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Gaeta R. Ancient DNA and paleogenetics: risks and potentiality. Pathologica 2021; 113:141-146. [PMID: 34042097 PMCID: PMC8167392 DOI: 10.32074/1591-951x-146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 06/19/2020] [Indexed: 11/30/2022] Open
Abstract
Paleopathology, the science that studies the diseases of the past, has always been addressed to the future in the use of new diagnostic methods. One of its relatively recent branches is paleogenetics, which is the study of genetic material from the past. Nuclear and mitochondrial DNA recovered from archaeological and paleontological specimens is called ancient DNA (aDNA), which can be extracted from a large variety of biological materials, of different origin, state of preservation and age, such as bones, teeth, coprolites, mummified tissues and hairs. There are many applications for ancient DNA research in the field of archaeology and paleopathology: population demography, genealogy, disease studies, archaeological reconstruction of plant vegetation, calibration of the molecular clock, phylogenetic relationship between different mammals and interpretation of the paleoclimate. However, the study of ancient genetic material is extremely difficult due to its poor quality and quantity, as well possible contamination with modern DNA. New advanced methods will allow extracting DNA from a greater variety of materials, and improvements in sequencing techniques will unveil data that are currently concealed. The aim of this paper is to provide initial insights into paleogenetics and ancient DNA study and to illustrate the limits, risks and potentiality of the research on the genetic material of ancient specimens, whose results have a strong impact on the present and future medicine.
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Affiliation(s)
- Raffaele Gaeta
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Italy
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2
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Serrage HJ, Joanisse S, Cooper PR, Palin W, Hadis M, Darch O, Philp A, Milward MR. Differential responses of myoblasts and myotubes to photobiomodulation are associated with mitochondrial number. JOURNAL OF BIOPHOTONICS 2019; 12:e201800411. [PMID: 30701682 PMCID: PMC7065641 DOI: 10.1002/jbio.201800411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/22/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Photobiomodulation (PBM) is the application of light to promote tissue healing. Current indications suggest PBM induces its beneficial effects in vivo through upregulation of mitochondrial activity. However, how mitochondrial content influences such PBM responses have yet to be evaluated. Hence, the current study assessed the biological response of cells to PBM with varying mitochondrial contents. METHODS DNA was isolated from myoblasts and myotubes (differentiated myoblasts), and mitochondrial DNA (mtDNA) was amplified and quantified using a microplate assay. Cells were seeded in 96-wellplates, incubated overnight and subsequently irradiated using a light-emitting diode array (400, 450, 525, 660, 740, 810, 830 and white light, 24 mW/cm2 , 30-240 seconds, 0.72-5.76J/cm2 ). The effects of PBM on markers of mitochondrial activity including reactive-oxygen-species and real-time mitochondrial respiration (Seahorse XFe96) assays were assessed 8 hours post-irradiation. Datasets were analysed using general linear model followed by one-way analysis of variance (and post hoc-Tukey tests); P = 0.05). RESULTS Myotubes exhibited mtDNA levels 86% greater than myoblasts (P < 0.001). Irradiation of myotubes at 400, 450 or 810 nm induced 53%, 29% and 47% increases (relative to non-irradiated control) in maximal respiratory rates, respectively (P < 0.001). Conversely, irradiation of myoblasts at 400 or 450 nm had no significant effect on maximal respiratory rates. CONCLUSION This study suggests that mitochondrial content may influence cellular responses to PBM and as such explain the variability of PBM responses seen in the literature.
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Affiliation(s)
- Hannah J. Serrage
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- Philips ResearchEindhovenThe Netherlands
| | - Sophie Joanisse
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
| | - Paul R. Cooper
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
| | - William Palin
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
| | - Mohammed Hadis
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
| | - Owen Darch
- Philips ResearchEindhovenThe Netherlands
| | - Andrew Philp
- School of Sport, Exercise and Rehabilitation SciencesUniversity of BirminghamBirminghamUK
- Garvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - Mike R. Milward
- School of DentistryCollege of Medical and Dental Sciences, Institute of Clinical Sciences, University of BirminghamBirminghamUK
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Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas. Sci Rep 2018; 8:6551. [PMID: 29695730 PMCID: PMC5917027 DOI: 10.1038/s41598-018-24497-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/03/2018] [Indexed: 12/12/2022] Open
Abstract
Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
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Caldararo N. Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept. J Mol Evol 2016; 83:78-87. [DOI: 10.1007/s00239-016-9755-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
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Lyons LA, Grahn RA, Kun TJ, Netzel LR, Wictum EE, Halverson JL. Acceptance of domestic cat mitochondrial DNA in a criminal proceeding. Forensic Sci Int Genet 2014; 13:61-7. [PMID: 25086413 DOI: 10.1016/j.fsigen.2014.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/20/2014] [Accepted: 07/07/2014] [Indexed: 02/06/2023]
Abstract
Shed hair from domestic animals readily adheres to clothing and other contact items, providing a source of transfer evidence for criminal investigations. Mitochondrial DNA is often the only option for DNA analysis of shed hair. Human mitochondrial DNA analysis has been accepted in the US court system since 1996. The murder trial of the State of Missouri versus Henry L. Polk, Jr. represents the first legal proceeding where cat mitochondrial DNA analysis was introduced into evidence. The mitochondrial DNA evidence was initially considered inadmissible due to concerns about the cat dataset and the scientific acceptance of the marker. Those concerns were subsequently addressed, and the evidence was deemed admissible. This report reviews the case in regards to the cat biological evidence and its ultimate admission as generally accepted and reliable. Expansion and saturation analysis of the cat mitochondrial DNA control region dataset supported the initial interpretation of the evidence.
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Affiliation(s)
- Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States.
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States; Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Teri J Kun
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Linda R Netzel
- Kansas City Police Crime Laboratory, 6633 Troost Avenue, Kansas City, MO 64131, United States
| | - Elizabeth E Wictum
- Forensics Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Joy L Halverson
- Zoogen Services, 1046 Olive Drive Suite 1, Davis, CA 95616, United States
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Theyab JB, Al-Bustan S, Crawford MH. The genetic structure of the Kuwaiti population: mtDNA Inter- and intra-population variation. Hum Biol 2013; 84:379-403. [PMID: 23249314 DOI: 10.3378/027.084.0403] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This study investigated: (1) the mitochondrial DNA (mtDNA) genetic variation in 116 unrelated individuals who originated from the Arabian Peninsula, Iran, or were of Bedouin ethnicity and (2) the genetic structure of Kuwaiti populations and compared it to their neighboring populations. These subpopulations were tested for genetic homogeneity and shown to be heterogeneous. Restriction fragment length polymorphism (RFLP) and mtDNA sequencing analyses of HVRI were used to reconstruct the genetic structure of Kuwait. The results indicated that the combined Kuwaiti population has a high frequency of haplogroup R0 (17%), J (12%), and U (12%) similar to other Arabian populations. In addition, contemporary African gene flow was detected through the presence of sub-haplogroup L (L1 and L2) (2%) and the absence of L3 which is reflective of an earlier migration. Furthermore, the multidimensional scaling (MDS) plot showed that the Kuwaiti population clusters with neighboring populations, including Iran and Saudi Arabia indicating gene flow into Kuwait. According to this study, the Kuwaiti population may be undergoing an expansion in a relatively short period of time, and the maternal genetic structure of Kuwait resembles both Saudi Arabia and Iran.
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Affiliation(s)
- Jasem B Theyab
- Department of Anthropology, University of Kansas, Lawrence, KS 66045, USA.
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Bandelt HJ, Kloss-Brandstätter A, Richards MB, Yao YG, Logan I. The case for the continuing use of the revised Cambridge Reference Sequence (rCRS) and the standardization of notation in human mitochondrial DNA studies. J Hum Genet 2013; 59:66-77. [PMID: 24304692 DOI: 10.1038/jhg.2013.120] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 09/29/2013] [Accepted: 10/25/2013] [Indexed: 02/06/2023]
Abstract
Since the determination in 1981 of the sequence of the human mitochondrial DNA (mtDNA) genome, the Cambridge Reference Sequence (CRS), has been used as the reference sequence to annotate mtDNA in molecular anthropology, forensic science and medical genetics. The CRS was eventually upgraded to the revised version (rCRS) in 1999. This reference sequence is a convenient device for recording mtDNA variation, although it has often been misunderstood as a wild-type (WT) or consensus sequence by medical geneticists. Recently, there has been a proposal to replace the rCRS with the so-called Reconstructed Sapiens Reference Sequence (RSRS). Even if it had been estimated accurately, the RSRS would be a cumbersome substitute for the rCRS, as the new proposal fuses--and thus confuses--the two distinct concepts of ancestral lineage and reference point for human mtDNA. Instead, we prefer to maintain the rCRS and to report mtDNA profiles by employing the hitherto predominant circumfix style. Tree diagrams could display mutations by using either the profile notation (in conventional short forms where appropriate) or in a root-upwards way with two suffixes indicating ancestral and derived nucleotides. This would guard against misunderstandings about reporting mtDNA variation. It is therefore neither necessary nor sensible to change the present reference sequence, the rCRS, in any way. The proposed switch to RSRS would inevitably lead to notational chaos, mistakes and misinterpretations.
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Affiliation(s)
| | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
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Kim HL, Schuster SC. Poor Man's 1000 Genome Project: Recent Human Population Expansion Confounds the Detection of Disease Alleles in 7,098 Complete Mitochondrial Genomes. Front Genet 2013; 4:13. [PMID: 23450075 PMCID: PMC3584485 DOI: 10.3389/fgene.2013.00013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/28/2013] [Indexed: 01/29/2023] Open
Abstract
Rapid growth of the human population has caused the accumulation of rare genetic variants that may play a role in the origin of genetic diseases. However, it is challenging to identify those rare variants responsible for specific diseases without genetic data from an extraordinarily large population sample. Here we focused on the accumulated data from the human mitochondrial (mt) genome sequences because this data provided 7,098 whole genomes for analysis. In this dataset we identified 6,110 single nucleotide variants (SNVs) and their frequency and determined that the best-fit demographic model for the 7,098 genomes included severe population bottlenecks and exponential expansions of the non-African population. Using this model, we simulated the evolution of mt genomes in order to ascertain the behavior of deleterious mutations. We found that such deleterious mutations barely survived during population expansion. We derived the threshold frequency of a deleterious mutation in separate African, Asian, and European populations and used it to identify pathogenic mutations in our dataset. Although threshold frequency was very low, the proportion of variants showing a lower frequency than that threshold was 82, 83, and 91% of the total variants for the African, Asian, and European populations, respectively. Within these variants, only 18 known pathogenic mutations were detected in the 7,098 genomes. This result showed the difficulty of detecting a pathogenic mutation within an abundance of rare variants in the human population, even with a large number of genomes available for study.
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Affiliation(s)
- Hie Lim Kim
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University University Park, PA, USA
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9
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Carter RW, Sanford JC. A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918. Theor Biol Med Model 2012; 9:42. [PMID: 23062055 PMCID: PMC3507676 DOI: 10.1186/1742-4682-9-42] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/04/2012] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The H1N1 influenza A virus has been circulating in the human population for over 95 years, first manifesting itself in the pandemic of 1917-1918. Initial mortality was extremely high, but dropped exponentially over time. Influenza viruses have high mutation rates, and H1N1 has undergone significant genetic changes since 1918. The exact nature of H1N1 mutation accumulation over time has not been fully explored. METHODS We have made a comprehensive historical analysis of mutational changes within H1N1 by examining over 4100 fully-sequenced H1N1 genomes. This has allowed us to examine the genetic changes arising within H1N1 from 1918 to the present. RESULTS We document multiple extinction events, including the previously known extinction of the human H1N1 lineage in the 1950s, and an apparent second extinction of the human H1N1 lineage in 2009. These extinctions appear to be due to a continuous accumulation of mutations. At the time of its disappearance in 2009, the human H1N1 lineage had accumulated over 1400 point mutations (more than 10% of the genome), including approximately 330 non-synonymous changes (7.4% of all codons). The accumulation of both point mutations and non-synonymous amino acid changes occurred at constant rates (μ = 14.4 and 2.4 new mutations/year, respectively), and mutations accumulated uniformly across the entire influenza genome. We observed a continuous erosion over time of codon-specificity in H1N1, including a shift away from host (human, swine, and bird [duck]) codon preference patterns. CONCLUSIONS While there have been numerous adaptations within the H1N1 genome, most of the genetic changes we document here appear to be non-adaptive, and much of the change appears to be degenerative. We suggest H1N1 has been undergoing natural genetic attenuation, and that significant attenuation may even occur during a single pandemic. This process may play a role in natural pandemic cessation and has apparently contributed to the exponential decline in mortality rates over time, as seen in all major human influenza strains. These findings may be relevant to the development of strategies for managing influenza pandemics and strain evolution.
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Posthuma-Trumpie GA, Wichers JH, Koets M, Berendsen LBJM, van Amerongen A. Amorphous carbon nanoparticles: a versatile label for rapid diagnostic (immuno)assays. Anal Bioanal Chem 2012; 402:593-600. [PMID: 21904801 PMCID: PMC3249172 DOI: 10.1007/s00216-011-5340-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 08/13/2011] [Accepted: 08/15/2011] [Indexed: 12/16/2022]
Abstract
Carbon nanoparticles (CNPs) labeled with reporter molecules can serve as signaling labels in rapid diagnostic assays as an alternative to gold, colored latex, silica, quantum dots, or up-converting phosphor nanoparticles. Detailed here is the preparation of biomolecule-labeled CNPs and examples of their use as a versatile label. CNPs can be loaded with a range of biomolecules, such as DNA, antibodies, and proteins (e.g., neutravidin or a fusion protein of neutravidin with an enzyme), and the resulting conjugates can be used to detect analytes of high or low molecular mass.
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Affiliation(s)
| | - Jan H. Wichers
- Food and Biobased Research, Wageningen University and Research Centre, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Marjo Koets
- Food and Biobased Research, Wageningen University and Research Centre, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Luciënne B. J. M. Berendsen
- Food and Biobased Research, Wageningen University and Research Centre, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Aart van Amerongen
- Food and Biobased Research, Wageningen University and Research Centre, P.O. Box 17, 6700 AA Wageningen, The Netherlands
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Mitochondrial genetic background plays a role in increasing risk to asthma. Mol Biol Rep 2011; 39:4697-708. [PMID: 21947849 DOI: 10.1007/s11033-011-1262-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
A number of studies suggest that mitochondrial dysfunction plays a role in the pathogenesis of asthma. To shed light for the first time on the role of the mitochondrial genome in the etiology of asthma we analyzed the mitochondrial tRNA genes and part of their flanking regions in patients with asthma compared with a set of healthy controls. We found a total of 10 mutations in 56 out of 76 asthmatic patients. Four of these mutations were not found in the control group, five were observed at a significantly lower frequency in controls, but none of the combinations of mutations detected in asthma patients was observed in the controls. Furthermore, we observed that 27.6% of the asthma patients (vs. 4% of the controls) belonged to the haplogroup U (Fisher test P = 0.00) and a positive significant correlation was found between the occurrence of the haplogroup U and the severity of the disease (Fisher test P = 0.02). Whereas further studies in larger cohorts are needed to confirm these observations we suggest that the mitochondrial genetic background plays a key role in asthma development.
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Pardiñas AF, Dopico E, Roca A, Garcia-Vazquez E, Lopez B. Introducing human population biology through an easy laboratory exercise on mitochondrial DNA. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2010; 38:110-115. [PMID: 21567805 DOI: 10.1002/bmb.20365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This article describes an easy and cheap laboratory exercise for students to discover their own mitochondrial haplogroup. Students use buccal swabs to obtain mucosa cells as noninvasive tissue samples, extract DNA, and with a simple polymerase chain reaction-restriction fragment length polymorphism analysis they can obtain DNA fragments of different sizes that can be visualized in agarose gels. The analysis of these fragments can reveal the mitochondrial haplogroup of each student. The results of the exercise can be used to provide additional insights into the genetic variation of human populations.
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Affiliation(s)
- Antonio F Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
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Webb K, Allard M. Assessment of minimum sample sizes required to adequately represent diversity reveals inadequacies in datasets of domestic dog mitochondrial DNA. ACTA ACUST UNITED AC 2010; 21:19-31. [DOI: 10.3109/19401730903532044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Lateral flow (immuno)assay: its strengths, weaknesses, opportunities and threats. A literature survey. Anal Bioanal Chem 2008; 393:569-82. [PMID: 18696055 DOI: 10.1007/s00216-008-2287-2] [Citation(s) in RCA: 941] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/01/2008] [Accepted: 07/03/2008] [Indexed: 10/21/2022]
Abstract
Lateral flow (immuno)assays are currently used for qualitative, semiquantitative and to some extent quantitative monitoring in resource-poor or non-laboratory environments. Applications include tests on pathogens, drugs, hormones and metabolites in biomedical, phytosanitary, veterinary, feed/food and environmental settings. We describe principles of current formats, applications, limitations and perspectives for quantitative monitoring. We illustrate the potentials and limitations of analysis with lateral flow (immuno)assays using a literature survey and a SWOT analysis (acronym for "strengths, weaknesses, opportunities, threats"). Articles referred to in this survey were searched for on MEDLINE, Scopus and in references of reviewed papers. Search terms included "immunochromatography", "sol particle immunoassay", "lateral flow immunoassay" and "dipstick assay".
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Yan CX, Chen F, Dang YH, Li T, Zheng HB, Chen T, Li SB. [Sequence polymorphism of mtDNA HVR Iand HVR II of Oroqen ethnic group in Inner Mongolia]. YI CHUAN = HEREDITAS 2008; 30:439-47. [PMID: 18424414 DOI: 10.3724/sp.j.1005.2008.00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Venous blood samples from 50 unrelated Oroqen individuals living in Inner Mongolia were collected and their mtDNA HVR I and HVR II sequences were detected by using ABI PRISM377 sequencers. The number of polymorphic loci, haplotype, haplotype frequence, average nucleotide variability and other polymorphic parameters were calculated. Based on Oroqen mtDNA sequence data obtained in our experiments and published data, genetic distance between Oroqen ethnic group and other populations were computered by Nei's measure. Phylogenetic tree was constructed by Neighbor Joining method. Comparing with Anderson sequence, 52 polymorphic loci in HVR I and 24 loci in HVR II were found in Oroqen mtDNA sequence, 38 and 27 haplotypes were defined herewith. Haplotype diversity and average nucleotide variability were 0.964+/-0.018 and 7.379 in HVR I, 0.929+/-0.019 and 2.408 in HVR II respectively. Fst and dA genetic distance between 12 populations were calculated based on HVR I sequence, and their relative coefficients were 0.993(P < 0.01). A phylogenetic tree was constructed based on genetic distances and included Oroqen, Taiwan and South Han population in a clade, which indicated near genetic relation between them, and far relation with northern Han, Mongolian and other foreign populations. The genetic polymorphism of mtDNA HVR I and HVR II in Oroqen ethnic group has some specificities compared with that of other populations. These data provide a useful tool in forensic identification, population genetic study and other research fields.
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Affiliation(s)
- Chun-Xia Yan
- Department of Forensic Sciences, Key Laboratory of the Health Ministry for Forensic Sciences, Xi'an Jiaotong University School of Medicire, Xi'an 710061, China.
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