNA hydrolysis in cellular lysates, by measuring their viscosity. This method only requires common laboratory supplies and a cell phone camera.
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Affiliation(s)
| | - Michael D. Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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29
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Van Asselt AJ, Ehli EA. Whole-Genome Genotyping Using DNA Microarrays for Population Genetics. Methods Mol Biol 2022; 2418:269-287. [PMID: 35119671 DOI: 10.1007/978-1-0716-1920-9_16] [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: 06/14/2023]
Abstract
The field of population genetics has exploded in the last two decades following the sequencing of the human genome in 2001 (Green et al. Nature 526:29-31, 2015). Tools to measure genetic variation have matured significantly throughout this advancement in knowledge (Lenoir and Giannella. J Biomed Discov Collab 1:11, 2006; Marzancola et al. Methods Mol Biol 1368:161-178, 2016). In this chapter, the focus is on the laboratory methods developed to perform genome-wide genotyping utilizing DNA microarrays, which is one of the most commonly used molecular techniques to assess global genetic variation (Heller MJ, Annu Rev Biomed Eng 4:129-153, 2002). DNA microarrays allow for the interrogation of hundreds of thousands of SNPs (single nucleotide polymorphisms) at once utilizing array-based technology in conjunction with fluorescent molecular labels in a process referred to as genotyping (Marzancola et al. Methods Mol Biol 1368:161-178, 2016). Genotype data can be utilized to associate certain phenotypes in relation with specific genetic variants within a population in a process known as genome-wide association studies or GWAS (Charlesworth and Charlesworth. Heredity (Edinb) 118(1):2-9, 2017; Casillas and Barbadilla. Genetics 205(3):1003-1035, 2017). This experimental technique is a multiple-day process involving the combination of DNA extraction, amplification, fragmentation, binding, and staining (Illumina Infinium HTS Assay Protocol Guide, 2013). Many vendors supply platforms and products to assess global genetic variation using DNA microarrays (Illumina Infinium HTS Assay Protocol Guide, 2013). In this chapter, the focus is on the methods utilized to generate high-quality genotype data with the Illumina® Infinium Global Screening Array. Although data analysis and quality control are not the focus for this chapter, they are also briefly addressed.
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Affiliation(s)
- Austin J Van Asselt
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Erik A Ehli
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD, USA.
- Department of Psychiatry, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA.
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30
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Ohni S, Yamaguchi H, Hirotani Y, Nakanishi Y, Midorikawa Y, Sugitani M, Naruse H, Nakayama T, Makishima M, Esumi M. Direct molecular evidence for both multicentric and monoclonal carcinogenesis followed by transdifferentiation from hepatocellular carcinoma to cholangiocarcinoma in a case of metachronous liver cancer. Oncol Lett 2022; 23:22. [PMID: 34868359 PMCID: PMC8630812 DOI: 10.3892/ol.2021.13140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/18/2021] [Indexed: 01/21/2023] Open
Abstract
Frequent recurrence is a major issue in liver cancer and histological heterogeneity frequently occurs in this cancer type. However, it has remained elusive whether such cancers are multicentric or monoclonal. To elucidate the clonal evolution of hepatocellular carcinoma (HCC) recurrence and combined hepatocellular-cholangiocarcinoma (cHCC-CCA) development, the somatic mutation frequency and signatures in a patient with triple occurrence of liver cancer every three years were examined, with samples designated as #1HCC, #2HCC and #3cHCC-CCA, respectively. A total of four tumor regions, including HCC (#3HCC) and intrahepatic CCA (#3iCCA) components of #3cHCC-CCA, and three nontumor regions (#1N, #2N and #3N) were precisely dissected from formalin-fixed paraffin-embedded tissues of each surgical specimen. DNA was extracted and subjected to tumor-specific somatic mutation determination. Of note, five nonsynonymous single-nucleotide variants (SNVs), namely those of KMT2D, TP53, DNMT3A, PKHD1 and TLR4, were identified in #3cHCC-CCA. All five SNVs were detected in both #3HCC and #3iCCA and #2HCC but not in #1HCC. The telomerase reverse transcriptase (TERT) promoter mutation C228T, but not C250T, was observed in all tumors. Digital PCR of C228T also indicated the presence of the TERT promoter mutation C228T in nontumorous liver tissues (#1N, #2N and #3N) at a frequency of 0.11-0.83% compared with normal liver and blood samples. These results suggest the following phylogenetic evolution of three metachronous liver cancers: #1HCC was not related to #2HCC, #3HCC and #3iCCA; both #3HCC and #3iCCA arose from #2HCC. From the above, three novel findings were deduced: i) Both multicentric occurrence and intrahepatic metastasis may be involved in liver cancer in a three-year interval; ii) transdifferentiation from HCC to iCCA is a possible pathogenic mechanism of cHCC-CCA; and iii) a nontumorous, noncirrhotic liver may contain a preneoplastic region with a cancer driver mutation in the TERT promoter.
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Affiliation(s)
- Sumie Ohni
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiromi Yamaguchi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yukari Hirotani
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yoko Nakanishi
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yutaka Midorikawa
- Department of Surgery, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Masahiko Sugitani
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiromu Naruse
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Tomohiro Nakayama
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Mariko Esumi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
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Paul P, Rajput S, Joshi P, Naithani M, Chowdhury N, Rao S, Pai MO. Comparison of Fluorometric and UV Spectrophotometric Findings for DNA Isolated From Formalin-Fixed Paraffin-Embedded Blocks, Fine Needle Aspiration Cytology Smears, and Blood. Cureus 2021; 13:e19583. [PMID: 34926054 PMCID: PMC8672151 DOI: 10.7759/cureus.19583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2021] [Indexed: 12/04/2022] Open
Abstract
Introduction: Fine needle aspiration cytology (FNAC) smear may serve as a convenient sample for DNA extraction for molecular pathology in addition to more commonly used formalin-fixed paraffin-embedded (FFPE) sections. DNA quantification done by fluorometer is more accurate than UV vis spectrophotometer regardless of the source. This study was conducted to compare DNA yield and quality from cytology smears, FFPE sections and peripheral blood using both fluorometer and spectrophotometer. Further, introspection was made to check for the adequacy of DNA extracted from cytology smears with respect to DNA extracted from core biopsies. Method: DNA was extracted from 10 fresh peripheral blood samples, core biopsies and FNAC smears. The DNA was quantified using a fluorimeter and UV vis spectrophotometer in all cases. Results: Statistically significant difference was seen between the data obtained from UV vis spectrophotometry and flourometry. The quantity of DNA extracted from FNAC smears was higher than that of core biopsy as per fluorometry data (mean DNA of core biopsy = 1.9ng/µl, of FNAC = 3.3ng/µl). Conclusion: DNA estimation by fluorometry is more accurate and precise than spectrophotometry in FFPE, FNAC and whole blood samples. DNA yield from FNAC slides is comparable to that from core biopsies.
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LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species. Life (Basel) 2021; 11:life11111163. [PMID: 34833039 PMCID: PMC8624210 DOI: 10.3390/life11111163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/19/2022] Open
Abstract
Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species. Advantages of the LoopTag system include having cheap conventional fluorescence dyes, easy primer design, no restrictions for PCR product lengths, robustness, high sequence specificity, applicability for multiplex real-time PCRs, melting curve analysis (single nucleotide polymorphism analysis) over a large temperature range, high sensitivity, and easy adaptation of conventional PCRs. Results: Using the LoopTag probe system we were able to detect all nine tested European species belonging to the Borrelia burgdorferi (sensu lato) complex and differentiated them from relapsing fever Borrelia species. As few as 10 copies of Borrelia in one PCR reaction were detectable. Conclusion: We established a novel multiplex probe real-time PCR system, designated LoopTag, that is simple, robust, and incorporates melting curve analysis for the detection and in the differentiation of European species belonging to the Borrelia burgdorferi s.l. complex.
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Kobayashi H, Nakai T, Nakanishi Y, Esumi M, Masuda S. Phylogenetic analysis of combined lobular and ductal carcinoma of the breast. Mol Med Rep 2021; 24:718. [PMID: 34396426 PMCID: PMC8383046 DOI: 10.3892/mmr.2021.12357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 07/12/2021] [Indexed: 11/18/2022] Open
Abstract
Breast cancer manifests in diverse forms, with particular reference to various cell types harboring different mutations and gene expression profiles. To elucidate the clonal relationship between cancer cells in tumors composed of both ductal and lobular phenotypes, two combined lobular and ductal carcinoma (CLDC) cases were analyzed, including one mixed ductal‑lobular carcinoma (MDL) lesion, by direct sequencing of the mitochondrial DNA D‑loop, digital PCR targeting of chromosomes 1q and 16q, as well as next‑generation sequencing. DNA was extracted from formalin‑fixed paraffin‑embedded tissue sections of different histological types, including invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, lobular carcinoma in situ, flat epithelial atypia, non‑neoplastic mammary gland and extramammary organs, using laser‑assisted microdissection. Mutations detected by the comprehensive cancer panel were validated by SYBR green allele‑specific quantitative PCR (RRM1, AKT1, PIK3CA, RALGDS, EGFR, TP53, IL21R, DPYD, SGK1, CDH1, TIMP3 and KMT2C). CLDC, which shared the basic genetic alterations of 1q gain or 16q loss, progresses to invasive lobular or ductual carcinoma with the accumulation of further mutations. Cancer cells contained in an MDL lesion shared closely related genetic alterations, suggesting that these cells have the same origin, despite different histological features, namely 'lobular' or 'ductal'. By contrast, multiple lesions located away from the main tumor, diagnosed as CLDC (excluding an MDL lesion) were not always identical with different genetic alterations, despite being diagnosed as ductal carcinoma in situ. Thus, MDL should be defined as a distinct category separate from CLDC, whose components of 'lobular' and 'ductal' may have the same cellular origin.
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MESH Headings
- Adult
- Breast
- Breast Neoplasms/classification
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/classification
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Lobular/classification
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/pathology
- Female
- Genotype
- High-Throughput Nucleotide Sequencing
- Humans
- Middle Aged
- Mutation
- Phylogeny
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Hiroko Kobayashi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Tokiko Nakai
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Yoko Nakanishi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Mariko Esumi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Shinobu Masuda
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
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Hu Y, Bai L, Zhao L, Wu L, Lv H, Li Q, Li X, Xie Q, Wang L, Liu C, Liu N, Cui S. Standardized Shiga-Toxin Encoding Genes Real-Time PCR Screening Methods Comparison and Development of an Internally Controlled Assay for Pan-stx2 Detection. J AOAC Int 2021; 104:1065-1071. [PMID: 33724375 DOI: 10.1093/jaoacint/qsab030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Various primer and probe sets have been developed and standardized, but certain sets may have low efficiency or miss some stx-subtypes. OBJECTIVE To compare the efficiency of the recommended stx screening primers and probe sets in four standardized methods and develop a new primers and probe system with an internal amplification control (IAC) for all known stx2 subtypes. METHOD The inclusivity and specificity of recommended screening primers and probe sets in four standardized methods were compared. A new pan-stx2 primer and probe set was adapted from the International Organization for Standardization (ISO) method for all known stx2 subtypes. The robustness of the new method was assessed in seven laboratories and also assessed in ground beef and bean sprout samples. RESULTS None of the recommended screening primers and probe sets in the four standardized methods could efficiently amplify all the stx2 subtypes because of various mismatches in the primers or the probe sequences. A new primers and probe system adapted from the ISO method, through introducing degenerate bases in primers and probe sequences with an IAC, showed high amplification efficiency and specificity for all known stx2 subtypes in ground beef and bean sprouts samples. The specificity of the new method was assessed in seven laboratories and showed robust and consistent results. CONCLUSIONS This study provided evidence for Shiga-toxin producing Escherichia coli (STEC) screening method development, and the newly developed primers and probes system should be considered in the revision of the standardized methods. HIGHLIGHTS None of the recommended screening primer and probe set in the four official methods could efficiently amplify all the stx2 subtypes. A new developed primer and probe set showed high amplification efficiency and specificity for all known stx2 subtypes in fresh ground beef and bean sprouts samples. The newly developed stx2 screening system showed robustness and consistency during interlaboratory study.
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Affiliation(s)
- Ying Hu
- College of Food Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, PR, China.,Department of Food Science, The National Institutes for Food and Drug Control, No.2 Tiantan Xili, Dongcheng District, Beijing 100050 , PR, China
| | - Li Bai
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Yard No.37, Guangqu Road, Chaoyang District, Beijing 100022, PR, China
| | - Linna Zhao
- Department of Food Science, The National Institutes for Food and Drug Control, No.2 Tiantan Xili, Dongcheng District, Beijing 100050 , PR, China
| | - Lingling Wu
- Center for Disease Control and Prevention of Henan Province, No.105 Nongye South Road, Zhengdong New District, Zhengzhou, 450016, PR, China
| | - Hong Lv
- Center for Disease Control and Prevention of Sichuan Province, No.6 Middle School Road, Chengdu, 610041, PR, China
| | - Qiongqiong Li
- Shanghai Institute of Food and Drug Control, No.1500 Zhangheng Road, Pudong New Area, Shanghai, 201203, PR, China
| | - Xinpeng Li
- Center for Disease Prevent and Control of Shandong Province, No. 16992 Jingshi Road, Jinan, 250014, PR, China
| | - Qingchao Xie
- Shanghai Ocean University, College of Food Science and Technology, No.999 Hucheng Ring Road, Pudong New Area, 201306, Shanghai, PR, China
| | - Lili Wang
- Beijing Centers for Disease Prevention and Control, Beijing Centers for Disease Preventive Medical Research, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, No.16 Heping Li Zhong Jie, Dongcheng District, Beijing, 100013, PR, China
| | - Chengwei Liu
- Center for Disease Prevent and Control of Jiangxi Province, No.555 Beijing Dong Lu, Nanchang, 330029, PR, China
| | - Na Liu
- Department of Food Science, The National Institutes for Food and Drug Control, No.2 Tiantan Xili, Dongcheng District, Beijing 100050 , PR, China
| | - Shenghui Cui
- Department of Food Science, The National Institutes for Food and Drug Control, No.2 Tiantan Xili, Dongcheng District, Beijing 100050 , PR, China
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Farajpour N, Lastra LS, Sharma V, Freedman KJ. Calibration-Less DNA Concentration Measurements Using EOF Volumetric Flow and Single Molecule Counting. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.689584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nanopore sensing is a promising tool well suited to capture and detect DNA and other single molecules. DNA is a negatively charged biomolecule that can be captured and translocated through a constricted nanopore aperture under an applied electric field. Precise assessment of DNA concentration is of crucial importance in many analytical processes and medical diagnostic applications. Recently, we found that hydrodynamic forces can lead to DNA motion against the electrophoretic force (EPF) at low ionic strength. This study utilized glass nanopores to investigate the DNA capture mechanism and detect DNA molecules due to volumetric flow at these low ionic strength conditions. We measured the DNA capture rate at five different pico-molar concentrations. Our findings indicated that the translocation rate is proportional to the concentration of DNA molecules and requires no calibration due to the volumetric flow rate and DNA counting directly correlates with concentration. Using finite element analysis, we calculated the volumetric flow and proposed a simple, straightforward approach for accurate DNA quantification. Furthermore, these experiments explore a unique transport mechanism where one of the most highly charged molecules enters a pore against electric field forces. This quantitative technique has the potential to provide distinct insight into nanopore-based biosensing and further enhance the nanopore’s capability as a biomolecule concentration sensor.
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Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. mSystems 2021; 6:e0029421. [PMID: 34254828 PMCID: PMC8409480 DOI: 10.1128/msystems.00294-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.
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37
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Sun C, Liu L, Vasudevan HN, Chang KC, Abate AR. Accurate Bulk Quantitation of Droplet Digital Polymerase Chain Reaction. Anal Chem 2021; 93:9974-9979. [PMID: 34252272 PMCID: PMC8829825 DOI: 10.1021/acs.analchem.1c00877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Droplet digital PCR
provides superior accuracy for nucleic acid
quantitation. The requirement of microfluidics to generate and analyze
the emulsions, however, is a barrier to its adoption, particularly
in low resource settings or clinical laboratories. Here, we report
a novel method to prepare ddPCR droplets by vortexing and readout
of the results by bulk analysis of recovered amplicons. We demonstrate
the approach by accurately quantitating SARS-CoV-2 sequences using
entirely bulk processing and no microfluidics. Our approach for quantitating
reactions should extend to all digital assays that generate amplicons,
including digital PCR and LAMP conducted in droplets, microchambers,
or nanoliter wells. More broadly, our approach combines important
attributes of ddPCR, including enhanced accuracy and robustness to
inhibition, with the high-volume sample processing ability of quantitative
PCR.
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Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Harish N Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94158, United States
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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38
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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Naue J, Winkelmann J, Schmidt U, Lutz-Bonengel S. Analysis of age-dependent DNA methylation changes in plucked hair samples using massive parallel sequencing. Rechtsmedizin (Berl) 2021. [DOI: 10.1007/s00194-021-00487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe analysis of age-dependent DNA methylation changes is a valuable tool in epigenetic research and forensic genetics. With some exceptions, most studies in the past concentrated on the analysis of blood, buccal, and saliva samples. Another important sample type in forensic investigations is hair, where age-dependent DNA methylation has not been investigated so far. In this pilot study a deeper look was taken at the possibilities and challenges of DNA methylation analysis in hair. The DNA methylation of selected age-dependent 5’-C-phosphate-G‑3’ (CpG) sites were characterized for their potential use as a biomarker for age prediction using plucked hair samples and massive parallel sequencing. Plucked hair roots of 49 individuals were included in the study. The DNA methylation of 31 hairs was successfully analyzed. The DNA methylation pattern of 10 loci, including ELOVL2, F5, KLF14, and TRIM59, was determined by amplicon-based massive parallel sequencing. Age-dependent changes were found for several markers. The results demonstrate the possible use of already established age-dependent markers but at the same time they have tissue/cell type-specific characteristics. Special challenges such as low amounts of DNA and degraded DNA as well as the possible heterogeneous cellular composition of plucked hair samples, have to be considered.
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40
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Sloan S, Jenvey CJ, Piedrafita D, Preston S, Stear MJ. Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes. BMC Biotechnol 2021; 21:35. [PMID: 34001079 PMCID: PMC8130168 DOI: 10.1186/s12896-021-00695-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. Results 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. Conclusions A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00695-6.
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Affiliation(s)
- S Sloan
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia.
| | - C J Jenvey
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
| | - D Piedrafita
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - S Preston
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - M J Stear
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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Nauwelaerts SJD, Van Geel D, Delvoye M, De Cremer K, Bernard A, Roosens NHC, De Keersmaecker SCJ. Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva? J Biomol Tech 2021; 31:27-35. [PMID: 32042275 DOI: 10.7171/jbt.20-3101-004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.
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Affiliation(s)
- Sarah J D Nauwelaerts
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Dirk Van Geel
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Maud Delvoye
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | - Koen De Cremer
- Platform Chromatography and Mass Spectrometry, Sciensano, 1050 Brussels, Belgium; and
| | - Alfred Bernard
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain Woluwe, 1200 Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
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Binyamin D, Nitzan O, Azrad M, Hamo Z, Koren O, Peretz A. The microbial diversity following antibiotic treatment of Clostridioides difficile infection. BMC Gastroenterol 2021; 21:166. [PMID: 33849457 PMCID: PMC8045228 DOI: 10.1186/s12876-021-01754-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/07/2021] [Indexed: 01/04/2023] Open
Abstract
Background Clostridioides difficile (C. difficile) is a major nosocomial pathogen that infects the human gut and can cause diarrheal disease. A dominant risk factor is antibiotic treatment that disrupts the normal gut microbiota. The aim of the study was to examine the correlation between antibiotic treatment received prior to C. difficile infection (CDI) onset and patient gut microbiota. Methods Stool samples were collected from patients with CDI, presenting at the Baruch Padeh Medical Center Poriya, Israel. Demographic and clinical information, including previous antibiotic treatments, was collected from patient charts, and CDI severity score was calculated. Bacteria were isolated from stool samples, and gut microbiome was analyzed by sequencing the 16S rRNA gene using the Illumina MiSeq platform and QIIME2. Results In total, 84 patients with CDI were enrolled in the study; all had received antibiotics prior to disease onset. Due to comorbidities, 46 patients (55%) had received more than one class of antibiotics. The most common class of antibiotics used was cephalosporins (n = 44 cases). The intestinal microbiota of the patients was not uniform and was mainly dominated by Proteobacteria. Differences in intestinal microbiome were influenced by the different combinations of antibiotics that the patients had received (p = 0.022) Conclusions The number of different antibiotics administered has a major impact on the CDI patients gut microbiome, mainly on bacterial richness.
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Affiliation(s)
- Dana Binyamin
- The Azrieli Faculty of Medicine, Bar Ilan University, 1311502, Safed, Israel
| | - Orna Nitzan
- Unit of Infectious Diseases, Baruch Padeh Medical Center, 15208, Poriya, Israel
| | - Maya Azrad
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Hanna Senesh 818/2, 15208, Poriya, Tiberias, Israel
| | - Zohar Hamo
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Hanna Senesh 818/2, 15208, Poriya, Tiberias, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar Ilan University, 1311502, Safed, Israel
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar Ilan University, 1311502, Safed, Israel. .,Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Hanna Senesh 818/2, 15208, Poriya, Tiberias, Israel.
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Baig MMFA, Zhang C, Akhtar MF, Saleem A, Mudassir J. The effective transfection of a low dose of negatively charged drug-loaded DNA-nanocarriers into cancer cells via scavenger receptors. J Pharm Anal 2021; 11:174-182. [PMID: 34012693 PMCID: PMC8116213 DOI: 10.1016/j.jpha.2020.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 12/26/2022] Open
Abstract
DNA-nanotechnology-based nano-architecture scaffolds based on circular strands were designed in the form of DNA-nanowires (DNA-NWs) as a polymer of DNA-triangles. Circularizing a scaffold strand (84-NT) was the critical step followed by annealing with various staple strands to make stiff DNA-triangles. Atomic force microcopy (AFM), native polyacrylamide gel electrophoresis (PAGE), UV-analysis, MTT-assay, flow cytometry, and confocal imaging were performed to assess the formulated DNA-NWs and cisplatin (CPT) loading. The AFM and confocal microscopy images revealed a uniform shape and size distribution of the DNA-NWs, with lengths ranging from 2 to 4 μm and diameters ranging from 150 to 300 nm. One sharp band at the top of the lane (500 bp level) with the loss of electrophoretic mobility during the PAGE (native) gel analysis revealed the successful fabrication of DNA-NWs. The loading efficiency of CPT ranged from 66.85% to 97.35%. MTT and flow cytometry results showed biocompatibility of the blank DNA-NWs even at 95% concentration compared with the CPT-loaded DNA-NWs. The CPT-loaded DNA-NWs exhibited enhanced apoptosis (22%) compared to the apoptosis (7%) induced by the blank DNA-NWs. The release of CPT from the DNA-NWs was sustained at < 75% for 6 h in the presence of serum, demonstrating suitability for systemic applications. The IC50 of CPT@DNA-NWs was reduced to 12.8 nM CPT, as compared with the free CPT solution exhibiting an IC50 of 51.2 nM. Confocal imaging revealed the targetability, surface binding, and slow internalization of the DNA-NWs in the scavenger-receptor-rich cancer cell line (HepG2) compared with the control cell line.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Laboratory of Biomedical & Pharmaceutical Engineering of Stem Cells Research, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, 999077, Hong Kong, PR China
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan
| | - Chengfei Zhang
- Laboratory of Biomedical & Pharmaceutical Engineering of Stem Cells Research, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, 999077, Hong Kong, PR China
| | - Muhammad Furqan Akhtar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University, Lahore, Pakistan
| | - Ammara Saleem
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Jahanzeb Mudassir
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60000, Pakistan
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Nicolás-Párraga S, Torres M, Alemany L, Félix A, Cruz E, de Sanjosé S, Bosch FX, Bravo IG. Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning 85 years. Virol J 2021; 18:65. [PMID: 33781303 PMCID: PMC8008572 DOI: 10.1186/s12985-021-01529-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/05/2021] [Indexed: 12/01/2022] Open
Abstract
Background Quality of the nucleic acids extracted from Formalin Fixed Paraffin Embedded (FFPE) samples largely depends on pre-analytic, fixation and storage conditions. We assessed the differential sensitivity of viral and human double stranded DNA (dsDNA) to degradation with storage time. Methods We randomly selected forty-four HPV16-positive invasive cervical cancer (ICC) FFPE samples collected between 1930 and 1935 and between 2000 and 2004. We evaluated through qPCR the amplification within the same sample of two targets of the HPV16 L1 gene (69 bp, 134 bp) compared with two targets of the human tubulin-β gene (65 bp, 149 bp). Results Both viral and human, short and long targets were amplified from all samples stored for 15 years. In samples archived for 85 years, we observed a significant decrease in the ability to amplify longer targets and this difference was larger in human than in viral DNA: longer fragments were nine times (CI 95% 2.6–35.2) less likely to be recovered from human DNA compared with 1.6 times (CI 95% 1.1–2.2) for viral DNA. Conclusions We conclude that human and viral DNA show a differential decay kinetics in FFPE samples. The faster degradation of human DNA should be considered when assessing viral DNA prevalence in long stored samples, as HPV DNA detection remains a key biomarker of viral-associated transformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01529-9.
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Affiliation(s)
- Sara Nicolás-Párraga
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Montserrat Torres
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Laia Alemany
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ana Félix
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Lisbon), Lisbon, Portugal
| | - Eugenia Cruz
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Coimbra), Coimbra, Portugal
| | - Silvia de Sanjosé
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Sexual and Reproductive Health, PATH, Seattle, USA.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francesc Xavier Bosch
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Biomedical Research Networking Centre On Cancer (CIBERONC), Madrid, Spain.,Universitat Oberta de Catalunya, Barcelona, Spain
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.,Laboratory MIVEGEC (CNRS IRD Univ Montpellier), French National Center for Scientific Research (CNRS), Montpellier, France.,Center for Research On the Ecology and Evolution of Diseases (CREES), Montpellier, France
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Strezsak SR, Beuning PJ, Skizim NJ. Complete enzymatic digestion of double-stranded RNA to nucleosides enables accurate quantification of dsRNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:179-185. [PMID: 33319868 DOI: 10.1039/d0ay01498b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The rapid growth of research focusing on RNA, especially for RNA interference applications, has created a need for a robust method that can accurately determine the concentration of long dsRNA. As it is difficult to find a source for pure dsRNA reference material, the most common method for quantitation is using a reversed-phase HPLC method to determine purity, which is linked to a calibration curve prepared by measurements obtained using UV absorbance at 260 nm. In this study we developed a nucleic acid digestion method that can digest both double- and single-stranded RNA and DNA to nucleosides. A reversed-phase HPLC/UV method was used to separate and quantitate the monomeric nucleosides. Using this method, we were able to calculate the absorptivity coefficient (proxy for the extinction coefficient) for dsRNA to be 45.9 ± 0.52 μg mL-1/A260. This value agrees with the one report we were able to find but uses an orthogonal method. Moreover, this study allowed us to understand that sequence design can dramatically change the extinction coefficient of the molecule. For molecules with ssRNA overhangs, we observed a 5% reduction in the calculated extinction coefficient.
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Affiliation(s)
- Steven R Strezsak
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA and Greenlight Biosciences, Medford, MA 02155, USA.
| | - Penny J Beuning
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA
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Gagnon P, Goricar B, Mencin N, Zvanut T, Peljhan S, Leskovec M, Strancar A. Multiple-Monitor HPLC Assays for Rapid Process Development, In-Process Monitoring, and Validation of AAV Production and Purification. Pharmaceutics 2021; 13:113. [PMID: 33477351 PMCID: PMC7830902 DOI: 10.3390/pharmaceutics13010113] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/08/2021] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
HPLC is established as a fast convenient analytical technology for characterizing the content of empty and full capsids in purified samples containing adeno-associated virus (AAV). UV-based monitoring unfortunately over-estimates the proportion of full capsids and offers little value for characterizing unpurified samples. The present study combines dual-wavelength UV monitoring with intrinsic fluorescence, extrinsic fluorescence, and light-scattering to extend the utility of HPLC for supporting development of therapeutic AAV-based drugs. Applications with anion exchange (AEC), cation exchange (CEC), and size exclusion chromatography (SEC) are presented. Intrinsic fluorescence increases sensitivity of AAV detection over UV and enables more objective estimation of empty and full capsid ratios by comparison of their respective peak areas. Light scattering enables identification of AAV capsids in complex samples, plus semiquantitative estimation of empty and full capsid ratios from relative peak areas of empty and full capsids. Extrinsic Picogreen fluorescence enables semiquantitative tracking of DNA with all HPLC methods at all stages of purification. It does not detect encapsidated DNA but reveals DNA associated principally with the exteriors of empty capsids. It also enables monitoring of host DNA contamination across chromatograms. These enhancements support many opportunities to improve characterization of raw materials and process intermediates, to accelerate process development, provide rapid in-process monitoring, and support process validation.
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Affiliation(s)
- Pete Gagnon
- BIA Separations, Sartorius Company, Mirce 21, 5270 Ajdovscina, Slovenia; (B.G.); (N.M.); (T.Z.); (S.P.); (M.L.); (A.S.)
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Sun C, Liu L, Vasudevan HN, Chang KC, Abate AR. Accurate bulk quantitation of droplet digital PCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.13.424628. [PMID: 33469578 PMCID: PMC7814815 DOI: 10.1101/2021.01.13.424628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Droplet digital PCR provides superior accuracy in nucleic acid quantitation. The requirement of microfluidics to generate and analyze the emulsions, however, is a barrier to its adoption, particularly in low resource or clinical settings. Here, we report a novel method to prepare ddPCR droplets by vortexing and readout the results by bulk analysis of recovered amplicons. We demonstrate the approach by accurately quantitating SARS-CoV-2 sequences using entirely bulk processing and no microfluidics. Our approach for quantitating reactions should extend to all digital assays that generate amplicons, including digital PCR and LAMP conducted in droplets, microchambers, or nanoliter wells. More broadly, our approach combines important attributes of ddPCR, including enhanced accuracy and robustness to inhibition, with the high-volume sample processing ability of quantitative PCR.
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Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Harish N. Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Shukla NI, Siva N, Sivakumar M, Parveen R, Mishra A, Shah A, Medicherla K, Suravajhala P. Extraction of DNA and RNA from Formalin-fixed Paraffin-embedded Tissue Specimens. Bio Protoc 2021. [DOI: 10.21769/bioprotoc.4095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Rohana H, Azrad M, Nitzan O, Adler A, Binyamin D, Koren O, Peretz A. Characterization of Clostridioides difficile Strains, the Disease Severity, and the Microbial Changes They Induce. J Clin Med 2020; 9:jcm9124099. [PMID: 33353133 PMCID: PMC7766075 DOI: 10.3390/jcm9124099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is a major nosocomial disease. The characteristics of different strains, the disease severity they cause, their susceptibility to antibiotics, and the changes they inflict on gut microbiome, have not been comprehensively studied in Israel. METHODS A severity score was calculated for 70 patients. Stool samples were tested for toxins presence using a special kit. Bacteria were isolated, identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and antibiotic susceptibility tests were performed for several antibiotics. Strains were classified by Multi-locus sequence typing (MLST), and changes in gut microbiome were tested. RESULTS ST04 (22.5%) and ST37 (12.7%) were the most frequent strains. Clade (phylogenetic lineage) 1 was the most (81.4%) prevalent. We found significant associations between ST and age (p = 0.024) and between ST and moxifloxacin susceptibility (p = 0.001). At the clade level, we found significant associations with binary toxin gene occurrence (p = 0.002), and with susceptibility to both metronidazole and vancomycin (p = 0.024, 0.035, respectively). Differences in intestine microbiome were affected by age, clades' distribution and STs. CONCLUSIONS By defining the characteristics of the different strains and clades, clinicians can choose medical interventions based on the predicted response or disease severity associated with each strain, enabling new advances in the field of personalized medicine.
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Affiliation(s)
- Hanan Rohana
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Maya Azrad
- Baruch Padeh Medical Center, Clinical Microbiology Laboratory, Poriya, Tiberias 1528001, Israel;
| | - Orna Nitzan
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
- Baruch Padeh Medical Center, Unit of Infectious Diseases, Poriya, Tiberias 1528001, Israel
| | - Amos Adler
- Tel Aviv Sourasky Medical Centre, Microbiology Laboratory, Tel Aviv 6423906, Israel;
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dana Binyamin
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
| | - Avi Peretz
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed 1311502, Israel; (H.R.); (O.N.); (D.B.); (O.K.)
- Baruch Padeh Medical Center, Clinical Microbiology Laboratory, Poriya, Tiberias 1528001, Israel;
- Correspondence: ; Tel.: +972-4-665-2322
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Kuwata T, Wakabayashi M, Hatanaka Y, Morii E, Oda Y, Taguchi K, Noguchi M, Ishikawa Y, Nakajima T, Sekine S, Nomura S, Okamoto W, Fujii S, Yoshino T. Impact of DNA integrity on the success rate of tissue-based next-generation sequencing: Lessons from nationwide cancer genome screening project SCRUM-Japan GI-SCREEN. Pathol Int 2020; 70:932-942. [PMID: 33030786 PMCID: PMC7820973 DOI: 10.1111/pin.13029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
In the nationwide cancer genome screening project SCRUM-Japan GI-SCREEN, 2590 archival formalin-fixed paraffin-embedded (FFPE) tumor tissues from 19 institutions were analyzed with two tissue-based next-generation sequencing (NGS) panels at the Clinical Laboratory Improvement Amendments (CLIA)-certified College of American Pathologists (CAP)-accredited central laboratory. The Oncomine Cancer Research Panel (OCP; 143 genes) succeeded in producing validated results for only 68.3% of the samples (%OCP-success). CE-IVD (25 genes) succeeded in 45.9% of the OCP-failed samples, leading to an overall NGS success (%combined-success) rate as high as 82.9%. Among 2573 samples, the DNA-integrity (ΔCt )-high (ΔCt < 4.4, n = 1253) samples showed significantly higher %OCP- and %combined-success rates (90.2% and 97.4%, respectively) than the DNA-integrity-intermediate (4.4 < ΔCt < 6.3, n = 911; 68.9% and 88.7%) and DNA-integrity-low ones (ΔCt > 6.3 or polymerase chain reaction-failed, n = 409; 5.6% and 24.7%). Other factors associated with NGS success included the FFPE-sample storage period (<4 years), the specimen type (surgical) and the primary tumor site (colorectal). Multivariable analysis revealed DNA integrity as the factor with the strongest independent association with NGS success, although it was suggested that other institution-specific factors contribute to the discordance of inter-institutional NGS success rates. Our results emphasize the importance of DNA quality in FFPE samples for NGS tests and the impact of DNA integrity on quality monitoring of pathology specimens for achieving successful NGS.
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Affiliation(s)
- Takeshi Kuwata
- Department of Genetic Medicine and ServicesNational Cancer Center Hospital EastChibaJapan
- Department of Pathology and Clinical LaboratoriesNational Cancer Center Hospital EastChibaJapan
| | - Masashi Wakabayashi
- Clinical Research Support OfficeNational Cancer Center Hospital EastChibaJapan
| | - Yutaka Hatanaka
- Research Division of Genome Companion DiagnosticsHokkaido University HospitalHokkaidoJapan
| | - Eiichi Morii
- Department of PathologyOsaka University Graduate School of MedicineOsakaJapan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Pathological Sciences, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kenichi Taguchi
- Department of PathologyNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Masayuki Noguchi
- Department of Diagnostic Pathology, Faculty of MedicineUniversity of TsukubaIbarakiJapan
| | - Yuichi Ishikawa
- Department of Pathology, the Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Takashi Nakajima
- Division of Diagnostic PathologyShizuoka Cancer Center HospitalShizuokaJapan
| | - Shigeki Sekine
- Department of PathologyNational Cancer Center HospitalTokyoJapan
| | - Shogo Nomura
- Clinical Research Support OfficeNational Cancer Center Hospital EastChibaJapan
| | - Wataru Okamoto
- Translational Research Support SectionNational Cancer Center Hospital EastChibaJapan
- Cancer Treatment CenterHiroshima University HospitalHiroshimaJapan
| | - Satoshi Fujii
- Department of Pathology and Clinical LaboratoriesNational Cancer Center Hospital EastChibaJapan
- Department of Molecular PathologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Takayuki Yoshino
- Department of Gastrointestinal OncologyNational Cancer Center Hospital EastChibaJapan
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