1
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Thongjued K, Garcia K, Scott D, Gonthier DJ, Dupuis JR. DNA metabarcoding diet analysis in a generalist omnivore: feeding trials reveal the efficacy of extraction kits and a multi-locus approach for identifying diverse diets. Integr Zool 2024; 19:790-806. [PMID: 38297429 DOI: 10.1111/1749-4877.12806] [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] [Indexed: 02/02/2024]
Abstract
Metabarcoding-based diet analysis is a valuable tool for understanding the feeding behavior of a wide range of species. However, many studies using these methods for wild animals assume accuracy and precision without experimental evaluation with known positive control food items. Here, we conducted a feeding trial experiment with a positive control community in pasture-raised chickens and assessed the efficacy of several commonly used DNA extraction kits and primer sets. We hand-fed 22 known food items, including insects and plants, to six backyard laying hens and collected their excreta for eight h. We evaluated the efficacy of three DNA extraction kits, three primer sets for plant identification (targeting rbcL, trnL, and internal transcribed spacer 2 [ITS2]), and three primer sets for arthropod identification (targeting cytochrome oxidase subunit I [COI]). The detection success rate of our positive control food items was highly variable, ranging from 2.04% to 93.88% for all kit/primer combinations and averaging 37.35% and 43.57% for the most effective kit/primer combination for plants and insects, respectively. Extraction kits using bead-based homogenization positively affected the recovery proportion of plant and insect DNA in excreta samples. The minimum time to detect known food items was 44 min post-feeding. Two COI primer sets significantly outperformed the third, and both recovery proportion and taxonomic resolution from ITS2 were significantly higher than those from rbcL and trnL. Taken together, these results display the potential variability that can be inherently present in DNA-based diet analyses and highlight the utility of experimental feeding trials in validating such approaches, particularly for omnivores with diverse diets.
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Affiliation(s)
- Kantima Thongjued
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Karina Garcia
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Delia Scott
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - David J Gonthier
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
| | - Julian R Dupuis
- Department of Entomology, University of Kentucky, Agricultural Science Center, Lexington, Kentucky, USA
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3
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Czado N, Houston R, Hughes S. Evaluation of metal ions and DNA recovery from the surface of fired and unfired brass ammunition to improve STR profiling. Int J Legal Med 2024; 138:1265-1272. [PMID: 38433135 DOI: 10.1007/s00414-024-03200-8] [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: 10/17/2023] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
Interest in recovering DNA from the surface of ammunition evidence for genotyping has increased over the past few years. Numerous studies have examined a variety of methods to maximize DNA recovery from these types of challenging samples, but successful DNA profiling has been inconsistent. Low amounts of DNA and PCR inhibition due to metal ions have been suggested as the leading causes of poor results; however, no study quantitatively examined the presence of metal ions at various stages of the DNA analysis workflow from DNA collection through to amplification. In this study, the effectiveness of six different DNA collection and purification methods commonly used by forensic laboratories to process brass ammunition for DNA evidence was investigated. The amount of copper, zinc, and other metals co-recovered from fired and unfired brass casings during DNA collection (using numerous soaking, swabbing, and direct PCR protocols) was quantified via Inductively Coupled Plasma - Optical Emission Spectrometry (ICP-OES). This same panel of metals was subsequently quantified after DNA lysis and purification steps. Results demonstrated that low amounts of DNA, DNA damage, and degradation are more detrimental to STR typing results than PCR inhibition, as metal ions were successfully removed by all DNA purification methods tested. Furthermore, the use of metal ion chelators increased the amount of DNA recovered and number of reportable STR alleles. This research informs the forensic community on the most effective way to collect and process trace amounts of biological material from brass ammunition and similar evidence.
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Affiliation(s)
- Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, USA
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, USA.
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4
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Schwaiger G, Matt M, Streich P, Bromann S, Clauß M, Elsner M, Seidel M. Standard addition method for rapid, cultivation-independent quantification of Legionella pneumophila cells by qPCR in biotrickling filters. Analyst 2024; 149:2978-2987. [PMID: 38602145 DOI: 10.1039/d3an02207b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Cultivation-independent molecular biological methods are essential to rapidly quantify pathogens like Legionella pneumophila (L. pneumophila) which is important to control aerosol-generating engineered water systems. A standard addition method was established to quantify L. pneumophila in the very complex matrix of process water and air of exhaust air purification systems in animal husbandry. Therefore, cryopreserved standards of viable L. pneumophila were spiked in air and water samples to calibrate the total bioanalytical process which includes cell lysis, DNA extraction, and qPCR. A standard addition algorithm was employed for qPCR to determine the initial concentration of L. pneumophila. In mineral water, the recovery rate of this approach (73%-134% within the concentration range of 100-5000 Legionella per mL) was in good agreement with numbers obtained from conventional genomic unit (GU) calibration with DNA standards. In air samples of biotrickling filters, in contrast, the conventional DNA standard approach resulted in a significant overestimation of up to 729%, whereas our standard addition gave a more realistic recovery of 131%. With this proof-of-principle study, we were able to show that the molecular biology-based standard addition approach is a suitable method to determine realistic concentrations of L. pneumophila in air and process water samples of biotrickling filter systems. Moreover, this quantification strategy is generally a promising method to quantify pathogens in challenging samples containing a complex microbiota and the classical GU approach used for qPCR leads to unreliable results.
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Affiliation(s)
- Gerhard Schwaiger
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Marco Matt
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Philipp Streich
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Sarah Bromann
- Thuenen-Institute for Agricultural Technology, Bundesallee 47, D-38116 Braunschweig, Germany
| | - Marcus Clauß
- Thuenen-Institute for Agricultural Technology, Bundesallee 47, D-38116 Braunschweig, Germany
| | - Martin Elsner
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Michael Seidel
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
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5
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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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6
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Dhar BC, Delgado Santander R, Aćimović SG. Improved Canker Processing and Viability Droplet Digital PCR Allow Detection of Erwinia amylovora Viable Nonculturable Cells in Apple Bark. Microorganisms 2024; 12:376. [PMID: 38399780 PMCID: PMC10893025 DOI: 10.3390/microorganisms12020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterium Erwinia amylovora causes fire blight and continues to threaten global commercial apple and pear production. Conventional microbiology techniques cannot accurately determine the presence of live pathogen cells in fire blight cankers. Several factors may prevent E. amylovora from growing on solid culture media, including competing microbiota and the release of bacterial-growth-inhibitory compounds by plant material during sample processing. We previously developed a canker processing methodology and a chip-based viability digital PCR (v-dPCR) assay using propidium monoazide (PMA) to bypass these obstacles. However, sample analysis was still time-consuming and physically demanding. In this work, we improved the previous protocol using an automatic tissue homogenizer and transferred the chip-based v-dPCR to the BioRad QX200 droplet dPCR (ddPCR) platform. The improved sample processing method allowed the simultaneous, fast, and effortless processing of up to six samples. Moreover, the transferred v-ddPCR protocol was compatible with the same PMA treatment and showed a similar dynamic range, from 7.2 × 102 to 7.6 × 107 cells mL-1, as the previous v-dPCR. Finally, the improved protocol allowed, for the first time, the detection of E. amylovora viable but nonculturable (VBNC) cells in cankers and bark tissues surrounding cankers. Our v-ddPCR assay will enable new ways to evaluate resistant pome fruit tree germplasm, further dissect the E. amylovora life cycle, and elucidate E. amylovora physiology, epidemiology, and new options for canker management.
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Affiliation(s)
- Bidhan Chandra Dhar
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, 595 Laurel Grove Rd, Winchester, VA 22602, USA;
| | - Ricardo Delgado Santander
- Irrigated Agriculture Research and Extension Center, College of Agricultural, Human and Natural Resource Sciences, Washington State University, Prosser, WA 99350, USA;
| | - Srđan G. Aćimović
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, 595 Laurel Grove Rd, Winchester, VA 22602, USA;
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7
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Kuffel A, Nic Daeid N, Gray A. Comparison of swabbing and cutting-out DNA collection methods from cotton, paper, and cardboard surfaces. Forensic Sci Int Synerg 2024; 8:100453. [PMID: 38283046 PMCID: PMC10821607 DOI: 10.1016/j.fsisyn.2023.100453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Choosing an inappropriate method of sample collection can often have a detrimental impact on DNA recovery. Multiple studies highlight the importance of selecting the recovery method based on the type of surface the DNA sample is located on. This study aimed to investigate the efficacy of sample collection via the single cotton swabbing method in comparison to recovery directly from the material cut from the surface. The three types of surfaces included cotton, paper, and cardboard. DNA sources comprised cell-free and cellular DNA, as well as blood and saliva as examples of body fluids commonly encountered at crime scenes. The data analysis revealed that the cutting-out method resulted in higher DNA recovery from all but cardboard surfaces, making it the more efficient collection method. Despite its limitations, the cutting-out method should be considered as the DNA recovery method of choice when suitable.
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Affiliation(s)
- Agnieszka Kuffel
- Leverhulme Research Centre for Forensic Science, Fleming Gym Building, University of Dundee, Small's Wynd, Dundee, United Kingdom
| | - Niamh Nic Daeid
- Leverhulme Research Centre for Forensic Science, Fleming Gym Building, University of Dundee, Small's Wynd, Dundee, United Kingdom
| | - Alexander Gray
- Leverhulme Research Centre for Forensic Science, Fleming Gym Building, University of Dundee, Small's Wynd, Dundee, United Kingdom
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8
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Hess J, Kreitlow A, Rohn K, Hennig-Pauka I, Abdulmawjood A. Rapid Diagnostic of Streptococcus suis in Necropsy Samples of Pigs by thrA-Based Loop-Mediated Isothermal Amplification Assay. Microorganisms 2023; 11:2447. [PMID: 37894105 PMCID: PMC10608932 DOI: 10.3390/microorganisms11102447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Streptococcus (S.) suis presents a serious threat to the pig industry as well as food safety and public health. Although several LAMP assays have been developed for the identification of S. suis, no universal assay is so far available for the field-suitable examination of clinical pig specimens. Based on the thrA housekeeping gene, a new loop-mediated isothermal amplification (LAMP) assay was developed and validated for the detection of S. suis in the brain and joints of pigs. For this LAMP assay, two different methods for the extraction of DNA from brain and joint swabs were compared. Using the LPTV boiling method, the detection limit of LAMP was 1.08 CFU/reaction, while the detection limit was 53.8 CFU/reaction using a commercial DNA extraction kit. The detection limits of thrA-LAMP in combination with the LPTV boiling method were 104-105 CFU/swab in the presence of brain tissue and 103-104 CFU/swab in the presence of joint tissue. The diagnostic quality criteria of LAMP were determined by the examination of 49 brain swabs and 34 joint swabs obtained during routine diagnostic necropsies. Applying the LPTV boiling method to brain swabs, the sensitivity, specificity, and positive and negative predictive values of thrA-LAMP were 88.0, 95.8, 95.7, and 88.5% using cultural investigation as a reference method, and 76.7, 100, 100, and 73.1% using real-time PCR as a reference method. Based on these results, the thrA-LAMP assay combined with the LPTV boiling method is suitable for rapid detection of S. suis from brain swabs.
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Affiliation(s)
- Julian Hess
- Field Station for Epidemiology (Bakum), University of Veterinary Medicine Hannover, Foundation, 49456 Bakum, Germany;
| | - Antonia Kreitlow
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany;
| | - Karl Rohn
- Institute for Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Isabel Hennig-Pauka
- Field Station for Epidemiology (Bakum), University of Veterinary Medicine Hannover, Foundation, 49456 Bakum, Germany;
| | - Amir Abdulmawjood
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany;
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9
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Evidentiary evaluation of single cells renders highly informative forensic comparisons across multifarious admixtures. Forensic Sci Int Genet 2023; 64:102852. [PMID: 36934551 DOI: 10.1016/j.fsigen.2023.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/09/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
The consistency between DNA evidence and person(s) of interest (PoI) is summarized by a likelihood ratio (LR): the probability of the data given the PoI contributed divided by the probability given they did not. It is often the case that there are several PoI who may have individually or jointly contributed to the stain. If there is more than one PoI, or the number of contributors (NoC) cannot easily be determined, then several sets of hypotheses are needed, requiring significant resources to complete the interpretation. Recent technological developments in laboratory systems offer a way forward, by enabling production of single cell data. Though single-cell data may be procured by next generation sequencing or capillary electrophoresis workflows, in this work we focus our attention on assessing the consistency between PoIs and a collection of single cell electropherograms (scEPGs) from diploid cells - i.e., leukocytes and epithelial cells. Specifically, we introduce a framework that: I) clusters scEPGs into collections, each originating from one genetic source; II) for each PoI, determines a LR for each cluster of scEPGs; and III) by averaging the likelihood ratios for each PoI across all clusters provides a whole-sample weight of evidence summary. By using Model Based Clustering (MBC) in step I) and an algorithm, named EESCIt for Evidentiary Evaluation of Single Cells, that computes single-cell LRs in step II), we show that 99% of the comparisons rendered log LR values > 0 for true contributors, and of these all but one gave log LR > 5, regardless of the number of donors or whether the smallest contributor donated less than 20% of the cells, greatly expanding the collection of cases for which DNA forensics provides informative results.
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10
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Kohlberger M, Gadermaier G. SELEX: Critical factors and optimization strategies for successful aptamer selection. Biotechnol Appl Biochem 2022; 69:1771-1792. [PMID: 34427974 PMCID: PMC9788027 DOI: 10.1002/bab.2244] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/22/2021] [Indexed: 12/30/2022]
Abstract
Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA- or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.
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Affiliation(s)
- Michael Kohlberger
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
| | - Gabriele Gadermaier
- Department of BiosciencesParis Lodron University SalzburgSalzburgAustria,Christian Doppler Laboratory for Biosimilar CharacterizationParis Lodron University SalzburgSalzburgAustria
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11
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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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12
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Elwick K, Gauthier Q, Rink S, Cropper E, Kavlick MF. Recovery of DNA from fired and unfired cartridge casings: comparison of two DNA collection methods. Forensic Sci Int Genet 2022; 59:102726. [PMID: 35660851 DOI: 10.1016/j.fsigen.2022.102726] [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: 11/16/2021] [Revised: 04/22/2022] [Accepted: 05/17/2022] [Indexed: 01/14/2023]
Abstract
For over 10 years, various studies have attempted to increase the recovery of DNA from ammunition by modifying the DNA collection, extraction, purification, and amplification procedures, with varying levels of success. This study focused on the "soaking" method of Montpetit & O'Donnell [1] and the "rinse-and-swab" method of Bille et al. [2]. First, testing for the presence of exogenous DNA, 210 boxed cartridges (brass, steel, and nickel-plated) from nine manufacturers were swabbed and DNA was extracted, concentrated, and quantified. Extracts that quantified > 0 ng/µL (44 of 210) were amplified and genotyped with GlobalFiler™. Of those, only one extract yielded two alleles indicating that the manufacturing and packaging of ammunition was virtually DNA free. Next, to obtain a baseline comparison of two DNA collection methods on a non-metallic substrate and identify a suitable number of cells to spot on cartridges, different DNA input amounts of primary human adult epidermal keratinocytes (HEKa) were tested. Thereafter, 300 brass and 300 nickel-plated, cartridges were spotted with HEKa cells containing ~5 ng of DNA, fired or unfired, and processed with either method. Finally, five methods representing hybrids of the soaking and rinse-and-swab methods were tested to determine if variations of those methods could be used to increase DNA yield and recovery. The results show that the soaking method consistently yielded more DNA than the rinse-and-swab method from a non-metallic substrate. However, the comparison study demonstrated that both methods performed comparably for cartridges. On average, the soaking method recovered 0.25 ng of DNA (5.1% recovery) and the rinse-and-swab method recovered 0.28 ng (5.8% recovery). However, average recoveries were significantly different among three analysts and considerable variation in yields were observed, possibly due to storage time. Furthermore, consistent with prior reports, the DNA recovered from brass casings was only 16% of that recovered from nickel-plated casings and the average yield of DNA from fired casings was reduced to 67% of unfired casings. Moreover, DNA extracts from brass or nickel-plated casings did not appear to contain amplification inhibitors and only 30/596 appeared severely degraded. Finally, both the published rinse-and-swab and soaking methods yielded more DNA than all modifications of the two methods. Overall, both methods yielded equivalent DNA quantities. Additionally, recovery of DNA from any given cartridge casing may be dependent on storage time as well as the skill, proficiency, and experience of the analyst and may reflect stochastic effects, particularly for casings containing low copy and/or degraded DNA.
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Affiliation(s)
- Kyleen Elwick
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Quentin Gauthier
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Stephanie Rink
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Emily Cropper
- Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA
| | - Mark F Kavlick
- Federal Bureau of Investigation Laboratory Division, Research and Support Unit, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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13
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Costa A, Giraldo G, Bishell A, He T, Kirker G, Wiedenhoeft AC. Organellar microcapture to extract nuclear and plastid DNA from recalcitrant wood specimens and trace evidence. PLANT METHODS 2022; 18:51. [PMID: 35443731 PMCID: PMC9019980 DOI: 10.1186/s13007-022-00885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Illegal logging is a global crisis with significant environmental, economic, and social consequences. Efforts to combat it call for forensic methods to determine species identity, provenance, and individual identification of wood specimens throughout the forest products supply chain. DNA-based methodologies are the only tools with the potential to answer all three questions and the only ones that can be calibrated "non-destructively" by using leaves or other plant tissue and take advantage of publicly available DNA sequence databases. Despite the potential that DNA-based methods represent for wood forensics, low DNA yield from wood remains a limiting factor because, when compared to other plant tissues, wood has few living DNA-containing cells at functional maturity, it often has PCR-inhibiting extractives, and industrial processing of wood degrades DNA. To overcome these limitations, we developed a technique-organellar microcapture-to mechanically isolate intact nuclei and plastids from wood for subsequent DNA extraction, amplification, and sequencing. RESULTS Here we demonstrate organellar microcapture wherein we remove individual nuclei from parenchyma cells in wood (fresh and aged) and leaves of Carya ovata and Tilia americana, amyloplasts from Carya wood, and chloroplasts from kale (Brassica sp.) leaf midribs. ITS (773 bp), ITS1 (350 bp), ITS2 (450 bp), and rbcL (620 bp) were amplified via polymerase chain reaction, sequenced, and heuristic searches against the NCBI database were used to confirm that recovered DNA corresponded to each taxon. CONCLUSION Organellar microcapture, while too labor-intensive for routine extraction of many specimens, successfully recovered intact nuclei from wood samples collected more than sixty-five years ago, plastids from fresh sapwood and leaves, and presents great potential for DNA extraction from recalcitrant plant samples such as tissues rich in secondary metabolites, old specimens (archaeological, herbarium, and xylarium specimens), or trace evidence previously considered too small for analysis.
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Affiliation(s)
- Adriana Costa
- Department of Sustainable Bioproducts, Mississippi State University, Starkville, MS USA
- Forest Products Laboratory, Madison, WI USA
| | - Giovanny Giraldo
- Department of Botany, University of Wisconsin, Madison, USA
- Forest Products Laboratory, Madison, WI USA
| | | | - Tuo He
- Department of Wood Anatomy and Utilization Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, China
| | - Grant Kirker
- Department of Sustainable Bioproducts, Mississippi State University, Starkville, MS USA
- Forest Products Laboratory, Madison, WI USA
| | - Alex C. Wiedenhoeft
- Department of Sustainable Bioproducts, Mississippi State University, Starkville, MS USA
- Department of Botany, University of Wisconsin, Madison, USA
- Forest Products Laboratory, Madison, WI USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN USA
- Departamento de Ciências Biológicas (Botânica), Universidade Estadual Paulista–Botucatu, São Paulo, Brasil
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14
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Chen C, Lin Y, Yu H, Xue Y, Xu Q, Jiang L, Zhu R, Chen A, Yang Y, Xia R, Zhang X, Yang Q, Tao R, Zhu B, Li C, Zhang S. Establishing an integrated pipeline for automatic and efficient detection of trace DNA encountered in forensic applications. Sci Justice 2022; 62:50-59. [PMID: 35033328 DOI: 10.1016/j.scijus.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/13/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022]
Abstract
The analysis of trace DNA is a crucial component in forensic applications. Biological materials containing low-level DNA collected at crime scenes, such as fingerprints, can be valuable as evidence. Automatic detection of biological samples has been largely embraced in forensic applications to meet the increasing throughput requirements. However, the amount of DNA automatically retrieved from trace evidence often tends to be small and unstable, ultimately resulting in poor detection of DNA profiles. Thus, in this work, we introduced a robust DNA extraction and purification platform named Bionewtech® BN3200 (Bionewtech®, Shanghai, China) with the goal of constructing a rapid automatic detection system for trace DNA. The establishment of automatic detection system for trace DNA mainly encompassed two parts: assessing the sensitivity of automatic extraction platform and screening the optimal short tandem repeat (STR) typing kit. The sensitivity of Bionewtech® BN3200 platform based on Ultra-sensitive DNA Extraction kit was initially estimated, demonstrating that this extraction platform might contain large potential in the trace DNA extraction. For the amplification part, three sets of commercial multiplex STR typing kits were selected as candidates, and the amplified products were further genotyped on the Applied Biosystems 3500xl Genetic Analyzer. After comparation, SiFa™ 23 Plex Kit was determined as the most suitable amplification system for trace DNA. Eventually, the newly exploited trace DNA detection system was successfully implemented in the detection of fingerprints derived from glass surfaces with the five-seconds contact time. As a result, the DNA recovered from the fingerprints fluctuated approximately from 57.60 pg to 18.05 ng, in addition, over 70% of the total STR loci were detected in 75% of the fingerprint samples.
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Affiliation(s)
- Chong Chen
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Yuan Lin
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Huan Yu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Yu Xue
- Bionewtech® Company., Ltd., Shanghai 201615, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Lei Jiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Ruxin Zhu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaochun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Qi Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China
| | - Bofeng Zhu
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China.
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China.
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15
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Shrivastava P, Jain T, Kumawat RK. Direct PCR amplification from saliva sample using non-direct multiplex STR kits for forensic DNA typing. Sci Rep 2021; 11:7112. [PMID: 33782478 PMCID: PMC8007628 DOI: 10.1038/s41598-021-86633-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Due to its proficiency to provide the most discriminating results for forensic applications, medical research and anthropological studies, multiplex PCR based STR analysis has been established as the most efficient technique in the forensic DNA analysis. Several multiplex amplification kits based on 4, 5 and 6 dyes chemistry are commercially available and used in forensic DNA typing across the globe. These multiplex PCR systems are routinely used for amplification of multiple STR loci (Autosomal, Y and/or X STR's) in the DNA extracted from various biological samples. In the routine forensic DNA testing, DNA profile obtained is compared with the DNA profile of the reference sample, which takes a certain turnaround time and employs costly lab resources. Successive development in forensic DNA typing have resulted in advent of improved multiplex kits which have reduced the effective analysis time, cost and minimized the number of steps required in comparison to conventional forensic DNA typing. Specialized direct amplification compatible multiplex kits are also available nowadays. These kits are relatively costlier but still require few pre-processing steps, which does not make them worth the hefty cost. Herein, this study, we have used non-direct multiplex STR kits to assess their efficacy for direct amplification. In the present study, 103 saliva samples were directly amplified without any pre-treatment of the samples using thirteen non-direct multiplex kits (4 dyes, 5 dyes and 6 dyes chemistry based) for forensic DNA typing. Here, we report a validated direct PCR amplification protocol from the reference saliva samples by omitting DNA extraction and quantification steps, which resulted in 80% reduction of the turnaround time. The developed protocol is cost effective, time efficient and it does not compromise with the quality of DNA profiles. To the best of our knowledge, this is the first report for direct amplification of DNA with the most commonly used non-direct multiplex STR kits without any pre-treatment of the sample. Complete DNA profiles matching all the essential quality parameters were obtained successfully from all the tested samples.
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Affiliation(s)
- Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, MP, 470001, India.
| | - Toshi Jain
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, MP, 470001, India
| | - R K Kumawat
- DNA Division, State Forensic Science Laboratory, Rajasthan, Jaipur, 302016, India
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16
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Hudson BC, Cox JO, Seashols-Williams SJ, Dawson Cruz T. The effects of dithiothreitol (DTT) on fluorescent qPCR dyes. J Forensic Sci 2020; 66:700-708. [PMID: 33284476 DOI: 10.1111/1556-4029.14637] [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: 09/18/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
DNA extractions of semen samples commonly utilize dithiothreitol (DTT) to reduce and disrupt disulfide bonds. Although traditional extraction techniques remove DTT before downstream analyses, the forensic DNA community has recently explored Y-screening, direct amplification, and direct cell lysis assays that omit purification but employ reducing agents to lyse spermatozoa. This study examined the impact of residual DTT on downstream processes involving fluorescent dyes. Quantification using Investigator® Quantiplex HYres revealed a significant increase in the male DNA yield (p = 0.00056) and a >150,000,000-fold increase in the male:human DNA ratio when DTT remained in extracts versus when it was filtered out using a traditional purification method. When DTT was present with Quantifiler™ Trio, the true mean DNA yield for the large autosomal target significantly increased (p = 0.038) and the average reported DNA yields increased 1.1-fold, >9.5-fold, and 1.3-fold for the small autosomal, large autosomal, and male targets, respectively. DTT-spiked DNA standards from both kits were impacted similarly to samples with residual DTT, demonstrating that observed effects were related to DTT and not the extraction method. This study corroborates other reports that DTT adversely affects multiple dyes (e.g., Cy5, Quasar 670, SYBR Green I, TMR, and Mustang Purple® ). Overall, DTT causes inaccurate quantities and, consequently, inaccurate calculated male:female ratios when used in conjunction with these kits. Thus, implementation of newer direct-to-PCR assays incorporating DTT should either be avoided or used only with carefully evaluated, compatible dyes.
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Affiliation(s)
- Brittany C Hudson
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.,Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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17
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Zhang W, Du H, Huang X, Wang C, Duan X, Liu Y, Shi B, Zhang W, Qu X, Wei L, Schiffman M, Belinson JL, Wu R. Evaluation of an isothermal amplification HPV detection assay for primary cervical cancer screening. Infect Agent Cancer 2020; 15:65. [PMID: 33110442 PMCID: PMC7583687 DOI: 10.1186/s13027-020-00328-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Objective The aim of this research was to evaluate independently the performance of a new isothermal amplification assay for cervical cancer screening compared to two previously validated PCR-based assays and histologic endpoints. Methods This is a sub-study from the Chinese multi-center screening trial (CHIMUST). The self-collected and clinician-collected specimens stored in PreservCyt at − 4 °C from 6042 women with complete data were tested with the AmpFire assay. These specimens had been previously tested with Cobas and SeqHPV assays. In the primary study all patients with an abnormal test were referred to colposcopy where all had directed and/or random biopsies plus ECC. No additional patients were called back based on the AmpFire results. Results 6042/6619 women had complete data (mean age 44.1). There were 57 cases of CIN 2, 35 cases of CIN 3 and 2 cancers. The sensitivity for CIN2+ and CIN3+ were similar among the three assays (both direct and self-collected). For the specificities in all categories (CIN2+/CIN3+ and self and direct collection), isothermal amplification assay was either equal to or more specific than Cobas but consistently less specific than SeqHPV. Conclusion The AmpFire HPV assay showed similar sensitivity to Cobas and SeqHPV for CIN2+ and CIN3+ on both self and clinician-collections (P>0.05), with good specificity. The speed, low cost, and simplicity of this assay will make it particularly suited for low and middle resource settings. Its accuracy with self-collection makes it applicable for mass screening programs.
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Affiliation(s)
- Wei Zhang
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Hui Du
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Xia Huang
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Chun Wang
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Xianzhi Duan
- Capital Medical University Beijing Tongren Hospital, Beijing, P. R. China
| | - Yan Liu
- Fudan University Huanshan Hospital, Shanghai, P. R. China
| | - Bin Shi
- The second Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Wei Zhang
- Wuhan University Zhongnan Hospital, Wuhan, P. R. China
| | - Xinfeng Qu
- Expert in Three Engineering Office, Shenzhen Maternal of Peking University Shenzhen Hospital, Shenzhen, 518036 China
| | - Lihui Wei
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, P. R. China
| | - M Schiffman
- National Cancer Institute, Division of Epidemiology and Genetics, Bethesda, USA
| | - J L Belinson
- Women's Health Institute, Cleveland Clinic, Cleveland, OH USA.,PPreventive Oncology International, Inc., Shaker Heights, USA
| | - Ruifang Wu
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
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18
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Martins WF, Longhi DA, de Aragão GMF, Melero B, Rovira J, Diez AM. A mathematical modeling approach to the quantification of lactic acid bacteria in vacuum-packaged samples of cooked meat: Combining the TaqMan-based quantitative PCR method with the plate-count method. Int J Food Microbiol 2019; 318:108466. [PMID: 31865245 DOI: 10.1016/j.ijfoodmicro.2019.108466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/04/2019] [Accepted: 11/27/2019] [Indexed: 01/01/2023]
Abstract
The TaqMan-based quantitative Polymerase Chain Reaction (qPCR) method and the Plate Count (PC) method are both used in combination with primary and secondary mathematical modeling, to describe the growth curves of Leuconostoc mesenteroides and Weissella viridescens in vacuum-packaged meat products during storage under different isothermal conditions. Vacuum-Packaged Morcilla (VPM), a typical cooked blood sausage, is used as a representative meat product, with the aim of improving shelf-life prediction methods for those sorts of meat products. The standard curves constructed by qPCR showed good linearity between the cycle threshold (CT) and log10 CFU/g, demonstrating the high precision and the reproducible results of the qPCR method. The curves were used for the quantification of L. mesenteroides and W. viridescens in artificially inoculated VPM samples under isothermal storage (5, 8, 13 and 18 °C). Primally, both the qPCR and the PC methods were compared, and a linear regression analysis demonstrated a statistically significant linear correlation between the methods. Secondly, the Baranyi and Roberts model was fitted to the growth curve data to estimate the kinetic parameters of L. mesenteroides and W. viridescens under isothermal conditions, and secondary models were used to establish the dependence of the maximum specific growth rate on the temperature. The results proved that primary and secondary models were adequate for describing the growth curves of both methods in relation to both bacteria. In conclusion, the results of all the experiments proved that the qPCR method in combination with the PC method can be used to construct microbial growth kinetics and that primary and secondary mathematical modeling can be successfully applied to describe the growth of L. mesenteroides and W. viridescens in vacuum-packaged morcilla and, by extension, other cooked meat products with similar characteristics.
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Affiliation(s)
- Wiaslan Figueiredo Martins
- Federal University of Santa Catarina, Department of Chemical Engineering and Food Engineering, Center of Technology, Florianópolis, SC 88040-901, Brazil; Federal Institute of Education, Science and Technology of Goiano, Food Technology, Campus Morrinhos, Morrinhos, GO 75650-000, Brazil
| | - Daniel Angelo Longhi
- Federal University of Paraná, Food Engineering, Campus Jandaia do Sul, Jandaia do Sul, PR 86900-000, Brazil
| | - Gláucia Maria Falcão de Aragão
- Federal University of Santa Catarina, Department of Chemical Engineering and Food Engineering, Center of Technology, Florianópolis, SC 88040-901, Brazil
| | - Beatriz Melero
- University of Burgos, Department of Biotechnology and Food Science, Burgos 09001, Spain
| | - Jordi Rovira
- University of Burgos, Department of Biotechnology and Food Science, Burgos 09001, Spain
| | - Ana M Diez
- University of Burgos, Department of Biotechnology and Food Science, Burgos 09001, Spain.
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19
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Young JM, Higgins D, Austin JJ. Hybridization Enrichment to Improve Forensic Mitochondrial DNA Analysis of Highly Degraded Human Remains. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Tang J, Ostrander J, Wickenheiser R, Hall A. Touch DNA in forensic science: The use of laboratory-created eccrine fingerprints to quantify DNA loss. Forensic Sci Int Synerg 2019; 2:1-16. [PMID: 32411992 PMCID: PMC7219128 DOI: 10.1016/j.fsisyn.2019.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022]
Abstract
Touch samples typically contain a limited quantity of DNA, which can be further reduced during collection and analysis. It is not clear, however, at which point(s) the majority of the DNA is lost because there is not a reliable positive control to track the quantity of DNA through the analysis procedures. To take the first step in bridging this gap, we established a set of laboratory-created eccrine, or mock, fingerprints containing known quantities of DNA. Next, we defined a set of process controls to quantify loss at key fail points in the collection/extraction procedures, analyzing a total of 1200 mock fingerprints deposited on four different surfaces. We quantified DNA loss to the surface, the swab and at extraction, completing the evaluation with ANOVA. With better understanding of DNA yields and the mechanisms of loss, targeted process improvements will bring touch DNA samples into even more routine use with standardized, optimized procedures.
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Affiliation(s)
- Jessica Tang
- University of Chicago at Illinois, Department of Biopharmaceutical Sciences, 833 S. Wood St, Chicago, IL, 60612, USA
| | - Jennifer Ostrander
- University of Chicago at Illinois, Department of Biopharmaceutical Sciences, 833 S. Wood St, Chicago, IL, 60612, USA
| | - Ray Wickenheiser
- New York State Police Crime Lab System, 1220 Washington Avenue, Building 30, Albany, NY, 12226, USA
| | - Ashley Hall
- University of Chicago at Illinois, Department of Biopharmaceutical Sciences, 833 S. Wood St, Chicago, IL, 60612, USA
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21
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Menchhoff SI, Delacruz MT, Hytinen ME, Cox JO, Miller MT, Dawson Cruz T. DNA Purification Cell Lysis and Wash Step Modifications for Low-Template DNA Sample Processing . J Forensic Sci 2019; 65:597-600. [PMID: 31577367 DOI: 10.1111/1556-4029.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/25/2019] [Accepted: 09/10/2019] [Indexed: 11/29/2022]
Abstract
As DNA technology becomes increasingly sensitive, forensic laboratories are receiving more low-template DNA samples. These samples, already low in DNA content, become even more challenging to process as the available DNA becomes further reduced during the extraction step. In this study, two extraction modifications were tested to determine if the cause of DNA loss could be identified and mitigated. A double lysis technique was used to test for DNA loss in the sample collection substrate, and lysate eluates were re-extracted to determine DNA loss from inefficient binding to the silica column. Both modifications showed DNA was lost at these steps. However, resulting STR profiles from these samples had fewer peaks and lower peak heights when compared to samples processed with no extraction modifications. Overall, the potential benefits of adding these extraction modifications for low-template DNA sample processing are not enough to justify the risk associated with additional manipulation.
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Affiliation(s)
- Sydney I Menchhoff
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Room 2015, Richmond, VA, 23284
| | - Milady T Delacruz
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Room 2015, Richmond, VA, 23284
| | - Madison E Hytinen
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Room 2015, Richmond, VA, 23284
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Room 2015, Richmond, VA, 23284
| | - Marilyn T Miller
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Room 2015, Richmond, VA, 23284
| | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Room 2015, Richmond, VA, 23284
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22
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Edson SM, Roberts M. Determination of materials present in skeletonized human remains and the associated DNA: Development of a GC/MS protocol. Forensic Sci Int Synerg 2019; 1:170-184. [PMID: 32411970 PMCID: PMC7219129 DOI: 10.1016/j.fsisyn.2019.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 11/24/2022]
Abstract
DNA testing of skeletonized human remains is considered to be challenging, especially when the remains have been exposed to inhibitory materials during decomposition. Inhibitors affect the processing of DNA, either by preventing efficient extraction or interfering with down-stream PCR-based processes. Limited studies have been performed on real-world samples that have been exposed to such inhibitors. This paper presents the development of a gas chromatography/mass spectrometry (GC/MS) protocol for the evaluation of materials present in skeletonized human remains recovered from the field, as well as the DNA extracted from the same materials. Twenty-one bone samples and seventeen DNA extracts were evaluated across three solvents and multiple GC/MS parameters to determine the optimal conditions for the recovery of trace materials present. The aim of this work is to provide a technique that can determine the presence of inhibitors prior to DNA extraction, allowing analysts to optimize removal of inhibitory materials.
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Affiliation(s)
- Suni M. Edson
- Flinders University, College of Science and Engineering, Adelaide, South Australia, Australia
- Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, 115 Purple Heart Drive, Dover AFB, DE, 19902, USA
| | - Marcel Roberts
- John Jay College of Criminal Justice, 524 W 59 St., New York, NY, 10019, USA
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23
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Edson SM. Getting Ahead: Extraction of DNA from Skeletonized Cranial Material and Teeth. J Forensic Sci 2019; 64:1646-1657. [DOI: 10.1111/1556-4029.14123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Suni M. Edson
- Armed Forces DNA Identification Laboratory Armed Forces Medical Examiner System 115 Purple Heart Drive Dover AFB DE 19902
- College of Science and Engineering Flinders University Adelaide South Australia Australia
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24
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Sherier AJ, Kieser RE, Novroski NM, Wendt FR, King JL, Woerner AE, Ambers A, Garofano P, Budowle B. Copan microFLOQ® Direct Swab collection of bloodstains, saliva, and semen on cotton cloth. Int J Legal Med 2019; 134:45-54. [DOI: 10.1007/s00414-019-02081-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/22/2019] [Indexed: 01/17/2023]
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25
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Comment on 'A DNA extraction method for small quantities of bone for high-qualitygenotyping' by Caputo et al. Forensic Sci Int Genet 2019; 40:e243-e244. [PMID: 30770290 DOI: 10.1016/j.fsigen.2019.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/30/2018] [Accepted: 01/30/2019] [Indexed: 01/20/2023]
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26
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Winters M, Monroe C, Barta JL, Kemp BM. Evaluating the Efficiency of Primer Extension Capture as a Method to Enrich DNA Extractions. J Forensic Sci 2018; 64:1145-1151. [PMID: 30550639 DOI: 10.1111/1556-4029.13973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/04/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022]
Abstract
In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of "copies in" to "copies out" by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are "lost" prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following "fishing" for DNA, an alternative method for DNA enrichment.
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Affiliation(s)
- Misa Winters
- Department of Anthropology, Washington State University, Pullman, WA, 99164-4236.,School of Biological Sciences, Washington State University, Pullman, WA, 99164-4910
| | - Cara Monroe
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, 73019.,Department of Anthropology, University of Oklahoma, Norman, OK, 73019
| | - Jodi Lynn Barta
- Department of Forensic Science, Madonna University, Livonia, MI, 48150
| | - Brian M Kemp
- Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK, 73019.,Department of Anthropology, University of Oklahoma, Norman, OK, 73019
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Porter BW, Venkatappa TK. Uncloaking an ancient adversary: Can pathogen biomarker elicitors play a role in confirming extrapulmonary TB and latent TB infection? Tuberculosis (Edinb) 2018; 113:30-37. [PMID: 30514511 DOI: 10.1016/j.tube.2018.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/07/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
Latent tuberculosis infection (LTBI) is diagnosed immunologically using the Mantoux tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). While widely used, immunodiagnostics can produce false negative or false positive results. Pathogen biomarkers provide an alternative, but direct detection in LTBI and extrapulmonary TB cases is challenging. Mycobacterium tuberculosis grows slowly, has limited hematogenous movement, is protected by a lipid rich cell wall, and produces low levels of secreted factors. Here we discuss the potential of elicitors by first considering pathogen markers that may be released following the administration of isoniazid. Isoniazid targets the cell wall of mycobacteria found in extracellular compartments and within monocytes, macrophages, dendritic cells, and lymphatic endothelial cells. Isoniazid's dual-purpose potential as an antibiotic and elicitor is supported by knowledge of latent infection dynamics, time-kill kinetics, and new detection techniques. Within hours, the bactericidal action of isoniazid likely enriches plasma with M. tuberculosis DNA, RNA, proteins/peptides, and lipids. Undoubtedly a portion of these biomarkers are eliminated as some bacilli undergo phagocytosis and lysosomal destruction. However, advances in immunoprecipitation and nucleic acid amplification, combined with the use of larger blood volumes during assay development, may overcome these losses. Other anticipated challenges include determining optimal sample collection times and designing diagnostic workflows that minimize processing-associated marker loss and degradation. Conventional, commercial, and emerging technologies that address these variables are discussed. If realized, isoniazid associated markers could provide proof of concept for novel elicitor-based diagnostic approaches capable of confirming LTBI and empirically treated extrapulmonary TB.
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Affiliation(s)
- Brad W Porter
- Independent Researcher; P.O. Box 56224, Atlanta, GA 30343, USA.
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28
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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29
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Winters M, Torkelson A, Booth R, Mailand C, Hoareau Y, Tucker S, Wasser S. Isolation of DNA from small amounts of elephant ivory: Sampling the cementum with total demineralization extraction. Forensic Sci Int 2018; 288:131-139. [DOI: 10.1016/j.forsciint.2018.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/11/2022]
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30
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Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Sci Rep 2018; 8:9822. [PMID: 29959351 PMCID: PMC6026117 DOI: 10.1038/s41598-018-28091-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/14/2018] [Indexed: 12/11/2022] Open
Abstract
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
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Carøe C, Gopalakrishnan S, Vinner L, Mak SST, Sinding MHS, Samaniego JA, Wales N, Sicheritz‐Pontén T, Gilbert MTP. Single‐tube library preparation for degraded
DNA. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12871] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Carøe
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Department of Bio and Health InformaticsCenter for Biological Sequence AnalysisTechnical University of Denmark Lyngby Denmark
| | | | - Lasse Vinner
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Sarah S. T. Mak
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Mikkel Holger S. Sinding
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Natural History MuseumUniversity of Oslo Blindern Oslo Norway
| | - José A. Samaniego
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Nathan Wales
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Thomas Sicheritz‐Pontén
- Department of Bio and Health InformaticsCenter for Biological Sequence AnalysisTechnical University of Denmark Lyngby Denmark
| | - M. Thomas P. Gilbert
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Trace and Environmental DNA LaboratoryDepartment of Environment and AgricultureCurtin University Perth WA Australia
- NTNU University Museum Trondheim Norway
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Emmons AL, DeBruyn JM, Mundorff AZ, Cobaugh KL, Cabana GS. The persistence of human DNA in soil following surface decomposition. Sci Justice 2017; 57:341-348. [PMID: 28889863 DOI: 10.1016/j.scijus.2017.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/06/2017] [Accepted: 05/12/2017] [Indexed: 02/07/2023]
Abstract
Though recent decades have seen a marked increase in research concerning the impact of human decomposition on the grave soil environment, the fate of human DNA in grave soil has been relatively understudied. With the purpose of supplementing the growing body of literature in forensic soil taphonomy, this study assessed the relative persistence of human DNA in soil over the course of decomposition. Endpoint PCR was used to assess the presence or absence of human nuclear and mitochondrial DNA, while qPCR was used to evaluate the quantity of human DNA recovered from the soil beneath four cadavers at the University of Tennessee's Anthropology Research Facility (ARF). Human nuclear DNA from the soil was largely unrecoverable, while human mitochondrial DNA was detectable in the soil throughout all decomposition stages. Mitochondrial DNA copy abundances were not significantly different between decomposition stages and were not significantly correlated to soil edaphic parameters tested. There was, however, a significant positive correlation between mitochondrial DNA copy abundances and the human associated bacteria, Bacteroides, as estimated by 16S rRNA gene abundances. These results show that human mitochondrial DNA can persist in grave soil and be consistently detected throughout decomposition.
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Affiliation(s)
- Alexandra L Emmons
- Dept. of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996-0720, United States.
| | - Jennifer M DeBruyn
- Dept. of Biosystems Engineering and Soil Science, University of Tennessee, 2506 E.J. Chapman Drive, Knoxville, TN 37996-4531, United States.
| | - Amy Z Mundorff
- Dept. of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996-0720, United States.
| | - Kelly L Cobaugh
- Dept. of Biosystems Engineering and Soil Science, University of Tennessee, 2506 E.J. Chapman Drive, Knoxville, TN 37996-4531, United States.
| | - Graciela S Cabana
- Dept. of Anthropology, University of Tennessee, 250 South Stadium Hall, Knoxville, TN 37996-0720, United States.
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Are we fishing or catching? Evaluating the efficiency of bait capture of CODIS fragments. Forensic Sci Int Genet 2017; 29:61-70. [PMID: 28371667 DOI: 10.1016/j.fsigen.2017.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 01/09/2017] [Accepted: 03/02/2017] [Indexed: 11/21/2022]
Abstract
This study sought to document the efficiency of DNA bait capture (i.e., "fishing") methods by two measures: (1) its ability to retain targeted DNA molecules, and (2) its ability to remove non-target DNA molecules from a pool containing both. DNA bait capture uses synthetic biotinylated DNA primers to bind target DNA, which are then immobilized onto streptavidin coated magnetic beads and drawn to a magnet. Bound DNA should, therefore, be isolated from non-target DNA and impurities (e.g., PCR inhibitors) and can be later eluted from the beads for downstream applications. Efficiencies were estimated by comparing the number of "copies in" to "copies out" with quantitative polymerase chain reaction (qPCR). Retention of target DNA molecules, ranging from 109 to 288 base pairs (bps) in length, averaged just 9.06-3.53% (i.e., loss of 90.94-96.47%) using the fishing protocol as originally described. Some improvement was achieved by employing a modified protocol (i.e., with a shortened hybridization time, use of twice the amount of M-270 streptavidin-coated beads, and modified bead washing), resulting in average retention of 31.41-12.08% of the same set of targeted molecules. Noted was the lack of efficacy in removing non-target DNA molecules as opposed to targeted molecules. It was also observed that most of the molecules (61.35-69.49%) are "lost" during the essential hybridization step of the fishing protocol, suggesting its suitability for high copy number samples only. While the bait capture method may be useful in the study of polymerase chain reaction (PCR) inhibited DNA samples as previously suggested, it is necessary to carefully weigh this possible advantage against the degree of expected DNA loss and the non-selectivity of the method for targeted over non-targeted DNA.
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34
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Farid AH, Rupasinghe PP. A fast and accurate method of detecting Aleutian mink disease virus in blood and tissues of chronically infected mink. Can J Microbiol 2017; 63:341-349. [PMID: 28177788 DOI: 10.1139/cjm-2016-0567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The objective of this study was to assess the sensitivity of the Omni Klentaq-LA DNA polymerase for detecting Aleutian mink disease virus (AMDV) in mink blood and tissues by PCR without DNA extraction. The presence of AMDV DNA was directly tested by Klentaq in the plasma, serum, whole blood, and spleen homogenates of 188 mink 4 and 16 months after inoculation with the virus. Samples from bone marrow, small intestine, liver, lungs, kidneys, and lymph nodes of 20 of the same mink were also tested by Klentaq. DNA was extracted from paired samples of plasma and the aforesaid tissues by a commercial nucleic acid extraction kit (Dynabeads Silane) and tested by PCR. Compared with the extracted DNA, Klentaq detected a significantly greater number of samples in the whole blood, serum, plasma, spleen, and small intestine. It was concluded that Klentaq is a preferred system for directly detecting AMDV DNA in mink blood and tissues. The lower success rate of extracted DNA compared with Klentaq could be the result of DNA losses during the extraction process. This is an important factor in chronically infected mink, which have a low AMDV copy number in the bloodstream. Direct AMDV detection also reduces the cost of PCR amplification and lowers the risk of sample contamination.
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Affiliation(s)
- A H Farid
- Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada.,Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada
| | - P P Rupasinghe
- Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada.,Department of Animal Science and Aquaculture, Dalhousie University Faculty of Agriculture, Truro, NS B2N 5E3, Canada
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