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Bathrick AS, Norsworthy S, Plaza DT, McCormick MN, Slack D, Ramotowski RS. DNA recovery after sequential processing of latent fingerprints on black polyethylene plastic. J Forensic Sci 2024; 69:993-1001. [PMID: 38402545 DOI: 10.1111/1556-4029.15498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
Latent fingerprints on plastic substrates can be visualized by using sequential treatments to enhance the contrast between the fingerprint residues and underlying substrate; however, the extent to which these processes affect subsequent DNA analysis is mostly unknown. Latent fingerprints deposited on black plastic by one donor were visualized with single-process fingerprint powders (i.e., white powder, bichromatic powder, or bichromatic magnetic powder) or sequential treatments (i.e., laser → reflected ultraviolet imaging system (RUVIS) → CA fuming → RUVIS → Rhodamine 6G, Ardrox, and MBD (RAM) or CA fuming → RAM/laser → bichromatic magnetic powder). Samples were examined after the addition of each treatment. DNA was collected using cotton swabs, extracted, quantified, and amplified. DNA yields, peak heights, number of alleles obtained, and percentage of DNA profiles eligible for CODIS upload were examined. Latent fingerprints processed with the laser and up to three sequential treatments generated DNA profiles with significantly higher peaks heights than those of the untreated samples. Fingerprints processed with the laser and up to two sequential treatments generated DNA profiles with significantly more alleles. All methods beginning with laser enhancement generated more CODIS-eligible profiles. Additional research is needed to determine the extent to which initial laser enhancement impacts the success of downstream DNA profiling results. Although DNA profile development is not guaranteed due to the variable quantities of DNA contained within latent fingerprints, the selection of an appropriate latent fingerprint visualization method could maximize both fingerprint detection and the generation of CODIS-eligible DNA profiles.
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Affiliation(s)
| | - Sarah Norsworthy
- Forensic Technology Center of Excellence, RTI International, Research Triangle Park, North Carolina, USA
| | | | - Mallory N McCormick
- Forensic Services Division, United States Secret Service, Washington, DC, USA
| | - Donia Slack
- Forensic Technology Center of Excellence, RTI International, Research Triangle Park, North Carolina, USA
| | - Robert S Ramotowski
- Forensic Services Division, United States Secret Service, Washington, DC, USA
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Nolan M, Linacre A. Cell counting to monitor swab efficiency. J Forensic Sci 2024; 69:1002-1010. [PMID: 38380584 DOI: 10.1111/1556-4029.15495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Plastic bags, such as ziplock bags, have been used to transport illicit materials worldwide; however, very few studies have tried to optimize the recovery of DNA from these items. This study reports on the best combination of swabs and moistening solution for the greatest recovery of cellular material from ziplock bags. Five swabs, two different variations of Copan Diagnostics nylon 4N6FLOQSwabs, one Medical Wire rayon DRYSWAB, one IsoHelix rayon swab, and one Livingstone cotton swab, were evaluated with two moistening solutions, Triton X-100 in either distilled water or isopropanol. Fingermarks were deposited on ziplock bags and stained with Diamond™ Nucleic Acid Dye to allow visualization of the cells pre- and post-swabbing to determine the number of cells recovered. Based on cell counting data, swabs moistened with Triton X-100 in distilled water performed better than those moistened with isopropanol. Livingstone cotton swabs had the worst recovery of cellular material, while the other swabs tested had no significant difference in their respective solutions. A comparison of the best three swabs for cellular recovery yielded no differences in the DNA concentration extracted. A linear relationship was observed between the log number of cells recovered by swabbing and the DNA concentration following extraction and quantification. The process of monitoring cell collection using fluorescence microscopy on ziplock bags allowed evaluation of swabbing efficacy. Additionally, this study highlights the ability to evaluate cellular recovery independently of traditional extraction, quantification, or profiling techniques which may unequally affect samples.
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Affiliation(s)
- Madison Nolan
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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3
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Larsen L. Why citizen scientists are gathering DNA from hundreds of lakes - on the same day. Nature 2024; 626:934-935. [PMID: 38383651 DOI: 10.1038/d41586-024-00520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
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Londero D, Merluzzi S, Dreossi C, Barillari G. Prenatal screening service for fetal RHD genotyping to guide prophylaxis: the two-year experience of the Friuli Venezia Giulia region in Italy. Blood Transfus 2023; 21:93-99. [PMID: 35848630 PMCID: PMC10072987 DOI: 10.2450/2022.0004-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/06/2022] [Indexed: 03/18/2023]
Abstract
BACKGROUND Fetal RHD genotyping of cell-free fetal DNA (cff-DNA) from RhD-negative pregnant women can be used to guide anti-D prophylaxis: the knowledge of fetal RhD type can direct and restrict the use of prenatal anti-D immunoglobulin exclusively to RhD-negative women carrying a RhD-positive fetus. Since November 2019 in the region of Friuli Venezia Giulia (Italy) a prenatal screening service has been offered to RhD-negative women at 22-24 weeks of gestation. MATERIALS AND METHODS The cff-DNA is extracted from a simple peripheral maternal blood sample to analyze the fetal RHD gene: the results are interpreted as RHD-positive fetus, RHD-negative fetus, or Inconclusive. The service is shared with all regional hospitals and tests are provided free of charge by the National Health System. RESULTS Overall, 142 RhD-negative pregnant women were recruited in nearly 2 years. Fetal RHD genotyping was negative in 53 pregnancies and positive in 89 pregnancies. Thus, unnecessary treatment of pregnant women and exposure to a scarce plasma-derived medicinal product was avoided, by the use of a single blood sample, in 37.8% of cases, representing 100% of the RhD-negative women carrying a RhD-negative fetus in our cohort. DISCUSSION The first Italian region-wide screening service for fetal RHD genotyping has been implemented for 2 years, despite the COVID-19 pandemic, in order to obtain the predicted fetal RhD phenotype before the 28th week of gestation, during which prenatal prophylaxis is usually administered. Giving prenatal anti-D immunoglobulin exclusively to RhD-negative women carrying a RhD-positive fetus reduces the overall use of anti-D immunoglobulin, which is becoming an ever more limited resource. The high sensitivity of the procedure provides evidence that the implementation of a diagnostic test in a reference laboratory guarantees the quality of the results, the concordance of reports and the sustainability of costs, representing an excellent guide to targeted use of prophylaxis.
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Abstract
There are several silica-based extraction methods that utilize silica-packed columns or silica-coated paramagnetic resin and are suitable for the needs of forensic DNA analysis and/or human identification. These rely on the use of chaotropic salts to alter the affinity of DNA such that it binds strongly to silica. A variety of samples can be successfully processed with these procedures, including buccal swabs, dried or liquid blood, saliva, semen, and other typical forensic-type samples. This chapter will describe the manual extraction process for Promega's DNA™ IQ System, as well as Qiagen's QIAamp® DNA Blood Mini Kit, QIAamp® DNA Mini Kit, and QIAamp® DNA Investigator Kit.
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van Bladel DAG, van der Last-Kempkes JLM, Scheijen B, Groenen PJTA. Next-Generation Sequencing-Based Clonality Detection of Immunoglobulin Gene Rearrangements in B-Cell Lymphoma. Methods Mol Biol 2022; 2453:7-42. [PMID: 35622318 DOI: 10.1007/978-1-0716-2115-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Immunoglobulin (IG) clonality assessment is a widely used supplementary test for the diagnosis of suspected lymphoid malignancies. The specific rearrangements of the immunoglobulin (IG) heavy and light chain genes act as a unique hallmark of a B-cell lymphoma, a feature that is used in clonality assessment. The widely used BIOMED-2/EuroClonality IG clonality assay, visualized by GeneScanning or heteroduplex analysis, has an unprecedented high detection rate because of the complementarity of this approach. However, the BIOMED-2/EuroClonality clonality assays have been developed for the assessment of specimens with optimal DNA quality. Further improvements for the assessment of samples with suboptimal DNA quality, such as from formalin-fixed paraffin-embedded (FFPE) specimens or specimens with a limited tumor burden, are required. The EuroClonality-NGS Working Group recently developed a next-generation sequencing (NGS)-based clonality assay for the detection of the IG heavy and kappa light chain rearrangements, using the same complementary approach as in the conventional assay. By employing next-generation sequencing, both the sensitivity and specificity of the clonality assay have increased, which not only is very useful for diagnostic clonality testing but also allows robust comparison of clonality patterns in a patient with multiple lymphoma's that have suboptimal DNA quality. Here, we describe the protocols for IG-NGS clonality assessment that are compatible for Ion Torrent and Illumina sequencing platforms including pre-analytical DNA isolation, the analytical phase, and the post-analytical data analysis.
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Affiliation(s)
- Diede A G van Bladel
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Jaskulak M, Rorat A, Vandenbulcke F, Pauwels M, Grzmil P, Plytycz B. Polymorphic microsatellite markers demonstrate hybridization and interspecific gene flow between lumbricid earthworm species, Eisenia andrei and E. fetida. PLoS One 2022; 17:e0262493. [PMID: 35180227 PMCID: PMC8856553 DOI: 10.1371/journal.pone.0262493] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/27/2021] [Indexed: 11/18/2022] Open
Abstract
The lumbricid earthworms Eisenia andrei (Ea) and E. fetida (Ef) have been used as model organisms for studies on hybridization. Previously they have been identified by species specific sequences of the mitochondrial COI gene of maternal origin ('a' or 'f') and the nuclear 28S gene of maternal/paternal origin ('A' or 'F'). In experimental crosses, these hermaphroditic species produce progeny of genotypes Ea (aAA), Ef (fFF) and hybrids (aAF and fFA) originating by self-fertilization or cross-fertilization. To facilitate studies on new aspects of the breeding biology and hybridization of earthworms, polymorphic microsatellite markers were developed based on 12 Ea and 12 Ef specimens and validated on DNA samples extracted from 24 genotyped specimens (aAA, fFF, aAF and fFA) from three laboratory-raised families and 10 of them were applied in the present study. The results indicate that microsatellite markers are valuable tools for tracking interspecific gene flow between these species.
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Affiliation(s)
- Marta Jaskulak
- Laboratoire de Génie Civil et géo-Environnement, Univ. Lille, IMT Lille Douai, Univ. Artois, Yncrea Hauts-de-France, ULR4515—LGCgE, Lille, France
- Department of Immunobiology and Environment Microbiology, Faculty of Health Sciences with Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement, Univ. Lille, IMT Lille Douai, Univ. Artois, Yncrea Hauts-de-France, ULR4515—LGCgE, Lille, France
| | - Franck Vandenbulcke
- Laboratoire de Génie Civil et géo-Environnement, Univ. Lille, IMT Lille Douai, Univ. Artois, Yncrea Hauts-de-France, ULR4515—LGCgE, Lille, France
| | - Maxime Pauwels
- Laboratoire de Génie Civil et géo-Environnement, Univ. Lille, IMT Lille Douai, Univ. Artois, Yncrea Hauts-de-France, ULR4515—LGCgE, Lille, France
- Univ. Lille, CNRS, UMR 8198 - EEP - Laboratoire Evolution Ecologie Paléontologie F-59000 Lille, France
| | - Paweł Grzmil
- Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
| | - Barbara Plytycz
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Jagiellonian University, Krakow, Poland
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Shvartsman E, Richmond MEI, Schellenberg JJ, Lamont A, Perciani C, Russell JNH, Poliquin V, Burgener A, Jaoko W, Sandstrom P, MacDonald KS. Comparative analysis of DNA extraction and PCR product purification methods for cervicovaginal microbiome analysis using cpn60 microbial profiling. PLoS One 2022; 17:e0262355. [PMID: 35025956 PMCID: PMC8758110 DOI: 10.1371/journal.pone.0262355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/21/2021] [Indexed: 11/19/2022] Open
Abstract
Background The microbiota of the lower female genital tract plays an important role in women’s health. Microbial profiling using the chaperonin60 (cpn60) universal target (UT) improves resolution of vaginal species associated with negative health outcomes compared to the more commonly used 16S ribosomal DNA target. However, the choice of DNA extraction and PCR product purification methods may bias sequencing-based microbial studies and should be optimized for the sample type and molecular target used. In this study, we compared two commercial DNA extraction kits and two commercial PCR product purification kits for the microbial profiling of cervicovaginal samples using the cpn60 UT. Methods DNA from cervicovaginal secretions and vaginal lavage samples as well as mock community standards were extracted using either the specialized QIAamp DNA Microbiome Kit, or the standard DNeasy Blood & Tissue kit with enzymatic pre-treatment for enhanced lysis of gram-positive bacteria. Extracts were PCR amplified using well-established cpn60 primer sets and conditions. Products were then purified using a column-based method (QIAquick PCR Purification Kit) or a gel-based PCR clean-up method using the QIAEX II Gel Extraction Kit. Purified amplicons were sequenced with the MiSeq platform using standard procedures. The overall quality of each method was evaluated by measuring DNA yield, alpha diversity, and microbial composition. Results DNA extracted from cervicovaginal samples using the DNeasy Blood and Tissue kit, pre-treated with lysozyme and mutanolysin, resulted in increased DNA yield, bacterial diversity, and species representation compared to the QIAamp DNA Microbiome kit. The column-based PCR product purification approach also resulted in greater average DNA yield and wider species representation compared to a gel-based clean-up method. In conclusion, this study presents a fast, effective sample preparation method for high resolution cpn60 based microbial profiling of cervicovaginal samples.
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Affiliation(s)
- Elinor Shvartsman
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Meika E. I. Richmond
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - John J. Schellenberg
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Alana Lamont
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, United States of America
- Department of Obstetrics and Gynecology, University of Manitoba, Winnipeg, Canada
| | - Catia Perciani
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Justen N. H. Russell
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Vanessa Poliquin
- Department of Obstetrics and Gynecology, University of Manitoba, Winnipeg, Canada
| | - Adam Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, United States of America
- Department of Obstetrics and Gynecology, University of Manitoba, Winnipeg, Canada
- Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Walter Jaoko
- Kenyan AIDS Vaccine Initiative–Institute of Clinical Research (KAVI-ICR), University of Nairobi, Nairobi, Kenya
| | - Paul Sandstrom
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Kelly S. MacDonald
- Department of Internal Medicine, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
- * E-mail:
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Sharma P, Singh M, Singh A, Bhardwaj D, Bhatia P. Experience of quantity and quality of DNA and RNA extraction from limited pediatric blood samples: A comparative analysis of automated and manual kit-based method. INDIAN J PATHOL MICR 2022; 65:105-110. [PMID: 35074973 DOI: 10.4103/ijpm.ijpm_946_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
INTRODUCTION Optimal DNA and RNA quantity and purity is essential for downstream molecular biology experimentation and to avoid re-processing of sample. Despite availability of different kits and automated systems for nucleic acid isolation there is limited data on their performance evaluation, more so with pediatric blood samples, that are usually compromised in quantity. Hence, we evaluated the performance of automated QIAcube platform using pediatric blood samples in parallel with manual Qiagen extraction kits. MATERIALS AND METHODS : A total of 500 samples were analyzed based on groups of PBMC and direct blood input. The isolated DNA and RNA were surveyed for quantity and quality tests by spectrophotometric and downstream analysis. RESULTS : There was no significant difference in the DNA quantity (ng/ul) between manual and automated method based on similar sample input but quality (260/280) was significantly better with the QIAcube platform when direct blood and or PBMCs were used for extraction respectively (1.82 ± 004 Vs. 1.84.002; P-0.000008 and 1.859 ± 005 Vs. 1.843 ± 0.003; P-0.02). Moreover, the standard error mean was low for both quantity and quality in the QIAcube method suggesting uniformity. Comparison of quality assessment by spectrophotometer and qubit fluorimeter showed that QIAcube sheared DNA less (P- 0.038) as compared to manual method (P-0.013). Also, time taken to process the samples in QIAcube was 23% less than the kit-based method. CONCLUSION Overall analysis of QIAcube platform suggests that it yields more better, uniform, and less-sheared quality of nucleic acid in a relatively less time as compared to manual extraction kits.
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Affiliation(s)
- Pankaj Sharma
- Pediatric Hematology-Oncology Laboratory, Advanced Pediatric Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Minu Singh
- Pediatric Hematology-Oncology Laboratory, Advanced Pediatric Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Aditya Singh
- Pediatric Hematology-Oncology Laboratory, Advanced Pediatric Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepshikha Bhardwaj
- Pediatric Hematology-Oncology Laboratory, Advanced Pediatric Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prateek Bhatia
- Pediatric Hematology-Oncology Laboratory, Advanced Pediatric Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Morita H, Akao S. The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks. PLoS One 2021; 16:e0260121. [PMID: 34793564 PMCID: PMC8601499 DOI: 10.1371/journal.pone.0260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.
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Affiliation(s)
- Hiroki Morita
- Graduate School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Satoshi Akao
- Graduate School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
- * E-mail:
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Ivanov AV, Popravko DS, Safenkova IV, Zvereva EA, Dzantiev BB, Zherdev AV. Rapid Full-Cycle Technique to Control Adulteration of Meat Products: Integration of Accelerated Sample Preparation, Recombinase Polymerase Amplification, and Test-Strip Detection. Molecules 2021; 26:6804. [PMID: 34833896 PMCID: PMC8622786 DOI: 10.3390/molecules26226804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/01/2022] Open
Abstract
Verifying the authenticity of food products is essential due to the recent increase in counterfeit meat-containing food products. The existing methods of detection have a number of disadvantages. Therefore, simple, cheap, and sensitive methods for detecting various types of meat are required. In this study, we propose a rapid full-cycle technique to control the chicken or pig adulteration of meat products, including 3 min of crude DNA extraction, 20 min of recombinase polymerase amplification (RPA) at 39 °C, and 10 min of lateral flow assay (LFA) detection. The cytochrome B gene was used in the developed RPA-based test for chicken and pig identification. The selected primers provided specific RPA without DNA nuclease and an additional oligonucleotide probe. As a result, RPA-LFA, based on designed fluorescein- and biotin-labeled primers, detected up to 0.2 pg total DNA per μL, which provided up to 0.001% w/w identification of the target meat component in the composite meat. The RPA-LFA of the chicken and pig meat identification was successfully applied to processed meat products and to meat after heating. The results were confirmed by real-time PCR. Ultimately, the developed analysis is specific and enables the detection of pork and chicken impurities with high accuracy in raw and processed meat mixtures. The proposed rapid full-cycle technique could be adopted for the authentication of other meat products.
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Affiliation(s)
| | | | | | | | | | - Anatoly V. Zherdev
- Research Centre of Biotechnology, A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.I.); (D.S.P.); (I.V.S.); (E.A.Z.); (B.B.D.)
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Mao J, Huang L, Fan L, Chen F, Lou J, Shan X, Yu D, Zhou J. 60-nt DNA Direct Detection without Pretreatment by Surface-Enhanced Raman Scattering with Polycationic Modified Ag Microcrystal Derived from AgCl Cube. Molecules 2021; 26:molecules26226790. [PMID: 34833883 PMCID: PMC8620099 DOI: 10.3390/molecules26226790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022] Open
Abstract
Direct detection of long-strand DNA by surface-enhanced Raman scattering (SERS) is a valuable method for diagnosis of hereditary diseases, but it is currently limited to less than 25-nt DNA strand in pure water, which makes this approach unsuitable for many real-life applications. Here, we report a 60-nt DNA label-free detection strategy without pretreatment by SERS with polyquaternium-modified Ag microcrystals derived from an AgCl cube. Through the reduction-induced decomposition, the size of the about 3 × 3 × 3 μm3 AgCl cube is reduced to Ag, and the surface is distributed with the uniform size of 63 nm silver nanoparticles, providing a large area of a robust and highly electromagnetic enhancement region. The modified polycationic molecule enhances the non-specific electrostatic interaction with the phosphate group, thereby anchoring DNA strands firmly to the SERS enhanced region intactly. As a result, the single-base recognition ability of this strategy reaches 60-nt and is successfully applied to detect thalassemia-related mutation genes.
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Affiliation(s)
- Jikai Mao
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
| | - Lvtao Huang
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
| | - Li Fan
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
| | - Fang Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
| | - Jingan Lou
- The Children’s Hospital Zhejiang University School of Medicine, Hangzhou 310000, China;
| | - Xuliang Shan
- Hangzhou Green Environment Science & Technology Co., Ltd., Hangzhou 310000, China;
| | - Dongdong Yu
- Hospital of Zhejiang University, Hangzhou 310027, China;
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, State Key Laboratory of Industrial Control Technology, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China; (J.M.); (L.H.); (L.F.)
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China;
- Correspondence:
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van Oorschot RAH, Meakin GE, Kokshoorn B, Goray M, Szkuta B. DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges. Genes (Basel) 2021; 12:genes12111766. [PMID: 34828372 PMCID: PMC8618004 DOI: 10.3390/genes12111766] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/16/2023] Open
Abstract
Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.
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Affiliation(s)
- Roland A. H. van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia
- School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Correspondence:
| | - Georgina E. Meakin
- Centre for Forensic Science, University of Technology Sydney, Ultimo, NSW 2007, Australia;
- Centre for the Forensic Sciences, Department of Security and Crime Science, University College London, London WC1H 9EZ, UK
| | - Bas Kokshoorn
- Netherlands Forensic Institute, 2497 GB The Hague, The Netherlands;
- Faculty of Technology, Amsterdam University of Applied Sciences, 1097 DZ Amsterdam, The Netherlands
| | - Mariya Goray
- College of Science and Engineering, Flinders University, Adelaide, SA 5042, Australia;
| | - Bianca Szkuta
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia;
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14
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Kumar N, Aparna R, Sharma S. Effect of postmortem interval and conditions of teeth on STR based DNA profiling from unidentified dead bodies. J Forensic Leg Med 2021; 83:102246. [PMID: 34438226 DOI: 10.1016/j.jflm.2021.102246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022]
Abstract
Teeth are important exhibits to establish the identity of unidentified dead bodies by DNA profiling. Tooth acts as a cage to protect DNA from harsh environmental conditions. Unidentified bodies are sometimes found many years after death causing loss of valuable soft tissues which can be used for DNA extraction. Skeletal remains and dental evidence provide the best alternative when decomposed or burnt bodies are examined to establish the identity. In this study, the powder-free method was used to extract DNA from ninety-five teeth of unidentified dead bodies across seven years (2014-2020). Intact and broken dental remains were analyzed majorly from decomposed remains. The present study reports successful STR profiles obtained from dental evidence using powder free method. Complete DNA profiles were obtained from intact teeth while damaged teeth either gave partial profiles or no results. This data suggest that intact teeth are excellent samples for DNA profiling from decomposed unidentified dead bodies even with greater post mortem interval. Findings from this study can hence be useful in establishing the identity in forensic and archeological casework.
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Affiliation(s)
- Naresh Kumar
- DNA Division, Regional Forensic Science Laboratory, Central Range, Mandi, 175001, Himachal Pradesh, India.
| | - R Aparna
- Department of Forensic Science, School of Sciences, JAIN (Deemed-to-be-University), Bengaluru, Karnataka, India.
| | - Shivkant Sharma
- Department of Genetics, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
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15
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Beckmann JF, Dormitorio T, Oladipupo SO, Bethonico Terra MT, Lawrence K, Macklin KS, Hauck R. Heterakis gallinarum and Histomonas meleagridis DNA persists in chicken houses years after depopulation. Vet Parasitol 2021; 298:109536. [PMID: 34365105 DOI: 10.1016/j.vetpar.2021.109536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/17/2021] [Accepted: 07/27/2021] [Indexed: 11/15/2022]
Abstract
The poultry pathogen Histomonas meleagridis is transmitted by chicken cecal worms (Heterakis gallinarum) and is potentially transmitted by second order insect vectors and paratenic hosts. Darkling beetles (Alphitobius diaperinus) are poultry farm pests that infest barns. An outstanding question is the degree to which darkling beetles transmit both Heterakis and Histomonas. In this study we monitored populations of darkling beetles and assessed their positivity for both Heterakis and Histomonas by PCR. Uniquely, this study was conducted during the scheduled deconstruction of Auburn University's Poultry Research Farm. Therefore, we were able to monitor beetle and litter infection status months and years after bird depopulation. The duration of our monitoring continued through three seasons. We show that environmental DNA from both Heterakis and Histomonas persist in the environment long after prior infections, even in the absence of living Heterakis and its hosts. Finally, in an intensive search for live Heterakis, we discovered reniform nematodes (plant parasitic nematodes) residing in the soil floor of poultry farms.
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Affiliation(s)
- John F Beckmann
- Auburn University, Department of Entomology and Plant Pathology, Auburn, AL, 36849, United States
| | - Teresa Dormitorio
- Auburn University, Department of Poultry Science, Auburn, AL, 36849, United States
| | - Seun O Oladipupo
- Auburn University, Department of Entomology and Plant Pathology, Auburn, AL, 36849, United States
| | | | - Kathy Lawrence
- Auburn University, Department of Entomology and Plant Pathology, Auburn, AL, 36849, United States
| | - Kenneth S Macklin
- Auburn University, Department of Poultry Science, Auburn, AL, 36849, United States
| | - Ruediger Hauck
- Auburn University, Department of Poultry Science, Auburn, AL, 36849, United States; Auburn University, Departmen of Pathobiology, Auburn, AL, 36849, United States.
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16
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Volarić M, Veseljak D, Mravinac B, Meštrović N, Despot-Slade E. Isolation of High Molecular Weight DNA from the Model Beetle Tribolium for Nanopore Sequencing. Genes (Basel) 2021; 12:1114. [PMID: 34440288 PMCID: PMC8394269 DOI: 10.3390/genes12081114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 12/31/2022] Open
Abstract
The long-read Nanopore sequencing has been recently applied for assembly of complex genomes and analysis of linear genome organization. The most critical factor for successful long-read sequencing is extraction of high molecular weight (HMW) DNA of sufficient purity and quantity. The challenges associated with input DNA quality are further amplified when working with extremely small insects with hard exoskeletons. Here, we optimized the isolation of HMW DNA from the model beetle Tribolium and tested for use in Nanopore sequencing. We succeeded in overcoming all the difficulties in HMW handling and library preparation that were encountered when using published protocols and commercial kits. Isolation of nuclei and subsequent purification of DNA on an anion-exchange chromatography column resulted in genomic HMW DNA that was efficiently relaxed, of optimal quality and in sufficient quantity for Nanopore MinION sequencing. DNA shearing increased average N50 read values up to 26 kb and allowed us to use a single flow cell in multiple library loads for a total output of more than 13 Gb. Although our focus was on T. castaneum and closely related species, we expect that this protocol, with appropriate modifications, could be extended to other insects, particularly beetles.
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Affiliation(s)
| | | | | | | | - Evelin Despot-Slade
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.V.); (D.V.); (B.M.); (N.M.)
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17
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Liu HW, Hu Y, Ren Y, Nam H, Santos JL, Ng S, Gong L, Brummet M, Carrington CA, Ullman CG, Pomper MG, Minn I, Mao HQ. Scalable Purification of Plasmid DNA Nanoparticles by Tangential Flow Filtration for Systemic Delivery. ACS Appl Mater Interfaces 2021; 13:30326-30336. [PMID: 34162211 PMCID: PMC9701136 DOI: 10.1021/acsami.1c05750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plasmid DNA (pDNA) nanoparticles synthesized by complexation with linear polyethylenimine (lPEI) are one of the most effective non-viral gene delivery vehicles. However, the lack of scalable and reproducible production methods and the high toxicity have hindered their clinical translation. Previously, we have developed a scalable flash nanocomplexation (FNC) technique to formulate pDNA/lPEI nanoparticles using a continuous flow process. Here, we report a tangential flow filtration (TFF)-based scalable purification method to reduce the uncomplexed lPEI concentration in the nanoparticle formulation and improve its biocompatibility. The optimized procedures achieved a 60% reduction of the uncomplexed lPEI with preservation of the nanoparticle size and morphology. Both in vitro and in vivo studies showed that the purified nanoparticles significantly reduced toxicity while maintaining transfection efficiency. TFF also allows for gradual exchange of solvents to isotonic solutions and further concentrating the nanoparticles for injection. Combining FNC production and TFF purification, we validated the purified pDNA/lPEI nanoparticles for future clinical translation of this gene nanomedicine.
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Affiliation(s)
- Heng-Wen Liu
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yizong Hu
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yong Ren
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jose Luis Santos
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Shirley Ng
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Like Gong
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mary Brummet
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | | | - Martin G. Pomper
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hai-Quan Mao
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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18
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Abstract
Police dogs are routinely deployed during criminal investigations under a variety of circumstances. In instances where police dogs are involved in apprehension of suspects, contact with a suspect may be observed or may occur out of the line of sight. The interactions between suspect and dog may include the dog biting the suspect, or the suspect touching or exuding bodily fluids onto the dog. In either form of contact, potentially valuable DNA may be left from the suspect on the dog. This paper describes a proof-of-concept study investigating collection of human DNA from the teeth and hair of dogs. It used controlled settings, where the human DNA sources were touch and saliva, and field cases, where the human DNA sources were unknown. The results of sample analysis to identify DNA short tandem repeats (STRs) from each of these scenarios are provided. They highlight the potential and importance of collecting trace DNA from police dogs who may have had contact with suspects during attempted apprehension.
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Affiliation(s)
- Alexandra Brower
- Department of Pathology and Population Medicine, Diagnostic Pathology Center, Midwestern University College of Veterinary Medicine, 5725 West Utopia Rd, Glendale, AZ 85308 USA
| | - Brice Akridge
- Department of Public Safety, DNA Technical Unit, Central Regional Crime Laboratory, AZ Arizona Phoenix, USA
| | - Nancy Siemens-Bradley
- Department of Pathology and Population Medicine, Diagnostic Pathology Center, Midwestern University College of Veterinary Medicine, 5725 West Utopia Rd, Glendale, AZ 85308 USA
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19
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Fenizia F, Alborelli I, Costa JL, Vollbrecht C, Bellosillo B, Dinjens W, Endris V, Heydt C, Leonards K, Merkelback-Bruse S, Pfarr N, van Marion R, Allen C, Chaudhary R, Gottimukkala R, Hyland F, Wong-Ho E, Jermann P, Machado JC, Hummel M, Stenzinger A, Normanno N. Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis: Results from the Onconetwork Immuno-Oncology Consortium. J Mol Diagn 2021; 23:882-893. [PMID: 33964449 DOI: 10.1016/j.jmoldx.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor mutation burden (TMB) is evaluated as a biomarker of response to immunotherapy. We present the efforts of the Onconetwork Immuno-Oncology Consortium to validate a commercial targeted sequencing test for TMB calculation. A three-phase study was designed to validate the Oncomine Tumor Mutational Load (OTML) assay at nine European laboratories. Phase 1 evaluated reproducibility and accuracy on seven control samples. In phase 2, six formalin-fixed, paraffin-embedded samples tested with FoundationOne were reanalyzed with the OTML panel to evaluate concordance and reproducibility. Phase 3 involved analysis of 90 colorectal cancer samples with known microsatellite instability (MSI) status to evaluate TMB and MSI association. High reproducibility of TMB was demonstrated among the sites in the first and second phases. Strong correlation was also detected between mean and expected TMB in phase 1 (r2 = 0.998) and phase 2 (r2 = 0.96). Detection of actionable mutations was also confirmed. In colorectal cancer samples, the expected pattern of MSI-high/high-TMB and microsatellite stability/low-TMB was present, and gene signatures produced by the panel suggested the presence of a POLE mutation in two samples. The OTML panel demonstrated robustness and reproducibility for TMB evaluation. Results also suggest the possibility of using the panel for mutational signatures and variant detection. Collaborative efforts between academia and companies are crucial to accelerate the translation of new biomarkers into clinical research.
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Affiliation(s)
- Francesca Fenizia
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | - Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jose Luis Costa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Claudia Vollbrecht
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Winand Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, France
| | - Katharina Leonards
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Nicole Pfarr
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
| | - Christopher Allen
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Ruchi Chaudhary
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Rajesh Gottimukkala
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Fiona Hyland
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Elaine Wong-Ho
- Clinical Next-Generation Sequencing Division, Thermo Fisher Scientific, Waltham, Massachusetts
| | - Philip Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Jose Carlos Machado
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Michael Hummel
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | | | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy.
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20
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Cotchim S, Thavarungkul P, Kanatharana P, Thanakiatkrai P, Kitpipit T, Limbut W. Extraction and electrochemical detection for quantification of trace-level DNA. Mikrochim Acta 2021; 188:180. [PMID: 33950304 DOI: 10.1007/s00604-021-04825-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/06/2021] [Indexed: 11/30/2022]
Abstract
A novel strategy was developed to extract, detect, and quantify trace-level DNA. For the extraction step, a composite of methylene blue (MB), poly(acrylic acid) (PAA), and modified iron oxide magnetic nanoparticles (IOMNPs) (PAA/IOMNPs) was used to adsorb DNA from the sample. MB-PAA/IOMNPs with adsorbed DNA were then separated from the solution with an external magnet and MB-DNA was eluted from PAA/IOMNPs with acetic acid. In the detection step, MB-DNA was adsorbed on the surface of 3-aminopropyltriethoxysilane (APTES)-modified glassy carbon electrode via electrostatic force. DNA was quantified by measuring the oxidation peak of MB at a potential -0.13 V vs. Ag/AgCl using differential pulse voltammetry. Under the optimal experimental conditions, the DNA sensor showed linear ranges from 0.001 to 0.005 pg μL-1, 0.005 to 0.070 pg μL-1, and 0.070 to 0.400 pg μL-1 and a limit of detection of 0.87 fg μL-1. The proposed sensor detected trace DNA in real samples with recoveries that ranged from 80.4 to 90.4%.
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Affiliation(s)
- Suparat Cotchim
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Panote Thavarungkul
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Proespichaya Kanatharana
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Phuvadol Thanakiatkrai
- Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Thitika Kitpipit
- Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Warakorn Limbut
- Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.
- Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.
- Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand.
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21
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Delfino D, Mori G, Rivetti C, Grigoletto A, Bizzotto G, Cavozzi C, Malatesta M, Cavazzini D, Pasut G, Percudani R. Actin-Resistant DNase1L2 as a Potential Therapeutics for CF Lung Disease. Biomolecules 2021; 11:biom11030410. [PMID: 33802146 PMCID: PMC8002113 DOI: 10.3390/biom11030410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
In cystic fibrosis (CF), the accumulation of viscous lung secretions rich in DNA and actin is a major cause of chronic inflammation and recurrent infections leading to airway obstruction. Mucolytic therapy based on recombinant human DNase1 reduces CF mucus viscosity and promotes airway clearance. However, the marked susceptibility to actin inhibition of this enzyme prompts the research of alternative treatments that could overcome this limitation. Within the human DNase repertoire, DNase1L2 is ideally suited for this purpose because it exhibits metal-dependent endonuclease activity on plasmid DNA in a broad range of pH with acidic optimum and is minimally inhibited by actin. When tested on CF artificial mucus enriched with actin, submicromolar concentrations of DNase1L2 reduces mucus viscosity by 50% in a few seconds. Inspection of superimposed model structures of DNase1 and DNase1L2 highlights differences at the actin-binding interface that justify the increased resistance of DNase1L2 toward actin inhibition. Furthermore, a PEGylated form of the enzyme with preserved enzymatic activity was obtained, showing interesting results in terms of activity. This work represents an effort toward the exploitation of natural DNase variants as promising alternatives to DNase1 for the treatment of CF lung disease.
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Affiliation(s)
- Danila Delfino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Antonella Grigoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
| | - Gloria Bizzotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
| | - Cristian Cavozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
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22
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England CJ, Gray TC, Malla SRL, Oliveira SA, Martin BR, Beall GW, Lewis LK. pH-dependent sedimentation of DNA in the presence of divalent, but not monovalent, metal ions. Anal Biochem 2021; 616:114099. [PMID: 33388294 PMCID: PMC7849029 DOI: 10.1016/j.ab.2020.114099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 10/22/2022]
Abstract
Precipitation of DNA is performed frequently in molecular biology laboratories for the purpose of purification and concentration of samples and also for transfer of DNA into cells. Metal ions are used to facilitate these processes, though their precise functions are not well characterized. In the current study we have investigated the precipitation of double-stranded DNA by group 1 and group 2 metal ions. Double-stranded DNAs were not sedimented efficiently by metals alone, even at high concentrations. Increasing the pH to 11 or higher caused strong DNA precipitation in the presence of the divalent group 2 metals magnesium, calcium, strontium and barium, but not group 1 metals. Group 2 sedimentation profiles were distinctly different from that of the transition metal zinc, which caused precipitation at pH 8. Analysis of DNAs recovered from precipitates formed with calcium revealed that structural integrity was retained and that sedimentation efficiency was largely size-independent above 400 bp. Several tests supported a model whereby single-stranded DNA regions formed by denaturation at high pH became bound by the divalent metal cations. Neutralization of negative surface charges reduced the repulsive forces between molecules, leading to formation of insoluble aggregates that could be further stabilized by cation bridging (ionic crosslinking).
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Affiliation(s)
- Corbin J England
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Tanner C Gray
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Shubha R L Malla
- Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - Samantha A Oliveira
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Benjamin R Martin
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - Gary W Beall
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA; Materials Science, Engineering and Commercialization Program, Texas State University, San Marcos, TX, 78666, USA.
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23
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Shiozaki T, Itoh F, Hirose Y, Onodera J, Kuwata A, Harada N. A DNA metabarcoding approach for recovering plankton communities from archived samples fixed in formalin. PLoS One 2021; 16:e0245936. [PMID: 33596231 PMCID: PMC7888612 DOI: 10.1371/journal.pone.0245936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/08/2021] [Indexed: 01/04/2023] Open
Abstract
Plankton samples have been routinely collected and preserved in formalin in many laboratories and museums for more than 100 years. Recently, attention has turned to use DNA information from formalin-fixed samples to examine changes in plankton diversity over time. However, no molecular ecological studies have evaluated the impact of formalin fixation on the genetic composition of the plankton community structure. Here, we developed a method for extracting DNA from archived formalin-preserved plankton samples to determine their community structure by a DNA metabarcoding approach. We found that a lysis solution consisting of borate-NaOH buffer (pH 11) with SDS and proteinase K effectively cleaved the cross-link formed by formalin fixation. DNA was extracted from samples preserved for decades in formalin, and the diatom community of the extracted DNA was in good agreement with the microscopy analysis. Furthermore, we stored a plankton sample for 1.5 years and demonstrated that 18S rRNA gene community structures did not change significantly from non-formalin-fixed, time-zero samples. These results indicate that our method can be used to describe the original community structure of plankton archived in formalin for years. Our approach will be useful for examining the long-term variation of plankton diversity by metabarcoding analysis of 18S rRNA gene community structure.
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Affiliation(s)
- Takuhei Shiozaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
- * E-mail:
| | - Fumihiro Itoh
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Jonaotaro Onodera
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Shiogama, Japan
| | - Naomi Harada
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
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24
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Sheth N, Swaminathan H, Gonzalez AJ, Duffy KR, Grgicak CM. Towards developing forensically relevant single-cell pipelines by incorporating direct-to-PCR extraction: compatibility, signal quality, and allele detection. Int J Legal Med 2021; 135:727-738. [PMID: 33484330 DOI: 10.1007/s00414-021-02503-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Current analysis of forensic DNA stains relies on the probabilistic interpretation of bulk-processed samples that represent mixed profiles consisting of an unknown number of potentially partial representations of each contributor. Single-cell methods, in contrast, offer a solution to the forensic DNA mixture problem by incorporating a step that separates cells before extraction. A forensically relevant single-cell pipeline relies on efficient direct-to-PCR extractions that are compatible with standard downstream forensic reagents. Here we demonstrate the feasibility of implementing single-cell pipelines into the forensic process by exploring four metrics of electropherogram (EPG) signal quality-i.e., allele detection rates, peak heights, peak height ratios, and peak height balance across low- to high-molecular-weight short tandem repeat (STR) markers-obtained with four direct-to-PCR extraction treatments and a common post-PCR laboratory procedure. Each treatment was used to extract DNA from 102 single buccal cells, whereupon the amplification reagents were immediately added to the tube and the DNA was amplified/injected using post-PCR conditions known to elicit a limit of detection (LoD) of one DNA molecule. The results show that most cells, regardless of extraction treatment, rendered EPGs with at least a 50% true positive allele detection rate and that allele drop-out was not cell independent. Statistical tests demonstrated that extraction treatments significantly impacted all metrics of EPG quality, where the Arcturus® PicoPure™ extraction method resulted in the lowest median allele drop-out rate, highest median average peak height, highest median average peak height ratio, and least negative median values of EPG sloping for GlobalFiler™ STR loci amplified at half volume. We, therefore, conclude the feasibility of implementing single-cell pipelines for casework purposes and demonstrate that inferential systems assuming cell independence will not be appropriate in the probabilistic interpretation of a collection of single-cell EPGs.
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Affiliation(s)
- Nidhi Sheth
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA
| | - Harish Swaminathan
- Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Amanda J Gonzalez
- Department of Chemistry, Rutgers University, 315 Penn Street R306C, Camden, NJ, 08102, USA
| | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Catherine M Grgicak
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, USA.
- Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, MA, 02118, USA.
- Department of Chemistry, Rutgers University, 315 Penn Street R306C, Camden, NJ, 08102, USA.
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25
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Dreskin BW, Luu K, Dong TS, Benhammou J, Lagishetty V, Vu J, Sanford D, Durazo F, Agopian VG, Jacobs JP, Pisegna JR, Hussain SK. Specimen Collection and Analysis of the Duodenal Microbiome. J Vis Exp 2021. [PMID: 33522511 DOI: 10.3791/61900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Shifts in the microbiome have been correlated with the physiology and pathophysiology of many organ systems both in humans and in mouse models. The gut microbiome has been typically studied through fecal specimen collections. The ease of obtaining fecal samples has resulted in many studies that have revealed information concerning the distal luminal gastrointestinal tract. However, few studies have addressed the importance of the microbiome in the proximal gut. Given that the duodenum is a major site for digestion and absorption, its microbiome is relevant to nutrition and liver disease and warrants further investigation. Here we detail a novel method for sampling the proximal luminal and mucosal gut microbiome in human subjects undergoing upper endoscopy by obtaining duodenal aspirate and biopsies. Specimen procurement is facile and unaffected by artifacts such as patient preparatory adherence, as might be the case in obtaining colonic samples during colonoscopy. The preliminary results show that the luminal and mucosal microbiomes differ significantly, which is likely related to environmental conditions and barrier functions. Therefore, a combination of duodenal aspirate and biopsies reveal a more comprehensive picture of the microbiome in the duodenum. Biopsies are obtained from the descending and horizontal segments of the duodenum, which are anatomically close to the liver and biliary tree. This is important in studying the role of bile acid biology and the gut-liver axis in liver disease. Biopsies and aspirate can be used for 16S ribosomal RNA sequencing, metabolomics, and other similar applications.
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Affiliation(s)
- Benjamin W Dreskin
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System;
| | - Kayti Luu
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System;
| | - Tien S Dong
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System; The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at University of California; UCLA Microbiome Center, David Geffen School of Medicine at University of California
| | - Jihane Benhammou
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System; The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at University of California; Department of Surgery, University of California, Los Angeles
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at University of California; UCLA Microbiome Center, David Geffen School of Medicine at University of California
| | - John Vu
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System
| | - Daniel Sanford
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System
| | - Francisco Durazo
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at University of California; Department of Surgery, University of California, Los Angeles
| | | | - Jonathan P Jacobs
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System; The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at University of California; UCLA Microbiome Center, David Geffen School of Medicine at University of California
| | - Joseph R Pisegna
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System; Department of Medicine and Human Genetics, David Geffen School of Medicine at University of California
| | - Shehnaz K Hussain
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center;
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26
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Coelho-Rocha ND, Barroso FAL, Tavares LM, Dos Santos ESS, Azevedo V, Drumond MM, Mancha-Agresti P. Main Features of DNA-Based Vectors for Use in Lactic Acid Bacteria and Update Protocols. Methods Mol Biol 2021; 2197:285-304. [PMID: 32827144 DOI: 10.1007/978-1-0716-0872-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA vaccines have been used as a promising strategy for delivery of immunogenic and immunomodulatory molecules into the host cells. Although, there are some obstacles involving the capability of the plasmid vector to reach the cell nucleus in great number to promote the expected benefits. In order to improve the delivery and, consequently, increase the expression levels of the target proteins carried by DNA vaccines, alternative methodologies have been explored, including the use of non-pathogenic bacteria as delivery vectors to carry, deliver, and protect the DNA from degradation, enhancing plasmid expression.
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Affiliation(s)
- Nina D Coelho-Rocha
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda A L Barroso
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Laísa M Tavares
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ester S S Dos Santos
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana M Drumond
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center of Federal Education of Minas Gerais (CEFET-MG), Belo Horizonte, Minas Gerais, Brazil
| | - Pamela Mancha-Agresti
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Carmona-Aldana F, Nuñez-Martinez HN, Peralta-Alvarez CA, Tapia-Urzua G, Recillas-Targa F. Generation of Functional Genetic Study Models in Zebrafish Using CRISPR-Cas9. Methods Mol Biol 2021; 2174:255-262. [PMID: 32813255 DOI: 10.1007/978-1-0716-0759-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CRISPR-Cas9 is a method for genome editing that can be used efficiently for in vivo applications; the basic implementation of this method is used to generate genome site-directed sequence eliminations. Here we describe a protocol for genome editing using CRISPR-Cas9 in zebrafish (Danio rerio) one-cell embryos.
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Affiliation(s)
- Francisco Carmona-Aldana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hober N Nuñez-Martinez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos A Peralta-Alvarez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gustavo Tapia-Urzua
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Abstract
Purification of high-quality plasmid DNA in large quantities is a crucial step in its production for therapeutic use and is usually conducted by different chromatographic techniques. Large-scale preparations require the optimization of yield and homogeneity, while maximizing removal of contaminants and preserving molecular integrity. The advantages of Convective Interaction Media® (CIM®) monolith stationary phases, including low backpressure, fast separation of macromolecules, and flow-rate-independent resolution qualified them to be used effectively in separation of plasmid DNA on laboratory as well as on large scale. A development and scale-up of plasmid DNA downstream process based on chromatographic monoliths is described and discussed below. Special emphasis is put on the introduction of process analytical technology principles and tools for optimization and control of a downstream process.
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29
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Maghini DG, Moss EL, Vance SE, Bhatt AS. Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome. Nat Protoc 2021; 16:458-471. [PMID: 33277629 PMCID: PMC8750633 DOI: 10.1038/s41596-020-00424-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/24/2020] [Indexed: 12/30/2022]
Abstract
Short-read metagenomic sequencing and de novo genome assembly of the human gut microbiome can yield draft bacterial genomes without isolation and culture. However, bacterial genomes assembled from short-read sequencing are often fragmented. Furthermore, these metagenome-assembled genomes often exclude repeated genomic elements, such as mobile genetic elements, compromising our understanding of the contribution of these elements to important bacterial phenotypes. Although long-read sequencing has been applied successfully to the assembly of contiguous bacterial isolate genomes, extraction of DNA of sufficient molecular weight, purity and quantity for metagenomic sequencing from stool samples can be challenging. Here, we present a protocol for the extraction of microgram quantities of high-molecular-weight DNA from human stool samples that are suitable for downstream long-read sequencing applications. We also present Lathe ( www.github.com/bhattlab/lathe ), a computational workflow for long-read basecalling, assembly, consensus refinement with long reads or Illumina short reads and genome circularization. Altogether, this protocol can yield high-quality contiguous or circular bacterial genomes from a complex human gut sample in approximately 10 d, with 2 d of hands-on bench and computational effort.
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Affiliation(s)
- Dylan G Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Eli L Moss
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Summer E Vance
- Divisions of Hematology and Blood & Marrow Transplantation, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Divisions of Hematology and Blood & Marrow Transplantation, Department of Medicine, Stanford University, Stanford, CA, USA.
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30
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Abstract
Identifying causative genes in a given phenotype or disease model is important for biological discovery and drug development. The recent development of the CRISPR/Cas9 system has enabled unbiased and large-scale genetic perturbation screens to identify causative genes by knocking out many genes in parallel and selecting cells with desired phenotype of interest. However, compared to cancer cell lines, human somatic cells including cardiomyocytes (CMs), neuron cells, and endothelial cells are not easy targets of CRISPR screens because CRISPR screens require a large number of isogenic cells to be cultured and thus primary cells from patients are not ideal. The combination of CRISPR screens with induced pluripotent stem cell (iPSC) technology would be a powerful tool to identify causative genes and pathways because iPSCs can be expanded easily and differentiated to any cell type in principle. Here we describe a robust protocol for CRISPR screening using human iPSCs. Because each screening is different and needs to be customized depending on the cell types and phenotypes of interest, we show an example of CRISPR knockdown screening using CRISPRi system to identify essential genes to differentiate iPSCs to CMs.
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Affiliation(s)
- Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.
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31
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Conner WR, Delaney EK, Bronski MJ, Ginsberg PS, Wheeler TB, Richardson KM, Peckenpaugh B, Kim KJ, Watada M, Hoffmann AA, Eisen MB, Kopp A, Cooper BS, Turelli M. A phylogeny for the Drosophila montium species group: A model clade for comparative analyses. Mol Phylogenet Evol 2020; 158:107061. [PMID: 33387647 DOI: 10.1016/j.ympev.2020.107061] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/22/2022]
Abstract
The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.
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Affiliation(s)
- William R Conner
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1)
| | - Emily K Delaney
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Michael J Bronski
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Paul S Ginsberg
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Department of Genetics, University of Georgia, Athens, GA 30602, USA(1)
| | - Timothy B Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1)
| | - Kelly M Richardson
- Bio21 Institute, School of BioScience, University of Melbourne, Victoria 3010, Australia
| | - Brooke Peckenpaugh
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA(1)
| | - Kevin J Kim
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
| | - Ary A Hoffmann
- Bio21 Institute, School of BioScience, University of Melbourne, Victoria 3010, Australia
| | - Michael B Eisen
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA(1)
| | - Michael Turelli
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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Carlsson ER, Fenger M, Henriksen T, Kjaer LK, Worm D, Hansen DL, Madsbad S, Poulsen HE. Reduction of oxidative stress on DNA and RNA in obese patients after Roux-en-Y gastric bypass surgery-An observational cohort study of changes in urinary markers. PLoS One 2020; 15:e0243918. [PMID: 33315915 PMCID: PMC7735613 DOI: 10.1371/journal.pone.0243918] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/18/2020] [Indexed: 01/14/2023] Open
Abstract
Increased oxidative stress in obesity and diabetes is associated with morbidity and mortality risks. Levels of oxidative damage to DNA and RNA can be estimated through measurement of 8-oxo-7,8-dihydro-2´-deoxyguanosine (8-oxodG) and 8-oxo-7,8-dihydroguanosine (8-oxoGuo) in urine. Both markers have been associated with type 2 diabetes, where especially 8-oxoGuo is prognostic for mortality risk. We hypothesized that Roux-en-Y gastric bypass (RYGB) surgery that has considerable effects on bodyweight, hyperglycemia and mortality, might be working through mechanisms that reduce oxidative stress, thereby reducing levels of the urinary markers. We used liquid chromatography coupled with tandem mass spectrometry to analyze the content of 8-oxodG and 8-oxoGuo in urinary samples from 356 obese patients treated with the RYGB-procedure. Mean age (SD) was 44.2 (9.6) years, BMI was 42.1 (5.6) kg/m2. Ninety-six (27%) of the patients had type 2 diabetes. Excretion levels of each marker before and after surgery were compared as estimates of the total 24-hour excretion, using a model based on glomerular filtration rate (calculated from cystatin C, age, height and weight), plasma- and urinary creatinine. The excretion of 8-oxodG increased in the first months after RYGB. For 8-oxoGuo, a gradual decrease was seen. Two years after RYGB and a mean weight loss of 35 kg, decreased hyperglycemia and insulin resistance, excretion levels of both markers were reduced by approximately 12% (P < 0.001). For both markers, mean excretion levels were about 30% lower in the female subgroup (P < 0.0001). Also, in this subgroup, excretion of 8-oxodG was significantly lower in patients with than without diabetes. We conclude, that oxidative damage to nucleic acids, reflected in the excretion of 8-oxodG and 8-oxoGuo, had decreased significantly two years after RYGB-indicating that reduced oxidative stress could be contributing to the many long-term benefits of RYGB-surgery in obesity and type 2 diabetes.
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Affiliation(s)
- Elin Rebecka Carlsson
- Department of Clinical Biochemistry, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical Biochemistry, Nordsjaellands Hospital, University of Copenhagen, Hilleroed, Denmark
| | - Mogens Fenger
- Department of Clinical Biochemistry, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Trine Henriksen
- Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Laura Kofoed Kjaer
- Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Dorte Worm
- Department of Medicine, Amager hospital, Copenhagen, Denmark
| | | | - Sten Madsbad
- Department of Endocrinology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Henrik Enghusen Poulsen
- Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, Copenhagen University Hospital, Copenhagen, Denmark
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Sesé B, Sanmartín JM, Ortega B, Llull R. Human Stromal Cell Aggregates Concentrate Adipose Tissue Constitutive Cell Population by In Vitro DNA Quantification Analysis. Plast Reconstr Surg 2020; 146:1285-1293. [PMID: 33234958 DOI: 10.1097/prs.0000000000007342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Regenerative cell strategies rely on stromal cell implants to attain an observable clinical outcome. However, the effective cell dose to ensure a therapeutic response remains unknown. To achieve a higher cell dose, the authors hypothesized that reducing the volume occupied by mature adipocytes in lipoaspirate will concentrate the stromal vascular fraction present in the original tissue. METHODS Human standardized lipoaspirate (n = 6) was centrifuged (1200 g for 3 minutes) and the water phase was discarded. Mechanical disaggregation was achieved by shearing tissue through 2.4- and 1.2-mm Luer-to-Luer transfers. After a second centrifugation (800 g for 10 minutes), stromal cell aggregates were separated from the supernatant oil phase. Lipoaspirate percentage composition was determined by its constituent weights. Cell content was measured by total DNA quantification, and partial cell viability was determined by image cytometry. Tissue sections were evaluated histologically (hematoxylin and eosin and Masson trichrome stains). RESULTS Stromal cell aggregates reduced the standardized lipoaspirate mass to 28.6 ± 4.2 percent. Accordingly, the cell density increased by 222.6 ± 63.3 percent (from 9.9 ± 1.4 million cells/g to 31.3 ± 6.6 million cells/g; p < 0.05). Cell viability was unaffected in stromal cell aggregates (71.3 ± 2.5 percent) compared to standardized lipoaspirate (72.2 ± 2.3 percent), and histologic analysis revealed high-density areas enriched with stromal cells (622.9 ± 145.6 percent) and extracellular matrix (871.2 ± 80.3 percent). CONCLUSION Stromal cell aggregates represent a biological agent that triplicates the cell density versus unprocessed lipoaspirate, low on oil and water fluids, and enriched extracellular matrix components.
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Affiliation(s)
- Borja Sesé
- From the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears; Servei de Genètica, Hospital Universitari Son Espases; Institut Català d'Oncologia, Hospital Germans Trias i Pujol; Cell Pro Tech Spain; and the University of Florida College of Medicine
| | - Javier M Sanmartín
- From the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears; Servei de Genètica, Hospital Universitari Son Espases; Institut Català d'Oncologia, Hospital Germans Trias i Pujol; Cell Pro Tech Spain; and the University of Florida College of Medicine
| | - Bernat Ortega
- From the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears; Servei de Genètica, Hospital Universitari Son Espases; Institut Català d'Oncologia, Hospital Germans Trias i Pujol; Cell Pro Tech Spain; and the University of Florida College of Medicine
| | - Ramon Llull
- From the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears; Servei de Genètica, Hospital Universitari Son Espases; Institut Català d'Oncologia, Hospital Germans Trias i Pujol; Cell Pro Tech Spain; and the University of Florida College of Medicine
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Nalbandian K, Piña-Aguilar RE, Morton CC. Resolving Breakpoints of Chromosomal Rearrangements at the Nucleotide Level Using Sanger Sequencing. Curr Protoc Hum Genet 2020; 108:e107. [PMID: 33369263 DOI: 10.1002/cphg.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Novel cytogenetic tools are increasingly based on genome sequencing for detecting chromosomal abnormalities. Different sequence-based techniques optimized for diagnosis of structural variants can be useful for narrowing down the localization of breakpoints of chromosomal abnormalities, but do not offer nucleotide resolution of breakpoints for proper interpretation of gene disruption. This protocol presents the characterization of structural variants at nucleotide resolution using Sanger sequencing after low-pass large-insert genome sequencing or other long-molecule methods. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Primer design for junction amplification at translocations and inversions Basic Protocol 2: Amplification of derivative chromosomes using a long-range polymerase Alternate Protocol: Amplification of derivative chromosomes using a hot-start polymerase Basic Protocol 3: Preparation of DNA for Sanger sequencing Basic Protocol 4: Interpretation and reporting of breakpoints based on Sanger sequencing.
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Affiliation(s)
- Katarena Nalbandian
- Massachusetts College of Pharmacy and Health Sciences University, Boston, Massachusetts
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts
- These authors contributed equally to this work
| | - Raul E Piña-Aguilar
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- These authors contributed equally to this work
| | - Cynthia C Morton
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
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Schyma C, Madea B, Müller R, Zieger M, Utz S, Grabmüller M. DNA-free does not mean RNA-free-The unwanted persistence of RNA. Forensic Sci Int 2020; 318:110632. [PMID: 33302243 DOI: 10.1016/j.forsciint.2020.110632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022]
Abstract
Contact shots to the head often provoke a transfer of biological traces into firearm barrels, which are not visible at endoscopic inspection. STR-PCR can amplify these latent traces and assign them to the victim. Via RNA-DNA-co-extraction also miRNA can be detected, which allow a conclusion to be drawn about the body fluid or tissue. Molecular genetic analysis of experimental stains in firearm barrels requires the guarantee that the barrel is initially free of any nucleic acid. Twelve shots were fired to so-called "reference cubes" (10 % gelatine, 12 cm edge length, embedded paint-blood-pad) using three current handguns: from 20 and 30 cm distance, four at close range (1-2.5 cm) and six contact shots. After endoscopic examination and swabbing of the barrels, a previously described mechanical and chemical cleaning using DNAExitusPlus™ was performed. The inner surface of the barrel was thoroughly wiped off using moistened forensic swabs, which were submitted to RNA-DNA-co-extraction. The combined thorough mechanical cleaning with Ballistol® and the application of DNAExitusPlus™ eliminated any profilable DNA in all samples. However, in 10 of 12 samples RNA concentrations between 0.11 - 0.79 ng/μl were measured. Furthermore, in 9 of 12 samples blood-specific miRNA (miR-451a) was detected. Summarizing, none of the experimentally contaminated barrels was RNA-free despite the performed cleaning procedure. Further investigation showed, that even "professional" cleaning by a gunsmith did not remove RNA.
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Affiliation(s)
- Christian Schyma
- Institute of Forensic Medicine of the University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland.
| | - Burkhard Madea
- Institute of Legal Medicine, University Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Rolf Müller
- Criminal Investigation Service of the Cantonal Police Department of Bern, Nordring 30, 3013 Bern, Switzerland
| | - Martin Zieger
- Institute of Forensic Medicine of the University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland
| | - Silvia Utz
- Institute of Forensic Medicine of the University of Bern, Bühlstrasse 20, 3012 Bern, Switzerland
| | - Melanie Grabmüller
- Institute of Legal Medicine, University Bonn, Stiftsplatz 12, 53111 Bonn, Germany
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Liu M, Zhao Y, Sun Y, Li Y, Wu P, Zhou S, Ren L. Comparative study on diatom morphology and molecular identification in drowning cases. Forensic Sci Int 2020; 317:110552. [PMID: 33147546 DOI: 10.1016/j.forsciint.2020.110552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
In the field of criminal investigations, in the event that a body is found in water, the ability to differentiate whether the cause of death was drowning or the body was murdered then dumped into water elsewhere is difficult but important for case detection. Detecting diatoms in human organs can be used to effectively identify if the cause of death was drowning. At present, diatom detection methods are roughly divided into morphological and molecular detection methods, but both methods have different limitations. In this study, a total of 79 samples from 23 victims in 19 known drowning deaths were collected. The diatom morphological identification combined with DNA metabarcoding technology was used to compare the reliability of the diatom detection method. Microscopic observations revealed that the positive detection rate of diatoms was 52.6 %, 26.3 % and 58.8 % respectively in the kidney, liver and lung samples. DNA metabarcoding analysis found that the positive detection rate of diatoms was 31.6 %, 31.6 % and 35.3 % respectively in kidney, liver and lung samples. When compared with barcode BacirbcL, barcode 18S605 detected more diatoms, while diatoms in BacirbcL were more consistent with environmental samples. The comparative analysis found that microscopic observations were not highly correlated with the identification results of DNA barcoding technology. There were no obvious differences in the effect of internal organs on diatom enrichment, and different organs should be tested at the same time. At present, the DNA barcode reference sequence is gravely insufficient and has many errors, which leads to restrictions in the application of this technology, resulting in many OTU not being accurately identified. This explains why the success rate of molecular identification is not higher than that of microscopic identification. Construction of a reliable diatom DNA barcode reference sequence database is an urgent task for drowning forensics.
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Affiliation(s)
- Mengyan Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China; Forensic Judicial Appraisal Center of Beijing Public Security Bureau, Beijing, 100192, China
| | - Yi Zhao
- Forensic Judicial Appraisal Center of Beijing Public Security Bureau, Beijing, 100192, China
| | - Yuzhe Sun
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Li
- Forensic Judicial Appraisal Center of Beijing Public Security Bureau, Beijing, 100192, China
| | - Ping Wu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Liang Ren
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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Cunha EN, de Souza MFB, Lanza DCF, Lima JPMS. A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum. PLoS One 2020; 15:e0240536. [PMID: 33057447 PMCID: PMC7561130 DOI: 10.1371/journal.pone.0240536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid detection by electrophoresis is still a quick and accessible technique for many diagnosis methods, primarily at research laboratories or at the point of care units. Standard protocols detect DNA/RNA molecules through specific bound chemical dyes using a UV-transilluminator or UV-photo documentation system. However, the acquisition costs and availability of these devices, mainly the ones with photography and internet connection capabilities, can be prohibitive, especially in developing countries public health units. Also, ultraviolet radiation is a common additional risk factor to professionals that use electrophoresis-based nucleic acid detection. With that in mind, this work describes the development of a low-cost DNA/RNA detection smart system capable of obtaining qualitative and semi-quantitative data from gel analysis. The proposed device explores the visible light absorption range of commonly used DNA/RNA dyes using readily available parts, and simple manufacturing processes, such as light-emitting diodes (LEDs) and 3D impression. By applying IoT techniques, our system covers a wide range of color spectrum in order to detect bands from various commercially used dyes, using Bluetooth communication and a smartphone for hardware control, image capturing, and sharing. The project also enables process scalability and has low manufacturing and maintenance costs. The use of LEDs at the visible spectrum can achieve very reproducible images, providing a high potential for rapid and point-of-care diagnostics as well as applications in several fields such as healthcare, agriculture, and aquaculture.
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Affiliation(s)
- Eduardo Nogueira Cunha
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
| | - Maria Fernanda Bezerra de Souza
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - Daniel Carlos Ferreira Lanza
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Departamento de Bioquímica, Laboratório de Biologia Molecular Aplicada (LAPLIC), Centro de Biociências, UFRN, Natal, Brazil
| | - João Paulo Matos Santos Lima
- Programa de Pós-graduação em Bioinformática (PPg-Bioinfo), Instituto Metrópole Digital (IMD), Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- Departamento de Bioquímica, Laboratório de Sistemas Metabólicos e Bioinformática (LASIS), Centro de Biociências, UFRN, Natal, Brazil
- Instituto de Medicina Tropical do Rio Grande do Norte (IMT-RN), UFRN, Natal, Brazil
- Programa de Pós-graduação em Bioquímica, Centro de Biociências, UFRN, Natal, Brazil
- Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Natal, Brazil
- * E-mail:
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Rasool N, Rasool M. DNA evidence in sexual assault cases in Pakistan. Med Sci Law 2020; 60:270-277. [PMID: 32576088 DOI: 10.1177/0025802420934240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sexual assault is becoming a global epidemic, affecting close to a billion women throughout the world. This paper explores the challenges in the admissibility of DNA evidence in rape cases in Pakistan. Delays in the medical examination of victims, and improper collection and packaging of evidentiary material, compromise the probative biological evidence. In the last few years, existing laws have been amended to increase the utility of DNA evidence during criminal trials. However, various issues - for example lack of proper knowledge of DNA evidence by lawyers and judicial officers, inadequacies in existing laws and conflicting decisions of apex courts - can affect the admissibility of DNA evidence during criminal trials.
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Affiliation(s)
- Nouman Rasool
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Pakistan
- Center for Professional Studies, Pakistan
| | - Muzamal Rasool
- Advocate, Lahore High Court, Pakistan
- Post Graduate Institute of Law, University of Lahore, Pakistan
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McManus KM, Kirk RD, Via CW, Lotti JS, Roduit AF, Teta R, Scarpato S, Mangoni A, Bertin MJ. Isolation of Isotrichophycin C and Trichophycins G-I from a Collection of Trichodesmium thiebautii. J Nat Prod 2020; 83:2664-2671. [PMID: 32816476 PMCID: PMC7815318 DOI: 10.1021/acs.jnatprod.0c00550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The trichophycin family of compounds are chlorinated polyketides first discovered from environmental collections of a bloom-forming Trichodesmium sp. cyanobacterium. In an effort to fully capture the chemical space of this group of metabolites, the utilization of MS/MS-based molecular networking of a Trichodesmium thiebautii extract revealed a metabolome replete with halogenated compounds. Subsequent MS-guided isolation resulted in the characterization of isotrichophycin C and trichophycins G-I (1-4). These new metabolites had intriguing structural variations from those trichophycins previously characterized, which allowed for a comparative study to examine structural features that are associated with toxicity to murine neuroblastoma cells. Additionally, we propose the absolute configuration of the previously characterized trichophycin A (5). Overall, the metabolome of the Trichodesmium bloom is hallmarked by an unprecedented amount of chlorinated molecules, many of which remain to be structurally characterized.
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Affiliation(s)
- Kelly M McManus
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Riley D Kirk
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Christopher W Via
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - James S Lotti
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Alexandre F Roduit
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Roberta Teta
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Silvia Scarpato
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Matthew J Bertin
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island 02881, United States
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Teixeira LPR, Lopes FEDM, Antunes ASLM, Alves MS, Miranda AM, Gaudencio Neto S, Martins LT, Moreira ACDOM, Tavares KCS. Application of a cost-effective DNA extraction protocol for screening transgenic and CRISPR-edited primary goat cells. PLoS One 2020; 15:e0239435. [PMID: 32946490 PMCID: PMC7500585 DOI: 10.1371/journal.pone.0239435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/06/2020] [Indexed: 11/18/2022] Open
Abstract
The genotyping of genetically-modified cells is a crucial step in studies of transgenics and genomic editing with systems such as CRISPR/Cas. The detection of genome editing events can be directly related to the genotyping methodology used, which is influenced by its costs, since many experiments require the analysis of a large number of samples. The aim of this study was to compare the performance of direct lysis methods of genomic DNA (gDNA) extraction for the detection of knockins and knockouts in primary goat cells. Initially, three gDNA extraction protocols (protocol A, heat denaturation/freeze-thaw in water; protocol B, heat denaturation/proteinase K; and protocol C, CellsDirect Kit) were tested using different quantities (1,000, 5,000 and 10,000 cells) and types of goat primary cells (fibroblasts and goat mammary epithelial cells—GMECs) for subsequent validation by PCR amplification of small (GAPDH) and large amplicons (hLF transgene). All protocols were successful in the detection of the small amplicon; however, in GMECs, only protocol B resulted efficient amplification (protocol A—0%, protocol B—93%, protocol C—13.33%, P <0.05). In a proof-of-principle experiment, the TP53 gene was knocked out in GMECs by CRISPR/Cas9-mediated deletion while constructs containing the anti-VEGF monoclonal antibody (pBC-anti-VEGF) and bacterial L-Asparaginase (pBC-ASNase) transgenes were knocked-in separately in fibroblasts. Detection of successful editing was performed using protocol B and PCR. The integration rates of the pBC-ASNase and pBC-anti-VEGF transgenes were 93.6% and 72%, respectively, as per PCR. The efficiency of biallelic editing in GMECs using CRISPR/Cas9 for the TP53 deletion was 5.4%. Our results suggest that protocol B (heat denaturation/proteinase K) can be used as an inexpensive and quick methodology for detecting genetic modifications in different types of primary goat cells, with efficiency rates consistent with values previously described in the literature when using extraction kits or more complex proteinase K formulations.
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Affiliation(s)
| | | | | | - Matheus Soares Alves
- Experimental Biology Center (NUBEX), University of Fortaleza (UNIFOR), Fortaleza, Ceara, Brazil
| | - André Marrocos Miranda
- Experimental Biology Center (NUBEX), University of Fortaleza (UNIFOR), Fortaleza, Ceara, Brazil
| | - Saul Gaudencio Neto
- Experimental Biology Center (NUBEX), University of Fortaleza (UNIFOR), Fortaleza, Ceara, Brazil
| | | | | | - Kaio Cesar Simiano Tavares
- Experimental Biology Center (NUBEX), University of Fortaleza (UNIFOR), Fortaleza, Ceara, Brazil
- * E-mail:
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41
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Wainwright BJ, Zahn GL, Afiq-Rosli L, Tanzil JTI, Huang D. Host age is not a consistent predictor of microbial diversity in the coral Porites lutea. Sci Rep 2020; 10:14376. [PMID: 32873814 PMCID: PMC7463248 DOI: 10.1038/s41598-020-71117-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
Corals harbour diverse microbial communities that can change in composition as the host grows in age and size. Larger and older colonies have been shown to host a higher diversity of microbial taxa and this has been suggested to be a consequence of their more numerous, complex and varied micro-niches available. However, the effects of host age on community structure and diversity of microbial associates remain equivocal in the few studies performed to date. To test this relationship more robustly, we use established techniques to accurately determine coral host age by quantifying annual skeletal banding patterns, and utilise high-throughput sequencing to comprehensively characterise the microbiome of the common reef-building coral, Porites lutea. Our results indicate no clear link between coral age and microbial diversity or richness. Different sites display distinct age-dependent diversity patterns, with more anthropogenically impacted reefs appearing to show a winnowing of microbial diversity with host age, possibly a consequence of corals adapting to degraded environments. Less impacted sites do not show a signature of winnowing, and we observe increases in microbial richness and diversity as the host ages. Furthermore, we demonstrate that corals of a similar age from the same reef can show very different microbial richness and diversity.
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Affiliation(s)
| | - Geoffrey L Zahn
- Biology Department, Utah Valley University, 800 W. University Parkway, Orem, UT, 84058, USA
| | - Lutfi Afiq-Rosli
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore
| | - Jani T I Tanzil
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore
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Veigl SJ, Harman O, Lamm E. Friedrich Miescher's Discovery in the Historiography of Genetics: From Contamination to Confusion, from Nuclein to DNA. J Hist Biol 2020; 53:451-484. [PMID: 32524311 DOI: 10.1007/s10739-020-09608-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher's name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher's reception in the historiography of genetics. To his critics, Miescher was a "contaminator," whose preparations were impure. Modern historians portrayed him as a "confuser," whose misunderstandings delayed the development of molecular biology. Each of these portrayals reflects the disciplinary context in which Miescher's work was evaluated. Using archival sources to unearth Miescher's unpublished speculations-including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation-this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago.
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Affiliation(s)
| | - Oren Harman
- Graduate Program in Science, Technology and Society, Bar Ilan University, Ramat Gan, Israel
| | - Ehud Lamm
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Ramat Aviv, 6997801, Tel Aviv, Israel.
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Kinkar L, Young ND, Sohn WM, Stroehlein AJ, Korhonen PK, Gasser RB. First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. PLoS Negl Trop Dis 2020; 14:e0008552. [PMID: 32845881 PMCID: PMC7449408 DOI: 10.1371/journal.pntd.0008552] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Background Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome—including the long, non-coding region—of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing. Methods The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach. Results From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719–809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation. Conclusions For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of a wide range of taxa. In the present study, we characterised the complete mitochondrial genome of Clonorchis sinensis—a carcinogenic liver fluke. To do this, we sequenced from total genomic DNA from multiple adult worms using a new method (Oxford Nanopore technology) to obtain data for long stretches of DNA, and then assembled these data to construct a mitochondrial genome of 18,304 bp, containing a > 4.5 kb-long tandem-repetitive region—not previously detected in this species. The results demonstrate that this method is effective at sequencing long and complex non-coding elements—not achievable using conventional techniques. The discovery of this long tandem-repetitive region in C. sinensis provides an opportunity to now explore its origin(s) and length/sequence diversity in populations of this species, and also to characterise its function(s). The technological approach employed here should have broad applicability to characterise previously-elusive non-coding mitochondrial genomic regions in a wide range of taxa.
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Affiliation(s)
- Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Andreas J. Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
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44
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Liu S, Piao X, Hou N, Cai P, Ma Y, Chen Q. Duplex real-time PCR for sexing Schistosoma japonicum cercariae based on W chromosome-specific genes and its applications. PLoS Negl Trop Dis 2020; 14:e0008609. [PMID: 32822351 PMCID: PMC7467314 DOI: 10.1371/journal.pntd.0008609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/02/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
As a unique feature among otherwise hermaphroditic trematodes, Schistosoma species are gonochoric parasites whose sex is genetically determined (ZZ for males and ZW for females). However, schistosome larvae are morphologically identical, and sex can only be discriminated by molecular methods. Here, we integrated published Schistosoma. japonicum transcriptome and genome data to identify W chromosome-specific genes as sex biomarkers. Three W chromosome-specific genes of S. japonicum were identified as sex biomarkers from a panel of 12 genes expressed only in females. An efficient duplex real-time PCR (qPCR) method for sexing cercariae was developed which could identify the sex of cercariae within 2 h without DNA extraction. Moreover, this method can be used to identify not only single-sex but also mixed-sex schistosome-infected snails. We observed a nearly equal proportion of single-male, single-female, and mixed-sex schistosome infections in artificially infected snails. Sex-known schistosome-infected snail models can be efficiently constructed with the aid of duplex qPCR. A field study revealed that single-sex schistosome infections were predominant among naturally infected snails. Finally, a schistosomiasis mouse model based on sex-known cercariae infection was shown to be more reliable than a model based on sex-unknown cercariae infection. The developed duplex qPCR method for sexing S. japonicum cercariae can be widely used for schistosomiasis modeling, genetic experiments, and field-based molecular epidemiological studies. Schistosoma japonicum is a major causative agent of human schistosomiasis. Unlike other parasitic worms, S. japonicum females are determined by the heterogametic sex chromosome (ZW) and males by the homogametic sex chromosome (ZZ). The life cycle of S. japonicum includes the egg, miracidium, mother sporocyst, daughter sporocyst, cercaria, schistosomulum, and adult stages. The sex of adult male and female worms can be morphologically distinguished, whereas the sex of larvae, such as cercariae, can only be discriminated by molecular methods. In this study, we established an efficient duplex real-time PCR method for sexing S. japonicum cercariae based on newly identified W chromosome-specific genes. The established duplex real-time PCR method will facilitate construction of sex-controlled schistosome-infected intermediate host or definitive host models for schistosome-host interplays and schistosomiasis studies. This method is also a powerful tool for investigating the epidemiology of single-sex and mixed-sex schistosome-infected snails in the field.
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Affiliation(s)
- Shuai Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
- * E-mail: (SL); (QC)
| | - Xianyu Piao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Nan Hou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Yu Ma
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Qijun Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agriculture University, Shenyang, P.R. China
- * E-mail: (SL); (QC)
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Goh PT, Kuah MK, Chew YS, Teh HY, Shu-Chien AC. The requirements for sterol regulatory element-binding protein (Srebp) and stimulatory protein 1 (Sp1)-binding elements in the transcriptional activation of two freshwater fish Channa striata and Danio rerio elovl5 elongase. Fish Physiol Biochem 2020; 46:1349-1359. [PMID: 32239337 DOI: 10.1007/s10695-020-00793-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
Fish are a major source of beneficial n-3 LC-PUFA in human diet, and there is considerable interest to elucidate the mechanism and regulatory aspects of LC-PUFA biosynthesis in farmed species. Long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis involves the activities of two groups of enzymes, the fatty acyl desaturase (Fads) and elongase of very long-chain fatty acid (Elovl). The promoters of elovl5 elongase, which catalyses the rate-limiting reaction of elongating polyunsaturated fatty acid (PUFA), have been previously described and characterized from several marine and diadromous teleost species. We report here the cloning and characterization of elovl5 promoter from two freshwater fish species, the carnivorous snakehead fish (Channa striata) and zebrafish. Results show the presence of sterol-responsive elements (SRE) in the core regulatory region of both promoters, suggesting the importance of sterol regulatory element-binding protein (Srebp) in the regulation of elovl5 for both species. Mutagenesis luciferase and electrophoretic mobility shift assays further validate the role of SRE for basal transcriptional activation. In addition, several Sp1-binding sites located in close proximity with SRE were present in the snakehead promoter, with one having a potential synergy with SRE in the regulation of elovl5 expression. The core zebrafish elovl5 promoter fragment also directed in vivo expression in the yolk syncytial layer of developing zebrafish embryos.
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Affiliation(s)
- Pei-Tian Goh
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Meng-Kiat Kuah
- Centre for Chemical Biology, Sains@USM, Blok B No. 10, Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Yen-Shan Chew
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Hui-Ying Teh
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Alexander Chong Shu-Chien
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
- Centre for Chemical Biology, Sains@USM, Blok B No. 10, Persiaran Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia.
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Krokidis MG, D’Errico M, Pascucci B, Parlanti E, Masi A, Ferreri C, Chatgilialoglu C. Oxygen-Dependent Accumulation of Purine DNA Lesions in Cockayne Syndrome Cells. Cells 2020; 9:cells9071671. [PMID: 32664519 PMCID: PMC7407219 DOI: 10.3390/cells9071671] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Cockayne Syndrome (CS) is an autosomal recessive neurodegenerative premature aging disorder associated with defects in nucleotide excision repair (NER). Cells from CS patients, with mutations in CSA or CSB genes, present elevated levels of reactive oxygen species (ROS) and are defective in the repair of a variety of oxidatively generated DNA lesions. In this study, six purine lesions were ascertained in wild type (wt) CSA, defective CSA, wtCSB and defective CSB-transformed fibroblasts under different oxygen tensions (hyperoxic 21%, physioxic 5% and hypoxic 1%). In particular, the four 5′,8-cyclopurine (cPu) and the two 8-oxo-purine (8-oxo-Pu) lesions were accurately quantified by LC-MS/MS analysis using isotopomeric internal standards after an enzymatic digestion procedure. cPu levels were found comparable to 8-oxo-Pu in all cases (3–6 lesions/106 nucleotides), slightly increasing on going from hyperoxia to physioxia to hypoxia. Moreover, higher levels of four cPu were observed under hypoxia in both CSA and CSB-defective cells as compared to normal counterparts, along with a significant enhancement of 8-oxo-Pu. These findings revealed that exposure to different oxygen tensions induced oxidative DNA damage in CS cells, repairable by NER or base excision repair (BER) pathways. In NER-defective CS patients, these results support the hypothesis that the clinical neurological features might be connected to the accumulation of cPu. Moreover, the elimination of dysfunctional mitochondria in CS cells is associated with a reduction in the oxidative DNA damage.
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Affiliation(s)
- Marios G. Krokidis
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; (M.G.K.); (A.M.); (C.F.)
- Institute of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos”, 15310 Agia Paraskevi Attikis, Athens, Greece
| | - Mariarosaria D’Errico
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.D.); (B.P.); (E.P.)
| | - Barbara Pascucci
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.D.); (B.P.); (E.P.)
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, Monterotondo Stazione, 00015 Rome, Italy
| | - Eleonora Parlanti
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (M.D.); (B.P.); (E.P.)
| | - Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; (M.G.K.); (A.M.); (C.F.)
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, Monterotondo Stazione, 00015 Rome, Italy
| | - Carla Ferreri
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; (M.G.K.); (A.M.); (C.F.)
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; (M.G.K.); (A.M.); (C.F.)
- Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
- Correspondence: ; Tel.: +39-051-639-8309
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Patzold F, Zilli A, Hundsdoerfer AK. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS One 2020; 15:e0235222. [PMID: 32639972 PMCID: PMC7343169 DOI: 10.1371/journal.pone.0235222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.
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Affiliation(s)
- Franziska Patzold
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Alberto Zilli
- Division Insects, Department Life Sciences, Natural History Museum, London, United Kingdom
| | - Anna K. Hundsdoerfer
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
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48
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Teillet J, Martinez Q, Tijunelyte I, Chami B, Bancaud A. Characterization and minimization of band broadening in DNA electrohydrodynamic migration for enhanced size separation. Soft Matter 2020; 16:5640-5649. [PMID: 32510064 DOI: 10.1039/d0sm00475h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The combination of hydrodynamic actuation with an opposing electrophoretic force in viscoelastic liquids enables the separation, concentration, and purification of DNA. Obtaining good analytical performances despite the use of hydrodynamic flow fields, which dramatically enhance band broadening due to Taylor dispersion, constitutes a paradox that remains to be clarified. Here, we study the mechanism of band broadening in electrohydrodynamic migration with an automated microfluidic platform that allows us to track the migration of a 600 bp band in the pressure-electric field parameter space. We demonstrate that diffusion in the electrohydrodynamic regime is controlled predominantly by the electric field and marginally by the hydrodynamic flow velocity. We explain this response with an analytical model of diffusion based on Taylor dispersion arguments. Furthermore, we demonstrate that the electric field can be modulated over time to monitor and minimize the breadth of a DNA band, and suggest guidelines to enhance the resolution of DNA separation experiments. Altogether, our report is a leap towards to the development of high-performance analytical technologies based on electrohydrodynamic actuation.
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Affiliation(s)
- Jeffrey Teillet
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France.
| | - Quentin Martinez
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France.
| | - Inga Tijunelyte
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France.
| | - Bayan Chami
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France.
| | - Aurélien Bancaud
- CNRS, LAAS, 7 Avenue du Colonel Roche, F-31400, Toulouse, France.
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49
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Lee S, Roh SM, Lee E, Park Y, Lee BC, Kwon Y, Kim HJ, Kim J. Applications of Converged Various Forces for Detection of Biomolecules and Novelty of Dielectrophoretic Force in the Applications. Sensors (Basel) 2020; 20:E3242. [PMID: 32517305 PMCID: PMC7309140 DOI: 10.3390/s20113242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022]
Abstract
Since separation of target biomolecules is a crucial step for highly sensitive and selective detection of biomolecules, hence, various technologies have been applied to separate biomolecules, such as deoxyribonucleic acid (DNA), protein, exosome, virus, etc. Among the various technologies, dielectrophoresis (DEP) has the significant advantage that the force can provide two different types of forces, attractive and repulsive DEP force, through simple adjustment in frequency or structure of microfluidic chips. Therefore, in this review, we focused on separation technologies based on DEP force and classified various separation technologies. First, the importance of biomolecules, general separation methods and various forces including DEP, electrophoresis (EP), electrothermal flow (ETF), electroosmosis (EO), magnetophoresis, acoustophoresis (ACP), hydrodynamic, etc., was described. Then, separating technologies applying only a single DEP force and dual force, moreover, applying other forces simultaneously with DEP force were categorized. In addition, advanced technologies applying more than two different kinds of forces, namely complex force, were introduced. Overall, we critically reviewed the state-of-the-art of converged various forces for detection of biomolecules with novelty of DEP.
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Affiliation(s)
- Seungjun Lee
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Korea; (S.L.); (S.M.R.); (E.L.); (Y.P.); (Y.K.)
| | - Seong Min Roh
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Korea; (S.L.); (S.M.R.); (E.L.); (Y.P.); (Y.K.)
| | - Eunji Lee
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Korea; (S.L.); (S.M.R.); (E.L.); (Y.P.); (Y.K.)
| | - Yejin Park
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Korea; (S.L.); (S.M.R.); (E.L.); (Y.P.); (Y.K.)
| | - Byung Chul Lee
- Center for BioMicrosystems, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea;
| | - Youngeun Kwon
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Korea; (S.L.); (S.M.R.); (E.L.); (Y.P.); (Y.K.)
| | - Hye Jin Kim
- Department of Clinical Pharmacology, Kyung Hee University, Seoul 02447, Korea
| | - Jinsik Kim
- Department of Medical Biotechnology, Dongguk University, Seoul 04620, Korea; (S.L.); (S.M.R.); (E.L.); (Y.P.); (Y.K.)
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50
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Ragazzo M, Melchiorri S, Manzo L, Errichiello V, Puleri G, Nicastro F, Giardina E. Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods. Genes (Basel) 2020; 11:E582. [PMID: 32456006 PMCID: PMC7288309 DOI: 10.3390/genes11050582] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/10/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This "swab in-profile out" method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality.
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Affiliation(s)
- Michele Ragazzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Stefano Melchiorri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Laura Manzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Giulio Puleri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | | | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
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