1
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Choe JA, Brinkman HM, Lee JS, Murphy WL. Optimized biomimetic minerals maintain activity of mRNA complexes after long term storage. Acta Biomater 2024; 174:428-436. [PMID: 38061679 DOI: 10.1016/j.actbio.2023.11.044] [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: 10/09/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
mRNA therapeutics can be readily designed, manufactured, and brought to scale, as demonstrated by widespread global vaccination against COVID-19. However, mRNA therapies require cold chain shipment and storage from manufacturing to administration, which may limit them to affluent communities. This problem could be addressed by mimicking the known ability of mineralized fossils to durably stabilize nucleic acids under extreme conditions. We synthesized and screened 40 calcium-phosphate minerals for their ability to store and maintain the activity of lyophilized mRNA complexes. The optimal mineral formulation incorporated mRNA complexes with high efficiency (77 %), and increased mRNA transfection efficiency by 5.6-fold. Lyophilized mRNA complexes stored with the optimized mineral formulation for 6 months at 25 °C were 3.2-fold more active than those stored with state-of-the-art excipients, but without a mineral. mRNA complexes stored with minerals at room temperature did not decline in transfection efficacy from 3 days to 6 months of storage, indicating that minerals can durably maintain activity of therapeutic mRNA complexes without cold chain storage. STATEMENT OF SIGNIFICANCE: Therapeutic mRNA, such as mRNA COVID-19 vaccines, require extensive cold chain storage that limits their general application. This work screened a library of minerals to maintain the activity of mRNA complexes with freeze-drying. The optimized mineral was able to maintain mRNA activity up to 6 months of storage at room temperature outperforming current methods of freeze-drying therapeutic mRNA complexes.
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Affiliation(s)
- Joshua A Choe
- Department of Biomedical Engineering, Madison, WI, USA; Department of Orthopedics and Rehabilitation, Madison, WI, USA; Medical Scientist Training Program, Madison, WI, USA
| | - Hannah M Brinkman
- Department of Orthopedics and Rehabilitation, Madison, WI, USA; Comparative Biomedical Sciences Program, University of Wisconsin - Madison, Madison, WI, USA
| | - Jae Sung Lee
- Department of Orthopedics and Rehabilitation, Madison, WI, USA
| | - William L Murphy
- Department of Biomedical Engineering, Madison, WI, USA; Department of Orthopedics and Rehabilitation, Madison, WI, USA.
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2
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Wegner CE, Stahl R, Velsko I, Hübner A, Fagernäs Z, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. A glimpse of the paleome in endolithic microbial communities. MICROBIOME 2023; 11:210. [PMID: 37749660 PMCID: PMC10518947 DOI: 10.1186/s40168-023-01647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. RESULTS By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. CONCLUSIONS Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.
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Affiliation(s)
- Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Irina Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Alex Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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3
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Rahmat RA, Humphries MA, Saedon NA, Self PG, Linacre AMT. Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth. Int J Legal Med 2023; 137:1353-1360. [PMID: 37306739 DOI: 10.1007/s00414-023-03017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Melissa A Humphries
- School and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, 5006, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, the University of Adelaide, Adelaide, South Australia, Australia
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor, 46661, Malaysia
| | - Peter G Self
- CSIRO, Land and Water, Locked Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, 5042, Australia
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4
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Essel E, Zavala EI, Schulz-Kornas E, Kozlikin MB, Fewlass H, Vernot B, Shunkov MV, Derevianko AP, Douka K, Barnes I, Soulier MC, Schmidt A, Szymanski M, Tsanova T, Sirakov N, Endarova E, McPherron SP, Hublin JJ, Kelso J, Pääbo S, Hajdinjak M, Soressi M, Meyer M. Ancient human DNA recovered from a Palaeolithic pendant. Nature 2023:10.1038/s41586-023-06035-2. [PMID: 37138083 DOI: 10.1038/s41586-023-06035-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.
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Affiliation(s)
- Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ellen Schulz-Kornas
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS) Research Network, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, London, UK
| | - Marie-Cécile Soulier
- Maison de la Recherche, Université de Toulouse-Jean Jaurès, CNRS UMR 5608 TRACES, Toulouse, France
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Merlin Szymanski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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5
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The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone. PLoS One 2022; 17:e0269348. [PMID: 36282813 PMCID: PMC9595551 DOI: 10.1371/journal.pone.0269348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/22/2022] [Indexed: 11/19/2022] Open
Abstract
The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.
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6
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Andreeva TV, Malyarchuk AB, Soshkina AD, Dudko NA, Plotnikova MY, Rogaev EI. Methodologies for Ancient DNA Extraction from Bones for Genomic Analysis: Approaches and Guidelines. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422090034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Chen X, Kong Y, Zhang S, Zhao J, Li S, Yao M. Comparative Evaluation of Common Materials as Passive Samplers of Environmental DNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10798-10807. [PMID: 35856738 DOI: 10.1021/acs.est.2c02506] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) technology has revolutionized biomonitoring in recent years; however, eDNA collection from aquatic environments generally relies on the time-consuming and equipment-dependent process of water filtration. Passive eDNA sampling deploys sorbent materials to capture eDNA from water, circumventing many problems associated with active filtration; yet, very few candidate materials have been systematically evaluated for this purpose. Here, we evaluated the ability of 12 different types of common loose sorbents and filter membranes to capture eDNA in laboratory and field experiments compared with conventional water filtration. Glass fiber filters (GF) outperformed all other materials in laboratory experiments with respect to their quantitative capacity to recover amphibian eDNA, with the eDNA yield increasing linearly with submersion time up to 72 h. Furthermore, GF rapidly (within 0.5 h) captured the eDNA of up to 71% of the total fish species in a lake, in addition to detecting the entire fish community by 8 h, as assessed by metabarcoding analysis. Our results demonstrate that GF could passively capture aqueous eDNA with a similar or greater efficiency than conventional methods, thus paving the way for convenient, effective, and eco-friendly eDNA sampling in aquatic environments.
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Affiliation(s)
- Xiaoyu Chen
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yueqiao Kong
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shan Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jindong Zhao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Sheng Li
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Meng Yao
- School of Life Sciences, Peking University, Beijing 100871, China
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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8
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Nardello LCL, Pinheiro ET, Gavini G, Prado LC, Romero RX, Gomes BPFA, Skelton-Macedo MC. Nature and Prevalence of Bacterial Taxa Persisting after Root Canal Chemomechanical Preparation in Permanent Teeth: A Systematic Review and Meta-analysis. J Endod 2022; 48:572-596. [PMID: 35114271 DOI: 10.1016/j.joen.2022.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 01/15/2022] [Accepted: 01/21/2022] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Culture-independent molecular studies have shown a broad spectrum of bacterial taxa that persist after chemomechanical procedures (CMP). Therefore, this study systematically reviewed these reports to explore the prevalence of bacteria in post-instrumentation samples of root canals from permanent teeth, especially of as-yet-uncultivated/difficult-to-culture bacteria. METHODS Electronic databases were searched from 2007 to January 2021. Clinical studies using culture-independent molecular methods to identify species-level taxa before and after CMP were included. Studies were critically appraised using the Joanna Briggs Institute Prevalence Critical Appraisal Checklist and the funnel plot analysis. The meta-analysis was performed on the prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa using RStudio. RESULTS A total of 3781 titles were screened, but only 20 studies were included. The most frequent species in post-instrumentation samples were Streptococcus spp., Leptotrichia buccalis, Fusobacterium nucleatum, and Capnocytophaga ochracea. The detection frequency of some species increased after CMP, including mainly Firmicutes members such as streptococci, Enterococcus faecium, Selenomonas noxia, and Solobacterium moorei. The prevalence (confidence interval) of difficult-to-culture species was as follows: Dialister invisus, 17% (7%-29%); Solobacterium moorei, 14% (8%-23%); Bacteroidaceae [G-1] bacterium HMT 272, 13% (5%-23%); and Filifactor alocis, 11% (3%-23%). CONCLUSIONS The prevalence of as-yet-uncultivated/difficult-to-culture bacterial taxa in post-instrumentation samples was low. The persistent species belonged mainly to the phylum Firmicutes, and streptococci were the major members. Future larger clinical studies on the composition of the whole bacterial community that persist after CMP are still necessary for a better understanding of bacterial interactions and their clinical significance in the treatment outcome.
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Affiliation(s)
- Laura C L Nardello
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Ericka T Pinheiro
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil.
| | - Giulio Gavini
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Laís C Prado
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Roberto X Romero
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Brenda P F A Gomes
- Department of Restorative Dentistry, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil
| | - Mary C Skelton-Macedo
- Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
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9
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Verdier H, Konecny-Dupre L, Marquette C, Reveron H, Tadier S, Grémillard L, Barthès A, Datry T, Bouchez A, Lefébure T. Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers. Mol Ecol Resour 2022; 22:2158-2170. [PMID: 35218316 DOI: 10.1111/1755-0998.13604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as water filtration and DNA precipitation are time consuming, require difficult-to-handle equipment and partially integrate eDNA signals. To overcome these limitations, we created the first proof of concept of a passive, 3D-printed and easy-to-use eDNA sampler. We designed the samplers from hydroxyapatite (HAp samplers), a natural mineral with a high DNA adsorption capacity. The porous structure and shape of the samplers were designed to optimise DNA adsorption and facilitate their handling in the laboratory and in the field. Here we show that HAp samplers can efficiently collect genomic DNA in controlled set-ups, but can also collect animal eDNA under controlled and natural conditions with yields similar to conventional methods. However, we also observed large variations in the amount of DNA collected even under controlled conditions. A better understanding of the DNA-hydroxyapatite interactions on the surface of the samplers is now necessary to optimise the eDNA adsorption and to allow the development of a reliable, easy-to-use and reusable eDNA sampling tool.
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Affiliation(s)
- Héloïse Verdier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France.,Eurofins Hydrobiologie France, Rue Lucien Cuenot, 54521, Maxéville, France.,INRAE, UR-Riverly, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, VILLEURBANNE Cedex, France
| | - Lara Konecny-Dupre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Christophe Marquette
- 3d.FAB, Univ Lyon, Université Lyon1, CNRS, INSA, CPE-Lyon, ICBMS, UMR 5246, 43, Bd du 11 novembre 1918, 69622, Villeurbanne cedex, France
| | - Helen Reveron
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Solène Tadier
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Laurent Grémillard
- Univ Lyon, INSA Lyon, UCBL, CNRS, MATEIS UMR 5510, 69621, Villeurbanne, France
| | - Amélie Barthès
- Eurofins Hydrobiologie France, Rue Lucien Cuenot, 54521, Maxéville, France
| | - Thibault Datry
- INRAE, UR-Riverly, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, VILLEURBANNE Cedex, France
| | - Agnès Bouchez
- INRAE, USMB, UMR CARRTEL, 75bis av. de Corzent, 742000, Thonon les Bains, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
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10
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Liu F, Chen B, Chen W, Chen S, Ma D, Xie M. Preparation of FA-targeted magnetic nanocomposites co-loading TFPI-2 plasmid and cis-platinum and its targeted therapy effects on nasopharyngeal carcinoma. Int J Med Sci 2021; 18:2355-2365. [PMID: 33967612 PMCID: PMC8100641 DOI: 10.7150/ijms.52643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/16/2021] [Indexed: 11/05/2022] Open
Abstract
The majority of patients diagnosed with nasopharyngeal carcinoma (NPC) present with advanced-stage disease. The main treatment for these patients is concurrent chemoradiotherapy, which has various side effects. To improve the therapeutic effects and reduce the side effects of NPC chemoradiotherapy, we constructed a multifunctional folic acid (FA)-targeted magnetic nanocomposite codelivering tissue factor pathway inhibitor-2 (TFPI-2) and cisplatin (CDDP). This novel nanocomposite (FA-MNP/CDDP/TFPI-2) was obtained by amidation and electrostatic adsorption between FA-methoxypolyethylene glycol-polyethyleneimine (FA-MPEG-PEI) containing the TFPI-2 plasmid and magnetic nanoparticles modified by aldehyde sodium alginate loaded with CDDP. Transmission electron microscopy (TEM) images showed that the size of the individual magnetite particle core was approximately 11.5 nm. The structure and composition of the nanocomposites were identified and examined by 1H nuclear magnetic resonance (NMR) spectroscopy and ultraviolet (UV) spectrophotometry. The fluorescence analysis, Prussian blue iron staining, magnetic resonance (MR) imaging and whole-body fluorescence imaging results demonstrated that FA-MNP/CDDP/TFPI-2 showed high gene transfection efficiency and could target tumor cells via folate receptor (FR)-mediated delivery. The codelivery analysis showed that the obtained FA-MNP/CDDP/TFPI-2 composite could cause significantly more apoptosis than treatment with CDDP or TFPI-2 alone. The results showed that the FA-MNP/CDDP/TFPI-2 composites were successfully synthesized and indicated to be a specific molecular target for the FR with significant inhibitory effects on the growth of HNE-1 cells.
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Affiliation(s)
- Fang Liu
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Bojie Chen
- Department of Joint Surgery, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, 341000, China
| | - Weifeng Chen
- Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Shuaijun Chen
- Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Dong Ma
- Key Laboratory of Biomaterials of Guangdong Higher Education Institutes, Department of Biomedical Engineering,Jinan University, Guangzhou, 510632, China
| | - Minqiang Xie
- Department of Otolaryngology, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
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11
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Komuro H, Yamazoe M, Nozaki K, Nagai A, Sasano T. Cardiomyocyte uptake mechanism of a hydroxyapatite nanoparticle mediated gene delivery system. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:1685-1692. [PMID: 33194517 PMCID: PMC7653333 DOI: 10.3762/bjnano.11.150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Gene therapy has been explored as a future alternative for treating heart disease. Among several gene delivery systems aimed at penetrating specific target cells, we focused on safe and non-viral gene delivery materials with a high transfection efficiency. Although various techniques have been developed, the mechanisms underlying the cellular uptake of gene delivery materials have not yet been sufficiently studied in cardiomyocytes. The aim of this study was to determine how hydroxyapatite (HAp) nanoparticles contribute to the delivery of plasmid DNA (pDNA) into cardiomyocytes. We fabricated HAp nanoparticles using the water-in-oil (W/O) emulsion method and used these nanoparticles as the delivery vector for transfecting cardiomyocyte-derived HL-1 cells. HAp exhibited particles on the nanoscale and with a low cytotoxicity in HL-1 cells. The transfection assay performed with several endocytosis inhibitors suggested that the HAp/pDNA complexes were internalized by HL-1 cells through macropinocytosis. Furthermore, this HL-1 cell uptake was generated in response to HAp stimulation. Thus, HAp is a positive regulator of macropinocytosis in HL-1 cells and a good system for gene delivery in cardiomyocytes.
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Affiliation(s)
- Hiroaki Komuro
- Department of Cardiovascular Physiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
| | - Masahiro Yamazoe
- Department of Bio-informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
| | - Kosuke Nozaki
- Department of Restorative Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
| | - Akiko Nagai
- Department of Anatomy, School of Dentistry, Aichi Gakuin University, Chikusa, Nagoya 464-8650, Japan
| | - Tetsuo Sasano
- Department of Cardiovascular Physiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
- Department of Cardiovascular Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
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12
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Nardello LC, Vilela BG, Fernandes FS, Bruno FP, Carvalho AP, Cazares RX, Nascimento LC, Honório HM, Ando ES, Mayer MP, Gavini G, Pinheiro ET. Analysis of Active Bacteria Persisting after Chemomechanical Procedures: An RNA- and DNA-based Molecular Study. J Endod 2020; 46:1570-1576. [DOI: 10.1016/j.joen.2020.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
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13
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Clinical and Molecular Microbiological Evaluation of Regenerative Endodontic Procedures in Immature Permanent Teeth. J Endod 2020; 46:1448-1454. [DOI: 10.1016/j.joen.2020.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/17/2020] [Accepted: 07/04/2020] [Indexed: 11/17/2022]
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14
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Peris D, Janssen K, Barthel HJ, Bierbaum G, Delclòs X, Peñalver E, Solórzano-Kraemer MM, Jordal BH, Rust J. DNA from resin-embedded organisms: Past, present and future. PLoS One 2020; 15:e0239521. [PMID: 32986737 PMCID: PMC7521698 DOI: 10.1371/journal.pone.0239521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
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Affiliation(s)
- David Peris
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - H. Jonas Barthel
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics and Biodiversity Research Institute (IRBio), Faculty of Earth Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Peñalver
- Geological and Mining Institute of Spain (Geominero Museum), Valencia, Spain
| | - Mónica M. Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Bjarte H. Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Jes Rust
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
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15
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Emmons AL, Mundorff AZ, Keenan SW, Davoren J, Andronowski J, Carter DO, DeBruyn JM. Characterizing the postmortem human bone microbiome from surface-decomposed remains. PLoS One 2020; 15:e0218636. [PMID: 32639969 PMCID: PMC7343130 DOI: 10.1371/journal.pone.0218636] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 05/19/2020] [Indexed: 01/19/2023] Open
Abstract
Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.
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Affiliation(s)
- Alexandra L. Emmons
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Amy Z. Mundorff
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sarah W. Keenan
- Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, United States of America
| | - Jonathan Davoren
- Bode Cellmark Forensics, Lorton, Virginia, United States of America
| | - Janna Andronowski
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - David O. Carter
- Division of Natural Sciences and Mathematics, Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Next-Generation Sequencing to Assess Potentially Active Bacteria in Endodontic Infections. J Endod 2020; 46:1105-1112. [PMID: 32497654 DOI: 10.1016/j.joen.2020.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Because active bacteria present a higher abundance of ribosomal RNA (rRNA) than DNA (rRNA gene), the rRNA/DNA ratio of next-generation sequencing (NGS) data was measured to search for active bacteria in endodontic infections. METHODS Paired complementary DNA and DNA samples from 5 root canals of teeth with apical periodontitis were subjected to polymerase chain reaction with bar-coded primers amplifying the 16S rRNA gene hypervariable regions V4-V5. High-throughput sequencing was performed using MiSeq (Illumina, San Deigo, CA), and data were analyzed using Quantitative Insights Into Microbial Ecology and Human Oral Microbiome Database. Statistical analysis was performed for relative abundance of bacteria in the DNA- and rRNA-based NGS data using the Mann-Whitney test, whereas differences in the diversity and richness indexes were assessed using a nonparametric 2-sample t test (P < .05). For bacterial taxa detected in both approaches, the rRNA/DNA ratios were calculated by dividing the average abundance of individual species in the respective analysis. RESULTS Although no significant difference was found in the indexes of bacterial richness and diversity, the relative abundance of bacterial members varied in both analyses. Comparing rRNA with DNA data, there was a significant decrease in the relative abundance of Firmicutes (P < .05). The bacterial taxa Bacteroidales [G-2] bacterium HMT 274, Porphyromonas endodontalis, Tannerella forsythia, Alloprevotella tannerae, Prevotella intermedia, Pseudoramibacter alactolyticus, Olsenella sp. HMT 809, Olsenella sp. HMT 939, Olsenella uli, and Fusobacterium nucleatum subsp. animalis were both dominant (DNA ≥ 1%) and active (rRNA/DNA ≥ 1). CONCLUSIONS The integrated DNA- and rRNA-based NGS strategy was particularly important to disclose the activity of as-yet-uncultivated or difficult-to-culture bacteria in endodontic infections.
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17
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Mckinnon M, Henneberg M, Simpson E, Higgins D. A comparison of crystal structure in fresh, burned and archaic bone - Implications for forensic sampling. Forensic Sci Int 2020; 313:110328. [PMID: 32502739 DOI: 10.1016/j.forsciint.2020.110328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
Abstract
Standard protocols for extracting DNA from bone are variable and are largely dependent on the state of preservation. In archaic samples, endogenous DNA is believed to be tightly bound to crystal aggregates in the Hydroxyapatite (HAp) matrix requiring prolonged demineralisation to allow its release. By comparison, fresh bone contains abundant cellular material, discounting the need for demineralisation. Recommendations for incinerated bone, specifically how viable sampling sites should be selected and the ideal techniques for DNA recovery are unclear, and the protocol used is often selected based on macroscopic sample appearance. It has been postulated that like archaic bone, burned bone is 'highly degraded' and therefore aDNA techniques may present better results for DNA recovery than using fresh protocols. However, little research has been undertaken comparing the crystal structure of burnt, fresh and archaic bone. This study uses a combination of XRPD and SEM analysis to compare the crystalline profile and microscopic appearance of burned bone subjected to temperatures ranging from 100-1000°C, with archaic and fresh samples. Although macroscopically visually different, fresh samples and samples heated up to 500°C showed no microscopic differences or significant changes in crystallinity. By comparison, samples heated above 500°C became significantly more crystalline, with HAp crystal size increasing dramatically. Archaic samples were different again, more closely resembling the amorphous fresh samples than the highly crystalline incinerated samples. These results suggests that, potentially, samples burned at 500°C or lower can be treated as fresh samples, whilst samples exposed to higher temperatures may require adapted protocols. Whether or not these highly burned samples require demineralisation needs to be investigated.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia.
| | - Maciej Henneberg
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Frome Road, Adelaide, SA 5000, Australia
| | | | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, the University of Adelaide, Adelaide, Australia
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18
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Catalano F, Ivanchenko P, Rebba E, Sakhno Y, Alberto G, Dovbeshko G, Martra G. Towards the control of the biological identity of nanobiomaterials: Impact of the structure of 011¯0 surface terminations of nanohydroxyapatite on the conformation of adsorbed proteins. Colloids Surf B Biointerfaces 2020; 188:110780. [PMID: 32004906 DOI: 10.1016/j.colsurfb.2020.110780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/18/2019] [Accepted: 01/04/2020] [Indexed: 11/24/2022]
Abstract
High-resolution transmission electron microscopy, ζ-potential and in-situ IR spectroscopy of adsorbed CO were combined for elucidating the ratio between {011¯0}_ Ca-rich: {011¯0}_ P-rich terminations of {011¯0} facets, i.e. the surfaces with the highest morphological importance, in two nanohydroxyapatite samples. Bovine serum albumin was found to form at least a monolayer on the surface left accessible to protein molecules by the agglomeration of nanoparticles when suspended in the buffered incubation medium. Noticeably, the conformation of adsorbed proteins appeared sensitive to the ratio between the two types of {011¯0} terminations, also resulting in a difference in the surface exposed toward the exterior by the adsorbed protein layer(s).
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Affiliation(s)
- Federico Catalano
- Department of Chemistry and Interdepartmental Nanostructured Interfaces and Surfaces (NIS) Centre, University of Torino, via P. Giuria 7, Torino, 10125, Italy
| | - Pavlo Ivanchenko
- Department of Chemistry and Interdepartmental Nanostructured Interfaces and Surfaces (NIS) Centre, University of Torino, via P. Giuria 7, Torino, 10125, Italy.
| | - Erica Rebba
- Department of Chemistry and Interdepartmental Nanostructured Interfaces and Surfaces (NIS) Centre, University of Torino, via P. Giuria 7, Torino, 10125, Italy
| | - Yuriy Sakhno
- Department of Chemistry and Interdepartmental Nanostructured Interfaces and Surfaces (NIS) Centre, University of Torino, via P. Giuria 7, Torino, 10125, Italy
| | - Gabriele Alberto
- Department of Chemistry and Interdepartmental Nanostructured Interfaces and Surfaces (NIS) Centre, University of Torino, via P. Giuria 7, Torino, 10125, Italy
| | - Galyna Dovbeshko
- Institute of Physics of the National Academy of Science of Ukraine, 46 Nauky Ave, Kyiv 03028, Ukraine
| | - Gianmario Martra
- Department of Chemistry and Interdepartmental Nanostructured Interfaces and Surfaces (NIS) Centre, University of Torino, via P. Giuria 7, Torino, 10125, Italy
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Effects of Contemporary Irrigant Activation Schemes and Subsequent Placement of an Interim Dressing on Bacterial Presence and Activity in Root Canals Associated with Asymptomatic Apical Periodontitis. J Clin Med 2020; 9:jcm9030854. [PMID: 32245051 PMCID: PMC7141523 DOI: 10.3390/jcm9030854] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 01/09/2023] Open
Abstract
New tools for activating endodontic irrigants have evolved, yet their impact on root canal disinfection, in comparison to the passive placing of an inter-visit medication, have not yet been fully elucidated. The use of DNA- and rRNA-based methods may cast some new light on this issue, as they allow a comparison to be made between microbial presence and activity. Therefore, the aim of this single-arm intervention trial is to evaluate the antibacterial effect of endodontic procedures using both molecular methods. Root canal samples were obtained from 20 patients with asymptomatic apical periodontitis after each treatment step: access cavity, chemo-mechanical preparation, adjunctive procedures (XP-endo Finisher file and passive ultrasonic irrigation), calcium hydroxide medication, and 2nd-visit root canal preparation. DNA and cDNA from the samples were subjected to quantitative polymerase chain reaction with universal primers for the bacterial 16S rRNA gene. Chemo-mechanical preparation promoted a drastic reduction in bacterial levels and activity, whereas the adjunctive procedures did not make a significant contribution to further disinfection. At the 2nd visit, bacteria were active after the use of calcium hydroxide medication; however, they were significantly reduced after a 2nd-visit preparation. Consequently, the lowest bacterial levels were found at the end of the treatment. This clinical trial, which used an rRNA and rDNA combined approach, confirmed previous studies showing that root canal preparation represents the main strategy for root canal disinfection.
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20
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Son J, Kim J, Lee K, Hwang J, Choi Y, Seo Y, Jeon H, Kang HC, Woo HM, Kang BJ, Choi J. DNA aptamer immobilized hydroxyapatite for enhancing angiogenesis and bone regeneration. Acta Biomater 2019; 99:469-478. [PMID: 31494292 DOI: 10.1016/j.actbio.2019.08.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 12/15/2022]
Abstract
In this study, we developed aptamer-conjugated hydroxyapatite (Apt-HA) that promotes bone regeneration and angiogenesis. The 3R02 bivalent aptamer specific to vascular endothelial growth factor (VEGF) was grafted to the hydroxyapatite (HA) surface. Apt-HA was tested for its VEGF protein capture ability to determine the optimal aptamer concentration immobilized on the HA. Apt-HA showed higher VEGF protein capture ability, and faster growth of human umbilical vein endothelial cell (HUVEC) compared to a neat HA with no cytotoxic effects on human osteoblasts. To examine in vivo angiogenesis and bone regeneration, Apt-HA and HA were bilaterally implanted into rabbit tibial metaphyseal defects and analyzed after eight weeks using micro-CT, histology, and histomorphometry. Apt-HA showed significantly increased the volume of new bones, the percentage of bone, and the density of bone mineral in cortical bone. Apt-HA also exhibited the enhanced bone formation at the cortical region in a histomorphometric analysis. Finally, Apt-HA showed significantly increased blood vessel number compared to a neat HA. In summary, the engineered Apt-HA has potential as a bone graft material that may simultaneously promote bone regeneration and angiogenesis. STATEMENT OF SIGNIFICANCE: This work presents a functional hydroxyapatite bone graft using a DNA-based aptamer which overcomes the limitations of existing bone graft materials, which use bound signaling peptides. DNA aptamer immobilized hydroxyapatite enhances the in vitro proliferation of human umbilical vascular endothelial cells as well as in vivo angiogenesis and bone regeneration. DNA aptamer immobilized hydroxyapatite shows no cytotoxic effect on human osteoblasts.
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21
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Cheang TY, Lei YY, Zhang ZQ, Zhou HY, Ye RY, Lin Y, Wang S. Graphene oxide-hydroxyapatite nanocomposites effectively deliver HSV-TK suicide gene to inhibit human breast cancer growth. J Biomater Appl 2019; 33:216-226. [PMID: 30096997 DOI: 10.1177/0885328218788242] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gene therapy with herpes simplex virus thymidine kinase gene (HSV-TK), which is also known as "suicide" gene therapy, is effective in various tumor models. The lack of a safe and efficient gene delivery system has become a major obstacle to "suicide" gene therapy. In this study, the cytotoxicity and transfection efficiency of graphene oxide-hydroxyapatite (GO-Hap) were analyzed by MTS and flow cytometry, respectively. A series of assays were performed to evaluate the effects of GO-HAp/p-HRE/ERE-Sur-TK combined with ganciclovir treatment on growth of human breast normal and cancer cells. The results showed that GO-HAp nanocomposites effectively transfected cells with minimum toxicity. GO-HAp/p-HRE/ERE-Sur-TK combined with ganciclovir treatment inhibited the proliferation and induced cell apoptosis in cancer cells, while the cytotoxic effects are tolerable in normal breast cells. We conclude that the GO-HAp nanocomposites have significant potential as a gene delivery vector for cancer therapy.
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Affiliation(s)
- Tuck-Yun Cheang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yi-Yan Lei
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhan-Qiang Zhang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hong-Yan Zhou
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Run-Yi Ye
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying Lin
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shenming Wang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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22
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Prado LC, Gavini G, Silveira ADC, Nakamura VC, Mayer MPA, Pinheiro ET. Comparison of rRNA-based reverse transcription PCR and rDNA-based PCR for the detection of streptococci in root canal infections. J Appl Oral Sci 2019; 27:e20180256. [PMID: 31365706 PMCID: PMC6690712 DOI: 10.1590/1678-7757-2018-0256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/26/2019] [Indexed: 11/21/2022] Open
Abstract
Objective The rDNA-based method is unable to distinguish between alive and dead cells. Alternatively, bacterial viability can be assessed by molecular methods based on ribosomal RNA (rRNA). Therefore, this study aimed to detect viable streptococci in root canal samples using rRNA-based reverse transcription polymerase chain reaction (RT-PCR), compared to an rDNA-based PCR assay. Methodology Microbiological root canal samples were obtained from 32 teeth with primary endodontic infections before (S1) and after chemomechanical preparation (S2), and after removal of intracanal medication (S3). RNA and DNA were extracted, and complementary DNA (cDNA) was synthesized from RNA using RT reaction. cDNA and genomic DNA were subjected to PCR with primers complementary to the 16S rRNA sequences of Streptococcus spp. McNemar’s test was used to compare the detection rate of both assays (P<0.05). Results Streptococci were detected in 28.12% (9/32) and 37.5% (12/32) of S1 samples using rRNA- and rDNA-based PCR assays, respectively. In contrast, they were detected in only 6.25% (2/32) of S2 samples using rRNA-based RT-PCR, compared to 15.62% (5/32) using rDNA-based PCR. Finally, in S3 samples, streptococci were not detected by rRNA, whereas rDNA-based PCR still detected the bacteria in 12.5% (4/32) of the samples. The total number of PCR-positive reactions in the rDNA-based PCR was higher than in the rRNA-based assay (P<0.05). Conclusions The rRNA-based RT-PCR showed a lower detection rate of streptococci when compared to the rDNA-based PCR, suggesting that the latter may have detected dead cells of streptococci in root canal samples.
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Affiliation(s)
- Laís Cunha Prado
- Universidade de São Paulo, Faculdade de Odontologia, São Paulo, SP, Brasil
| | - Giulio Gavini
- Universidade de São Paulo, Faculdade de Odontologia, São Paulo, SP, Brasil
| | | | | | - Marcia Pinto Alves Mayer
- Universidade de São Paulo, Faculdade de Odontologia, Instituto de Ciências Biomédicas, São Paulo, SP, Brasil
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23
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Zoss R, Medina Ferrer F, Flood BE, Jones DS, Louw DC, Bailey J. Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system. GEOBIOLOGY 2019; 17:76-90. [PMID: 30369004 DOI: 10.1111/gbi.12318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/20/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.
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Affiliation(s)
- Roman Zoss
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| | | | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| | - Daniel S Jones
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
- BioTechnology Institute, University of Minnesota, St. Paul, Minneapolis
| | - Deon C Louw
- Ministry of Fisheries and Marine Resources, National Marine Information and Research Centre, Swakopmund, Namibia
| | - Jake Bailey
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
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Komuro H, Sasano T, Horiuchi N, Yamashita K, Nagai A. The effect of glucose modification of hydroxyapatite nanoparticles on gene delivery. J Biomed Mater Res A 2018; 107:61-66. [PMID: 30394681 DOI: 10.1002/jbm.a.36523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/05/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022]
Abstract
Surface modification techniques have been employed for the use of biocompatible and bioresorbable hydroxyapatite (HAp) nanoparticles in cell biology and medicine for the delivery of bioactive molecules. We demonstrated the effects of glucose modification of HAp (GlcHAp) on the transfection efficiency in endothelial cells. After preparing homogeneous HAp nanoparticles with a microemulsion technique, the particles with or without glucose modification and plasmid DNA (pDNA) complexes were transfected into endothelial cells. The transfection efficiency of GlcHAp/pDNA was higher than that of HAp/pDNA. To elucidate the mechanism underlying the improvement in the transfection efficiency following glucose modification, the uptake route into the cells and the inhibition of DNA degradation were investigated. GlcHAp/pDNA enhanced the transfection efficiency after interacting with the glucose transporter 1, as observed by the selective inhibitor assay. In addition, GlcHAp/pDNA was more stable than HAp/pDNA in the DNA degradation assay. Our results suggest that the glucose modification could promote the uptake of HAp nanoparticles by cells and protect the internalized DNA; properties essential for non-viral transfection carriers. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 61-66, 2019.
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Affiliation(s)
- Hiroaki Komuro
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo, 101-0062, Japan.,Department of Cardiovascular Physiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Tetsuo Sasano
- Department of Cardiovascular Physiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8519, Japan
| | - Naohiro Horiuchi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo, 101-0062, Japan
| | - Kimihiro Yamashita
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo, 101-0062, Japan
| | - Akiko Nagai
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo, 101-0062, Japan.,School of Dentistry, Aichi Gakuin University, 1-100 Kusumoto, Chikusa, Nagoya, 464-8650, Japan
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Samsuwan J, Somboonchokepisal T, Akaraputtiporn T, Srimuang T, Phuengsukdaeng P, Suwannarat A, Mutirangura A, Kitkumthorn N. A method for extracting DNA from hard tissues for use in forensic identification. Biomed Rep 2018; 9:433-438. [PMID: 30402227 DOI: 10.3892/br.2018.1148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/10/2018] [Indexed: 11/05/2022] Open
Abstract
With deceased and decayed bodies, personal identification is performed using hard tissue DNA, commonly extracted from bone. The quantity and quality of DNA used in the polymerase chain reaction (PCR) amplification step is critical for a successful outcome. Since enamel is the strongest tissue in the human body, it was hypothesized that teeth may preserve DNA better than bones. In the present study, porcine teeth and bone samples were exposed to a variety of environments that imitated personal identification conditions, and DNA extracted from the teeth and bone samples was compared, using a PCR amplification method. The porcine teeth and bones were exposed to 11 different conditions for 5 different time periods to imitate a series of common crime scenes. DNA was extracted by a standard phenol-chloroform method. To test DNA quality, PCR was performed with primers designed to amplify porcine β-actin (ACTB) and mitochondrial DNA (mtDNA) sequences. The results demonstrated that the quality of DNA extracted from teeth was greater than that extracted from bone in the following environments: Buried in sand, soaked in caustic soda and burnt with rubber. By contrast, the quality of DNA extracted from bone was greater than that extracted from teeth when samples were buried in soil or submerged in water. There was no discernable difference in the quality of DNA extracted from bones and teeth in several environments, including being submerged in seawater, soaked in sulfuric acid, left in open air, and stored at 4, -20 and -80°C. Additionally, the results suggested that PCR using mtDNA primers performed better than that using ACTB primers. Finally, it was indicated that components of seawater may inhibit PCR amplification. The preliminary data reported here may provide basic guidelines for selecting the optimum source of DNA in each case.
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Affiliation(s)
- Jarunya Samsuwan
- Sub Division of Forensic Biochemistry, Institute of Forensic Medicine, Police General Hospital, Royal Thai Police, Bangkok 10330, Thailand
| | | | | | | | | | | | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
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Controlled Non-Viral Gene Delivery in Cartilage and Bone Repair: Current Strategies and Future Directions. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Culture-independent Characterization of the Microbiome of Healthy Pulp. J Endod 2018; 44:1132-1139.e2. [DOI: 10.1016/j.joen.2018.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 02/08/2023]
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Abstract
Current protocols for ancient DNA and radiocarbon analysis of ancient bones and teeth call for multiple destructive samplings of a given specimen, thereby increasing the extent of undesirable damage to precious archaeological material. Here we present a method that makes it possible to obtain both ancient DNA sequences and radiocarbon dates from the same sample material. This is achieved by releasing DNA from the bone matrix through incubation with either EDTA or phosphate buffer prior to complete demineralization and collagen extraction utilizing the acid-base-acid-gelatinization and ultrafiltration procedure established in most radiocarbon dating laboratories. Using a set of 12 bones of different ages and preservation conditions we demonstrate that on average 89% of the DNA can be released from sample powder with minimal, or 38% without any, detectable collagen loss. We also detect no skews in radiocarbon dates compared to untreated samples. Given the different material demands for radiocarbon dating (500 mg of bone/dentine) and DNA analysis (10-100 mg), combined DNA and collagen extraction not only streamlines the sampling process but also drastically increases the amount of DNA that can be recovered from limited sample material.
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29
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Liu Q, Liu L, Zhang M, Zhang Q, Wang Q, Ding X, Shao L, Zhou Z, Wang S. A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth. J Forensic Sci 2017; 63:824-828. [PMID: 29240980 DOI: 10.1111/1556-4029.13603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/27/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique.
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Affiliation(s)
- Qiqi Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liyan Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Minli Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qingzhen Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qiong Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiaoran Ding
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhe Zhou
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
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Gonzalez-Fernandez T, Tierney EG, Cunniffe GM, O'Brien FJ, Kelly DJ. Gene Delivery of TGF-β3 and BMP2 in an MSC-Laden Alginate Hydrogel for Articular Cartilage and Endochondral Bone Tissue Engineering. Tissue Eng Part A 2017; 22:776-87. [PMID: 27079852 DOI: 10.1089/ten.tea.2015.0576] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Incorporating therapeutic genes into three-dimensional biomaterials is a promising strategy for enhancing tissue regeneration. Alginate hydrogels have been extensively investigated for cartilage and bone tissue engineering, including as carriers of transfected cells to sites of injury, making them an ideal gene delivery platform for cartilage and osteochondral tissue engineering. The objective of this study was to develop gene-activated alginate hydrogels capable of supporting nanohydroxyapatite (nHA)-mediated nonviral gene transfer to control the phenotype of mesenchymal stem cells (MSCs) for either cartilage or endochondral bone tissue engineering. To produce these gene-activated constructs, MSCs and nHA complexed with plasmid DNA (pDNA) encoding for transforming growth factor-beta 3 (pTGF-β3), bone morphogenetic protein 2 (pBMP2), or a combination of both (pTGF-β3-pBMP2) were encapsulated into alginate hydrogels. Initial analysis using reporter genes showed effective gene delivery and sustained overexpression of the transgenes were achieved. Confocal microscopy demonstrated that complexing the plasmid with nHA before hydrogel encapsulation led to transport of the plasmid into the nucleus of MSCs, which did not happen with naked pDNA. Gene delivery of TGF-β3 and BMP2 and subsequent cell-mediated expression of these therapeutic genes resulted in a significant increase in sulfated glycosaminoglycan and collagen production, particularly in the pTGF-β3-pBMP2 codelivery group in comparison to the delivery of either pTGF-β3 or pBMP2 in isolation. In addition, stronger staining for collagen type II deposition was observed in the pTGF-β3-pBMP2 codelivery group. In contrast, greater levels of calcium deposition were observed in the pTGF-β3- and pBMP2-only groups compared to codelivery, with a strong staining for collagen type X deposition, suggesting these constructs were supporting MSC hypertrophy and progression along an endochondral pathway. Together, these results suggest that the developed gene-activated alginate hydrogels were able to support transfection of encapsulated MSCs and directed their phenotype toward either a chondrogenic or an osteogenic phenotype depending on whether TGF-β3 and BMP2 were delivered in combination or isolation.
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Affiliation(s)
- Tomas Gonzalez-Fernandez
- 1 Trinity Centre for Bioengineering (TCBE), Trinity Biomedical Sciences Institute , Trinity College Dublin, Dublin, Ireland .,2 Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin , Dublin, Ireland .,3 Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin , Dublin, Ireland .,4 Tissue Engineering Research Group (TERG), Department of Anatomy, Royal College of Surgeons in Ireland , Dublin, Ireland
| | - Erica G Tierney
- 4 Tissue Engineering Research Group (TERG), Department of Anatomy, Royal College of Surgeons in Ireland , Dublin, Ireland
| | - Grainne M Cunniffe
- 1 Trinity Centre for Bioengineering (TCBE), Trinity Biomedical Sciences Institute , Trinity College Dublin, Dublin, Ireland .,2 Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin , Dublin, Ireland .,3 Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin , Dublin, Ireland
| | - Fergal J O'Brien
- 1 Trinity Centre for Bioengineering (TCBE), Trinity Biomedical Sciences Institute , Trinity College Dublin, Dublin, Ireland .,3 Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin , Dublin, Ireland .,4 Tissue Engineering Research Group (TERG), Department of Anatomy, Royal College of Surgeons in Ireland , Dublin, Ireland
| | - Daniel J Kelly
- 1 Trinity Centre for Bioengineering (TCBE), Trinity Biomedical Sciences Institute , Trinity College Dublin, Dublin, Ireland .,2 Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin , Dublin, Ireland .,3 Advanced Materials and Bioengineering Research Centre (AMBER), Royal College of Surgeons in Ireland and Trinity College Dublin , Dublin, Ireland .,4 Tissue Engineering Research Group (TERG), Department of Anatomy, Royal College of Surgeons in Ireland , Dublin, Ireland
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Wadsworth C, Procopio N, Anderung C, Carretero JM, Iriarte E, Valdiosera C, Elburg R, Penkman K, Buckley M. Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites. J Proteomics 2017; 158:1-8. [DOI: 10.1016/j.jprot.2017.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/23/2022]
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Effect of X-ray irradiation on ancient DNA in sub-fossil bones - Guidelines for safe X-ray imaging. Sci Rep 2016; 6:32969. [PMID: 27615365 PMCID: PMC5018823 DOI: 10.1038/srep32969] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([μ]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200 Gy. Dosimetry shows that conventional μCT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studies.
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33
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Weiß CL, Schuenemann VJ, Devos J, Shirsekar G, Reiter E, Gould BA, Stinchcombe JR, Krause J, Burbano HA. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160239. [PMID: 27429780 PMCID: PMC4929915 DOI: 10.1098/rsos.160239] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/24/2016] [Indexed: 05/04/2023]
Abstract
Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.
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Affiliation(s)
- Clemens L. Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Verena J. Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
| | - Jane Devos
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
| | - Billie A. Gould
- Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S
- University of Toronto, Toronto, Ontario, CanadaM5S
| | - Johannes Krause
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
- Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tuebingen 72076, Germany
- Max Planck Institute for the Science of Human History, Jena 07743, Germany
| | - Hernán A. Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
- Author for correspondence: Hernán A. Burbano e-mail:
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34
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Figdor D, Brundin M. Contamination Controls for Analysis of Root Canal Samples by Molecular Methods: An Overlooked and Unsolved Problem. J Endod 2016; 42:1003-8. [PMID: 27236203 DOI: 10.1016/j.joen.2016.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Abstract
INTRODUCTION It has been almost 20 years since molecular methods were first described for the analysis of root canal microbial flora. Contamination control samples are essential to establish DNA decontamination before taking root canal samples, and this review assessed those studies. METHODS Using PubMed, a search was conducted for studies using molecular microbial analysis for the investigation of endodontic samples. Studies were grouped according to the cleaning protocol, acquisition methods, and processing of control samples taken to check for contamination. RESULTS Of 136 studies applying molecular analysis to root canal samples, 21 studies performed surface cleaning and checking nucleotide decontamination with contamination control samples processed by polymerase chain reaction. Only 1 study described disinfection, sampling from the access cavity, and processing by polymerase chain reaction and reported the result; that study reported that all samples contained contaminating bacterial DNA. CONCLUSIONS Cleaning, disinfection, and checking for contamination are basic scientific prerequisites for this type of investigation; yet, this review identifies it as an overlooked issue. On the basis of this review, we call for improved scientific practice in this field.
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Affiliation(s)
- David Figdor
- Department of Microbiology, Monash University, Melbourne, Australia
| | - Malin Brundin
- Department of Odontology/Endodontics, Faculty of Medicine, Umeå University, Umeå, Sweden.
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35
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Pinheiro ET, Neves VD, Reis CC, Longo PL, Mayer MPA. Evaluation of the Propidium Monoazide-quantitative Polymerase Chain Reaction Method for the Detection of Viable Enterococcus faecalis. J Endod 2016; 42:1089-92. [PMID: 27179593 DOI: 10.1016/j.joen.2016.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/17/2016] [Accepted: 04/03/2016] [Indexed: 11/26/2022]
Abstract
INTRODUCTION One limitation of DNA-based molecular assays is their inability to distinguish between live and dead cells. A sample treatment with propidium monoazide (PMA) before DNA amplification has been proposed to overcome this problem. The aim of this in vitro study was to test different concentrations of PMA coupled with quantitative polymerase chain reaction (qPCR) for the detection of viable Enterococcus faecalis. METHODS Viable or heat-killed suspensions of E. faecalis (10⁶ colony-forming units/mL) were treated with PMA at 10, 50, and 100 μg/mL before DNA extraction. qPCR was performed using primers complementary for E. faecalis 16S ribosomal RNA sequence. PMA was also tested on bacteria suspensions containing different proportions of viable and dead cells. Bacterial suspensions without PMA treatment were used as positive controls. RESULTS The treatment of heat-killed suspensions with PMA at different concentrations significantly reduced the DNA amplification when compared with the group without treatment (P < .0001), indicating that DNA from dead cells was not used as templates. The greatest reduction in qPCR amplification of dead cell DNA was found when 100 μg/mL PMA was used (P < .005). In mixtures containing live/dead cells, PMA allowed selective detection of viable cells. CONCLUSIONS PMA was effective in inhibiting qPCR amplification from the DNA of dead cells, enabling in vitro detection and quantification of viable cells of E. faecalis.
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Affiliation(s)
- Ericka T Pinheiro
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil.
| | - Viviane D Neves
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Caroline C Reis
- Discipline of Endodontics, Department of Dentistry, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Priscila L Longo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Márcia P A Mayer
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Johnston E, Stephenson M. DNA Profiling Success Rates from Degraded Skeletal Remains in Guatemala. J Forensic Sci 2016; 61:898-902. [PMID: 27364268 DOI: 10.1111/1556-4029.13087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 09/14/2015] [Accepted: 10/04/2015] [Indexed: 11/28/2022]
Abstract
No data are available regarding the success of DNA Short Tandem Repeat (STR) profiling from degraded skeletal remains in Guatemala. Therefore, DNA profiling success rates relating to 2595 skeletons from eleven cases at the Forensic Anthropology Foundation of Guatemala (FAFG) are presented. The typical postmortem interval was 30 years. DNA was extracted from bone powder and amplified using Identifiler and Minifler. DNA profiling success rates differed between cases, ranging from 50.8% to 7.0%, the overall success rate for samples was 36.3%. The best DNA profiling success rates were obtained from femur (36.2%) and tooth (33.7%) samples. DNA profiles were significantly better from lower body bones than upper body bones (p = <0.0001). Bone samples from males gave significantly better profiles than samples from females (p = <0.0001). These results are believed to be related to bone density. The findings are important for designing forensic DNA sampling strategies in future victim recovery investigations.
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Affiliation(s)
- Emma Johnston
- Department of Forensic Genetics, Fundación de Antropología Forense de Guatemala, 1ra Calle 1-53, Zona 2, Guatemala, Guatemala
| | - Mishel Stephenson
- Department of Forensic Genetics, Fundación de Antropología Forense de Guatemala, 1ra Calle 1-53, Zona 2, Guatemala, Guatemala
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Pinheiro ET, Candeiro GT, Teixeira SR, Shin RC, Prado LC, Gavini G, Mayer MP. RNA-based Assay Demonstrated Enterococcus faecalis Metabolic Activity after Chemomechanical Procedures. J Endod 2015; 41:1441-4. [DOI: 10.1016/j.joen.2015.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/22/2015] [Accepted: 04/28/2015] [Indexed: 10/23/2022]
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38
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TRIzol and Alu qPCR-based quantification of metastatic seeding within the skeleton. Sci Rep 2015; 5:12635. [PMID: 26271202 PMCID: PMC4536516 DOI: 10.1038/srep12635] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/02/2015] [Indexed: 11/08/2022] Open
Abstract
Current methods for detecting disseminated tumor cells in the skeleton are limited by expense and technical complexity. We describe a simple and inexpensive method to quantify, with single cell sensitivity, human metastatic cancer in the mouse skeleton, concurrently with host gene expression, using TRIzol-based DNA/RNA extraction and Alu sequence qPCR amplification. This approach enables precise quantification of tumor cells and corresponding host gene expression during metastatic colonization in xenograft models.
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Korlević P, Gerber T, Gansauge MT, Hajdinjak M, Nagel S, Aximu-Petri A, Meyer M. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 2015; 59:87-93. [PMID: 26260087 DOI: 10.2144/000114320] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/08/2015] [Indexed: 11/23/2022] Open
Abstract
Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem.
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Affiliation(s)
- Petra Korlević
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Coulson-Thomas YM, Norton AL, Coulson-Thomas VJ, Florencio-Silva R, Ali N, Elmrghni S, Gil CD, Sasso GRS, Dixon RA, Nader HB. DNA and bone structure preservation in medieval human skeletons. Forensic Sci Int 2015; 251:186-94. [PMID: 25912776 DOI: 10.1016/j.forsciint.2015.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/29/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified.
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Affiliation(s)
- Yvette M Coulson-Thomas
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil; School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK.
| | | | - Vivien J Coulson-Thomas
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil; John van Geest Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK
| | - Rinaldo Florencio-Silva
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil
| | - Nadir Ali
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Samir Elmrghni
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Cristiane D Gil
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil
| | - Gisela R S Sasso
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil
| | - Ronald A Dixon
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Helena B Nader
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil
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Warinner C, Speller C, Collins MJ. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130376. [PMID: 25487328 PMCID: PMC4275884 DOI: 10.1098/rstb.2013.0376] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.
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Rivas M, Casanovas J, del Valle LJ, Bertran O, Revilla-López G, Turon P, Puiggalí J, Alemán C. An experimental-computer modeling study of inorganic phosphates surface adsorption on hydroxyapatite particles. Dalton Trans 2015; 44:9980-91. [DOI: 10.1039/c5dt00209e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The adsorption of different phosphates and a triphosphonate onto hydroxyapatite has been highlighted combining experiments and theoretical calculations.
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Affiliation(s)
- Manuel Rivas
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Jordi Casanovas
- Departament de Química
- Escola Politècnica Superior
- Universitat de Lleida
- Lleida E-25001
- Spain
| | - Luis J. del Valle
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Oscar Bertran
- Departament de Física Aplicada
- EEI
- Universitat Politècnica de Catalunya
- 08700 Igualada
- Spain
| | - Guillermo Revilla-López
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Pau Turon
- B. Braun Surgical
- 08191 Rubí (Barcelona)
- Spain
| | - Jordi Puiggalí
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- E. T. S. d'Enginyeria Industrial de Barcelona
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
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del Valle LJ, Bertran O, Chaves G, Revilla-López G, Rivas M, Casas MT, Casanovas J, Turon P, Puiggalí J, Alemán C. DNA adsorbed on hydroxyapatite surfaces. J Mater Chem B 2014; 2:6953-6966. [DOI: 10.1039/c4tb01184h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Young JM, Rawlence NJ, Weyrich LS, Cooper A. Limitations and recommendations for successful DNA extraction from forensic soil samples: A review. Sci Justice 2014; 54:238-44. [DOI: 10.1016/j.scijus.2014.02.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/12/2014] [Accepted: 02/18/2014] [Indexed: 11/15/2022]
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Brundin M, Figdor D, Sundqvist G, Sjögren U. Preservation of Fusobacterium nucleatum and Peptostreptococcus anaerobius DNA after loss of cell viability. Int Endod J 2014; 48:37-45. [PMID: 24611977 DOI: 10.1111/iej.12273] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 02/22/2014] [Indexed: 01/30/2023]
Abstract
AIM To investigate whether DNA from two obligate anaerobes, Fusobacterium nucleatum and Peptostreptococcus anaerobius, is recoverable after loss of cell viability induced by air exposure. METHODOLOGY Harvested cultures of F. nucleatum and P. anaerobius were killed by exposure to air and stored in phosphate-buffered saline. Dead cells were incubated aerobically for up to 6 months. Every month, the presence of detectable DNA in the cell pellet and supernatant was assessed by conventional and quantitative PCR. Cell staining techniques were used to characterize the cell wall permeability of air-killed cells. Scanning electron microscopy was used to examine viable, freshly killed and stored cells. RESULTS With conventional PCR, amplifiable DNA was detectable over 6 months in all samples. Quantitative PCR showed a progressive fall in DNA concentration in nonviable cell pellets and a concomitant rise in DNA concentration in the supernatant. DNA staining showed that some air-killed cells retained an intact cell wall. After storage, SEM of both air-killed species revealed shrivelling of the cells, but some cells of P. anaerobius retained their initial form. CONCLUSION Amplifiable DNA from F. nucleatum and P. anaerobius was detectable 6 months after loss of viability. Air-killed anaerobes initially retained their cell form, but cells gradually shriveled over time. The morphological changes were more pronounced with the gram-negative F. nucleatum than the gram-positive P. anaerobius. Over 6 months, there was a gradual increase in cell wall permeability with progressive leakage of DNA. Bacterial DNA was recoverable long after loss of cell viability.
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Affiliation(s)
- M Brundin
- Department of Odontology/Endodontics, Faculty of Medicine, Umeå University, Umeå, Sweden
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Bertran O, del Valle LJ, Revilla-López G, Chaves G, Cardús L, Casas MT, Casanovas J, Turon P, Puiggalí J, Alemán C. Mineralization of DNA into nanoparticles of hydroxyapatite. Dalton Trans 2014; 43:317-27. [DOI: 10.1039/c3dt52112e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Preservation of bacterial DNA by human dentin. J Endod 2013; 40:241-5. [PMID: 24461411 DOI: 10.1016/j.joen.2013.08.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 02/01/2023]
Abstract
INTRODUCTION The capacity of dentin and collagen to bind DNA and protect against spontaneous and nuclease-induced degradation was evaluated individually and by the incubation of DNA with nuclease-producing bacteria in a mixed culture. METHODS Extracted Fusobacterium nucleatum DNA was incubated with dentin shavings or collagen for 90 minutes. The DNA-bound substrates were incubated in different media (water, sera, and DNase I) for up to 3 months. Amplifiable DNA was released from dentin using EDTA,or from collagen using proteinase K, and evaluated by polymerase chain reaction (PCR). The stability of dentin-bound DNA was also assessed in a mixed culture (Parvimonas micra and Pseudoramibacter alactolyticus) containing a DNase-producing species, Prevotella intermedia. Samples were analyzed for amplifiable DNA. RESULTS In water, dentin-bound DNA was recoverable by PCR at 3 months compared with no detectable DNA after 4 weeks in controls (no dentin). DNA bound to collagen was detectable by PCR after 3 months of incubation in water. In 10% human sera, amplifiable DNA was detectable at 3 months when dentin bound and in controls (no dentin). In mixed bacterial culture, dentin-bound DNA was recoverable throughout the experimental period (3 months), compared with no recoverable F. nucleatum DNA within 24 hours in controls (no dentin). CONCLUSIONS There is a strong binding affinity between DNA and dentin, and between DNA and serum proteins or collagen. These substrates preserve DNA against natural decomposition and protect DNA from nuclease activity, factors that may confound molecular analysis of the endodontic microbiota yet favor paleomicrobiological studies of ancient DNA.
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Keyser C, Crubézy É, Ludes B. L’analyse ADN dans l’approche anthropologique des populations du passé. Med Sci (Paris) 2013; 29:637-41. [DOI: 10.1051/medsci/2013296017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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