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Kampmann ML, Tfelt-Hansen J, Børsting C. Cleaning protocols in forensic genetic laboratories. Int J Legal Med 2024:10.1007/s00414-024-03232-0. [PMID: 38649547 DOI: 10.1007/s00414-024-03232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
It is pivotal to avoid cross-sample contamination in forensic genetic laboratories and optimal cleaning protocols for the removal of DNA are essential. A survey was performed, and ten forensic genetic laboratories shared their cleaning protocols in pre-PCR and post-PCR laboratories. The cleaning frequencies on different surface areas were somewhat similar, whereas none of the laboratories used the same cleaning reagents. Therefore, the efficiencies of the cleaning protocol utilised were tested and compared. The results showed that freshly made household bleach and Virkon® removed all amplifiable DNA from the surfaces, whereas DNA AWAY™ and the disinfection reagents ethanol, isopropanol, and ChemGene HLD4L did not.
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Affiliation(s)
- Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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2
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Lynggaard C, Frøslev TG, Johnson MS, Olsen MT, Bohmann K. Airborne environmental DNA captures terrestrial vertebrate diversity in nature. Mol Ecol Resour 2024; 24:e13840. [PMID: 37497670 DOI: 10.1111/1755-0998.13840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/12/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
The current biodiversity and climate crises highlight the need for efficient tools to monitor terrestrial ecosystems. Here, we provide evidence for the use of airborne eDNA analyses as a novel method for detecting terrestrial vertebrate communities in nature. Metabarcoding of 143 airborne eDNA samples collected during 3 days in a mixed forest in Denmark yielded 64 bird, mammal, fish and amphibian taxa, of which the detected 57 'wild' taxa represent over a quarter of the around 210 terrestrial vertebrates that occur in the overall area. We provide evidence for the spatial movement and temporal patterns of airborne eDNA and for the influence of weather conditions on vertebrate detections. This study demonstrates airborne eDNA for high-resolution biomonitoring of vertebrates in terrestrial systems and elucidates its potential to guide global nature management and conservation efforts in the ongoing biodiversity crisis.
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Affiliation(s)
- Christina Lynggaard
- Section for Molecular Ecology & Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Guldberg Frøslev
- Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew S Johnson
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- DevLabs, Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Molecular Ecology & Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Molecular Ecology & Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Kampmann ML, Simonsen BT, Børsting C. Test of chlorine wipes for efficient removal of DNA from forensic genetics laboratories. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Bini C, Giorgetti A, Giovannini E, Pelletti G, Fais P, Pelotti S. Technical note: Human DNA contamination of postmortem examination facilities: Impact of COVID-19 cleaning procedure. J Forensic Sci 2022; 67:1867-1875. [PMID: 35844155 PMCID: PMC9349986 DOI: 10.1111/1556-4029.15096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022]
Abstract
The DNA contamination of evidentiary trace samples, included those collected in the autopsy room, has significant detrimental consequences for forensic genetics investigation. After the COVID‐19 pandemic, methods to prevent environmental contamination in the autopsy room have been developed and intensified. This study aimed to evaluate the level of human DNA contamination of a postmortem examination facility before and after the introduction of COVID‐19‐related disinfection and cleaning procedures. Ninety‐one swabs were collected from the surfaces and the dissecting instruments, analyzed by real‐time quantitative PCR (q‐PCR) and typed for 21 autosomal STRs. Sixty‐seven out of 91 samples resulted in quantifiable human DNA, ranging from 1 pg/μl to 12.4 ng/μl, including all the samples collected before the implementation of COVID‐19 cleaning procedures (n = 38) and 29 out of 53 (54.7%) samples taken afterward. All samples containing human DNA were amplified, resulting in mixed (83.6%), single (13.4%), and incomplete (3%) profiles. A statistically significant decrease in DNA contamination was found for dissecting instruments after treatment with chlorhexidine and autoclave (p < 0.05). Environmental decontamination strategies adopted during COVID‐19 pandemic only partially solved the long‐standing issue of DNA contamination of postmortem examination facilities. The pandemic represents an opportunity to further stress the need for standardized evidence‐based protocols targeted to overcome the problem of DNA contamination in the autopsy room.
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Affiliation(s)
- Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Arianna Giorgetti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Elena Giovannini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Guido Pelletti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Paolo Fais
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
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5
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Moshynets OV, Baranovskyi TP, Iungin OS, Kysil NP, Metelytsia LO, Pokholenko I, Potochilova VV, Potters G, Rudnieva KL, Rymar SY, Semenyuta IV, Spiers AJ, Tarasyuk OP, Rogalsky SP. eDNA Inactivation and Biofilm Inhibition by the PolymericBiocide Polyhexamethylene Guanidine Hydrochloride (PHMG-Cl). Int J Mol Sci 2022; 23:ijms23020731. [PMID: 35054915 PMCID: PMC8775615 DOI: 10.3390/ijms23020731] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/03/2022] [Accepted: 01/03/2022] [Indexed: 01/05/2023] Open
Abstract
The choice of effective biocides used for routine hospital practice should consider the role of disinfectants in the maintenance and development of local resistome and how they might affect antibiotic resistance gene transfer within the hospital microbial population. Currently, there is little understanding of how different biocides contribute to eDNA release that may contribute to gene transfer and subsequent environmental retention. Here, we investigated how different biocides affect the release of eDNA from mature biofilms of two opportunistic model strains Pseudomonas aeruginosa ATCC 27853 (PA) and Staphylococcus aureus ATCC 25923 (SA) and contribute to the hospital resistome in the form of surface and water contaminants and dust particles. The effect of four groups of biocides, alcohols, hydrogen peroxide, quaternary ammonium compounds, and the polymeric biocide polyhexamethylene guanidine hydrochloride (PHMG-Cl), was evaluated using PA and SA biofilms. Most biocides, except for PHMG-Cl and 70% ethanol, caused substantial eDNA release, and PHMG-Cl was found to block biofilm development when used at concentrations of 0.5% and 0.1%. This might be associated with the formation of DNA–PHMG-Cl complexes as PHMG-Cl is predicted to bind to AT base pairs by molecular docking assays. PHMG-Cl was found to bind high-molecular DNA and plasmid DNA and continued to inactivate DNA on surfaces even after 4 weeks. PHMG-Cl also effectively inactivated biofilm-associated antibiotic resistance gene eDNA released by a pan-drug-resistant Klebsiella strain, which demonstrates the potential of a polymeric biocide as a new surface-active agent to combat the spread of antibiotic resistance in hospital settings.
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Affiliation(s)
- Olena V. Moshynets
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
- Correspondence: (O.V.M.); (S.P.R.)
| | - Taras P. Baranovskyi
- Department of Dermatovenerology, Allergology, Clinical and Laboratory Immunology, Shupyk National Healthcare University of Ukraine, 9 Dorohozhytska Str., 03680 Kiev, Ukraine;
- Kyiv Regional Clinical Hospital, 1 Baggovutivska Street, 04107 Kiev, Ukraine; (V.V.P.); (K.L.R.)
| | - Olga S. Iungin
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
- Department of Biotechnology, Leather and Fur, Faculty of Chemical and Biopharmaceutical Technologies, Kyiv National University of Technologies and Design, Nemyrovycha-Danchenka Street, 2, 01011 Kiev, Ukraine
| | - Nadiia P. Kysil
- National Children’s Specialized Hospital “Okhmatdyt”, 28/1 Chornovola Str., 01135 Kiev, Ukraine;
| | - Larysa O. Metelytsia
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
| | - Ianina Pokholenko
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
| | - Viktoria V. Potochilova
- Kyiv Regional Clinical Hospital, 1 Baggovutivska Street, 04107 Kiev, Ukraine; (V.V.P.); (K.L.R.)
| | - Geert Potters
- Antwerp Maritime Academy, Noordkasteel Oost 6, 2030 Antwerp, Belgium;
- Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Kateryna L. Rudnieva
- Kyiv Regional Clinical Hospital, 1 Baggovutivska Street, 04107 Kiev, Ukraine; (V.V.P.); (K.L.R.)
| | - Svitlana Y. Rymar
- Biofilm Study Group, Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho Str., 03680 Kiev, Ukraine; (O.S.I.); (I.P.); (S.Y.R.)
| | - Ivan V. Semenyuta
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Bell Street, Dundee DD1 1HG, UK;
| | - Oksana P. Tarasyuk
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
| | - Sergiy P. Rogalsky
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Science of Ukraine, 50 Kharkivske Schose, 01135 Kiev, Ukraine; (L.O.M.); (I.V.S.); (O.P.T.)
- Correspondence: (O.V.M.); (S.P.R.)
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6
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Silva DP, Epstein HE, Vega Thurber RL. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics. Front Microbiol 2022; 13:1007877. [PMID: 36891260 PMCID: PMC9987214 DOI: 10.3389/fmicb.2022.1007877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/30/2022] [Indexed: 02/22/2023] Open
Abstract
Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.
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Affiliation(s)
- Denise P Silva
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Hannah E Epstein
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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7
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Alvarez MM, Bravo-González S, González-González E, Trujillo-de Santiago G. Portable and Label-Free Quantitative Loop-Mediated Isothermal Amplification (LF-qLamp) for Reliable COVID-19 Diagnostics in Three Minutes of Reaction Time: Arduino-Based Detection System Assisted by a pH Microelectrode. BIOSENSORS 2021; 11:bios11100386. [PMID: 34677342 PMCID: PMC8533988 DOI: 10.3390/bios11100386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been recently studied as an alternative method for cost-effective diagnostics in the context of the current COVID-19 pandemic. Recent reports document that LAMP-based diagnostic methods have a comparable sensitivity and specificity to that of RT-qPCR. We report the use of a portable Arduino-based LAMP-based amplification system assisted by pH microelectrodes for the accurate and reliable diagnosis of SARS-CoV-2 during the first 3 min of the amplification reaction. We show that this simple system enables a straightforward discrimination between samples containing or not containing artificial SARS-CoV-2 genetic material in the range of 10 to 10,000 copies per 50 µL of reaction mix. We also spiked saliva samples with SARS-CoV-2 synthetic material and corroborated that the LAMP reaction can be successfully monitored in real time using microelectrodes in saliva samples as well. These results may have profound implications for the design of real-time and portable quantitative systems for the reliable detection of viral pathogens including SARS-CoV-2.
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Affiliation(s)
- Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Correspondence: (M.M.A.); (G.T.-d.S.)
| | - Sergio Bravo-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Ingeniería Mecatrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Correspondence: (M.M.A.); (G.T.-d.S.)
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8
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Alvarez FJ, Perez-Cardenas M, Gudiño M, Tellkamp MP. Tips for a reduction of false positives in manual RT-PCR diagnostics of SARS-CoV-2. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.03.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
RT-PCR is the standard gold technique for testing the presence of RNA of the coronavirus causing Severe Acute Respiratory Syndrome (SARS-CoV-2) due to its high specificity and sensitivity. Despite its general use and reliability, no lab in the world is immune to the generation of false positives. These errors cause a loss of confidence in the technique's power and damage the image of laboratories. More importantly, they can take a toll on tested individuals and have economic, psychological, and health-associated effects. Most false positives are caused during a manual operation inside the laboratory. However, not much has been published about the errors associated with particular laboratory techniques used to detect the virus since the beginning of the actual pandemic. This work precisely reflects on events that occur during manual RT-PCR diagnostics in a COVID-19 laboratory, providing tips for reducing false-positive results.
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Affiliation(s)
- Francisco J. Alvarez
- Yachay Tech University, School of Biological Sciences and Engineering, Hda. San José s/n y Proyecto Yachay, 100119, Urcuquí, Ecuador
| | - Mariela Perez-Cardenas
- Yachay Tech University, School of Biological Sciences and Engineering, Hda. San José s/n y Proyecto Yachay, 100119, Urcuquí, Ecuador
| | - Marco Gudiño
- Yachay Tech University, School of Biological Sciences and Engineering, Hda. San José s/n y Proyecto Yachay, 100119, Urcuquí, Ecuador
| | - Markus P. Tellkamp
- Yachay Tech University, School of Biological Sciences and Engineering, Hda. San José s/n y Proyecto Yachay, 100119, Urcuquí, Ecuador
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9
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Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA. Nat Protoc 2020; 15:2279-2300. [PMID: 32612278 DOI: 10.1038/s41596-020-0338-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/17/2020] [Indexed: 01/20/2023]
Abstract
It has been shown that highly fragmented DNA is most efficiently converted into DNA libraries for sequencing if both strands of the DNA fragments are processed independently. We present an updated protocol for library preparation from single-stranded DNA, which is based on the splinted ligation of an adapter oligonucleotide to the 3' ends of single DNA strands, the synthesis of a complementary strand using a DNA polymerase and the addition of a 5' adapter via blunt-end ligation. The efficiency of library preparation is determined individually for each sample using a spike-in oligonucleotide. The whole workflow, including library preparation, quantification and amplification, requires two work days for up to 16 libraries. Alternatively, we provide documentation and electronic protocols enabling automated library preparation of 96 samples in parallel on a Bravo NGS Workstation (Agilent Technologies). After library preparation, molecules with uninformative short inserts (shorter than ~30-35 base pairs) can be removed by polyacrylamide gel electrophoresis if desired.
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10
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Hoffmann A, Fingerle V, Noll M. Analysis of Tick Surface Decontamination Methods. Microorganisms 2020; 8:microorganisms8070987. [PMID: 32630152 PMCID: PMC7409031 DOI: 10.3390/microorganisms8070987] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 11/23/2022] Open
Abstract
Various microbial pathogens have been found in ticks such as Ixodes ricinus. However, most studies assessed tick microbiomes without prior decontamination of the tick surface, which may alter the results and mislead conclusions regarding the composition of the tick-borne microbiome. The aim of this study was to test four different decontamination methods, namely (i.) 70% ethanol, (ii.) DNA Away, (iii.) 5% sodium hypochlorite and (iv.) Reactive Skin Decontamination Lotion (RSDL), which have been previously reported for tick surface and animal or human skin decontamination. To test the efficiency of decontamination, we contaminated each tick with a defined mixture of Escherichia coli, Micrococcus luteus, Pseudomonas fluorescens, dog saliva and human sweat. No contamination was used as a negative control, and for a positive control, a no decontamination strategy was carried out. After nucleic acid extraction, the recovery rate of contaminants was determined for RNA and DNA samples by qPCR and tick-borne microbiome analyses by bacterial 16S rRNA and 16S rRNA gene amplicon sequencing. Ticks treated with 5% sodium hypochlorite revealed the lowest number of contaminants followed by DNA Away, RSDL and 70% ethanol. Moreover, tick microbiomes after 5% sodium hypochlorite decontamination clustered with negative controls. Therefore, the efficiency of decontamination was optimal with 5% sodium hypochlorite and is recommended for upcoming studies to address the unbiased detection of tick-borne pathogens.
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Affiliation(s)
- Angeline Hoffmann
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany;
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority (LGL), National Reference Center for Borrelia, 85764 Oberschleißheim, Germany;
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Sciences, Coburg University of Applied Sciences and Arts, 96450 Coburg, Germany;
- Correspondence: ; Tel.: +49-9561-317-645
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11
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Sun X, Kosman E, Sharon O, Ezrati S, Sharon A. Significant host- and environment-dependent differentiation among highly sporadic fungal endophyte communities in cereal crops-related wild grasses. Environ Microbiol 2020; 22:3357-3374. [PMID: 32483901 DOI: 10.1111/1462-2920.15107] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/19/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022]
Abstract
Endophytic fungi compose a significant part of plant microbiomes. However, while a small number of fungal taxa have proven beneficial impact, the vast majority of fungal endophytes remain uncharacterized, and the drivers of fungal endophyte community (FEC) assembly are not well understood. Here, we analysed FECs in three cereal crops-related wild grasses - Avena sterilis, Hordeum spontaneum and Aegilops peregrina - that grow in mixed populations in natural habitats. Taxa in Ascomycota class Dothideomycetes, particularly the genera Alternaria and Cladosporium, were the most abundant and prevalent across all populations, but there was also high incidence of basidiomyceteous yeasts of the class Tremellomycetes. The fungal community was shaped to large extent by stochastic processes, as indicated by high level of variation even between individuals from local populations of the same plant species, and confirmed by the neutral community model and Raup-Crick index. Nevertheless, we still found strong determinism in FEC assembly with both incidence and abundance data sets. Substantial differences in community composition across host species and locations were revealed. Our research demonstrated that assembly of FECs is affected by stochastic as well as deterministic processes and suggests strong effects of environment heterogeneity and plant species on community composition. In addition, a small number of taxa had high incidence and abundance in all of the 15 populations. These taxa represent an important part of the core FEC and might be of general functional importance.
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Affiliation(s)
- Xiang Sun
- Institute of Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Evsey Kosman
- Institute of Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Or Sharon
- Institute of Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Smadar Ezrati
- Institute of Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Amir Sharon
- Institute of Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
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12
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Rojas EC, Sapkota R, Jensen B, Jørgensen HJL, Henriksson T, Jørgensen LN, Nicolaisen M, Collinge DB. Fusarium Head Blight Modifies Fungal Endophytic Communities During Infection of Wheat Spikes. MICROBIAL ECOLOGY 2020; 79:397-408. [PMID: 31448388 PMCID: PMC7033075 DOI: 10.1007/s00248-019-01426-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/13/2019] [Indexed: 05/29/2023]
Abstract
Fusarium head blight (FHB) is a devastating disease of wheat heads. It is caused by several species from the genus Fusarium. Several endophytic fungi also colonize wheat spikes asymptomatically. Pathogenic and commensal fungi share and compete for the same niche and thereby influence plant performance. Understanding the natural dynamics of the fungal community and how the pre-established species react to pathogen attack can provide useful information on the disease biology and the potential use of some of these endophytic organisms in disease control strategies. Fungal community composition was assessed during anthesis as well as during FHB attack in wheat spikes during 2016 and 2017 in two locations. Community metabarcoding revealed that endophyte communities are dominated by basidiomycete yeasts before anthesis and shift towards a more opportunistic ascomycete-rich community during kernel development. These dynamics are interrupted when Fusarium spp. colonize wheat spikes. The Fusarium pathogens appear to exclude other fungi from floral tissues as they are associated with a reduction in community diversity, especially in the kernel which they colonize rapidly. Similarly, the presence of several endophytes was negatively correlated with Fusarium spp. and linked with spikes that stayed healthy despite exposure to the pathogen. These endophytes belonged to the genera Cladosporium, Itersonillia and Holtermanniella. These findings support the hypothesis that some naturally occurring endophytes could outcompete or prevent FHB and represent a source of potential biological control agents in wheat.
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Affiliation(s)
- Edward C Rojas
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
| | - Rumakanta Sapkota
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Birgit Jensen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Hans J L Jørgensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | | | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
| | - David B Collinge
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences & Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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13
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Effect of sodium hypochlorite decontamination on the DNA recovery from human teeth. Int J Legal Med 2019; 134:93-99. [PMID: 31691839 DOI: 10.1007/s00414-019-02174-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/07/2019] [Indexed: 10/25/2022]
Abstract
Genetic identification of skeletal human remains is often realized by short tandem repeat (STR) genotyping of nuclear DNA. Dental DNA is preferred to DNA from bone for the better protection of the endogenous DNA. Especially if whole tooth grinding is intended to access the DNA, contaminations with exogenous DNA have to be avoided. The immersion of the tooth in sodium hypochlorite (NaOCl, known as bleach) is one common procedure to clean the outer surface from extraneous DNA and PCR inhibitors. To investigate the impact of bleaching on endogenous DNA and the decontamination success, 71 recently extracted teeth were differently treated with sodium hypochlorite (2.5 or 5.0% NaOCl for 30 or 60 s, 5.0% NaOCl for 10 min, and control group) in the beginning of the extraction process, whereas equally handled afterwards. Quantitative and qualitative evaluation of the extracted DNA was performed. There was a great variation for the DNA concentration of the extracts even within a group of the same NaOCl treatment. Complete DNA profiles from single persons with alleles for the 16 ESS (European Standard Set) STR loci were obtained for all regarded teeth. A statistically significant difference between the DNA yields of the treatment groups was not determined. Moreover, a negative effect of NaOCl (2.5% and 5.0%) on the DNA recovery could not be observed. Significant larger amounts of DNA were extracted from anterior teeth in contrast to posterior teeth.
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14
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van Oorschot RA, Szkuta B, Meakin GE, Kokshoorn B, Goray M. DNA transfer in forensic science: A review. Forensic Sci Int Genet 2019; 38:140-166. [DOI: 10.1016/j.fsigen.2018.10.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
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15
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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16
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Noël S, Lagacé K, Raymond S, Granger D, Loyer M, Bourgoin S, Jolicoeur C, Séguin D. Repeatedly washed semen stains: Optimal screening and sampling strategies for DNA analysis. Forensic Sci Int Genet 2018; 38:9-14. [PMID: 30312967 DOI: 10.1016/j.fsigen.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 01/27/2023]
Abstract
In many sexual assault cases, bedding and clothing are essential pieces of evidence that are screened for semen stains to gather DNA from the assailant. In some cases, these items have been washed before being seized and sent to the forensic lab. However, few data exist on the optimal methods for detecting and sampling semen stains on washed fabrics. In this paper, we used semen stains washed up to six times to evaluate the efficiency of commonly used screening methods for the detection of semen: alternate light source (ALS), acid phosphatase (AP), prostate specific antigen (PSA) and microscopy (sperm Hy-Liter™, SHL). We also assessed different washing conditions (detergents, washing machines, addition of bleach) and sampling methods (cutting and swabbing). The results show that some semen stain detection strategies, such as ALS, PSA, and SHL, are effective even when the item was washed multiple times. We also show that a complete genetic profile could be obtained from semen stains washed six times. Based on these findings, we present different strategies for the detection and sampling of semen stains depending on the circumstances of the case.
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Affiliation(s)
- Sarah Noël
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Karine Lagacé
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Sylvain Raymond
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Dominic Granger
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Magali Loyer
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Sarah Bourgoin
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Christine Jolicoeur
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
| | - Diane Séguin
- Laboratoire de sciences judiciaires et de médecine légale, 1701 Parthenais, Montréal, Québec, H2K 3S7, Canada.
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17
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Morono Y, Hoshino T, Terada T, Suzuki T, Sato T, Yuasa H, Kubota Y, Inagaki F. Assessment of Capacity to Capture DNA Aerosols by Clean Filters for Molecular Biology Experiments. Microbes Environ 2018; 33:222-226. [PMID: 29910221 PMCID: PMC6031387 DOI: 10.1264/jsme2.me18012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Experimental contamination by exogenous DNA is a major issue in molecular biological studies for data quality and its management. We herein assessed DNA aerosols for the risk of contamination and tested the capacity of clean air filters to trap and remove DNA aerosols. DNA aerosols were generated by atomizing a DNA solution and introduced into a laminar flow clean air unit. Capture and detection performed upstream and downstream of the clean air unit showed that a significant fraction (>99.96%) of introduced molecules was trapped and removed by the filter. Although DNA aerosols appear to be an avoidable source of exogenous contamination, a clearer understanding and careful experimental procedures are needed in order to perform contamination-free, high-quality molecular biology experiments.
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Affiliation(s)
- Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC
| | - Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC
| | | | | | | | | | | | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Geobiotechnology Group, Research and Development Center for Submarine Resources, JAMSTEC.,Research and Development Center for Ocean Drilling Science, JAMSTEC
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