Isolation of Mitochondrial DNA from Single, Short Hairs without Roots Using Pressure Cycling Technology

Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT extracts exceeded the requirements for forensic analysis, with the DNA quality confirmed through sequencing. Automated extraction of mtDNA from hairs without roots using PCT could be useful for forensic laboratories processing numerous samples.

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Genetic variability of farmed fur animals of the Canidae family assessed by nuclear and mitochondrial DNA analysis

Medycyna Weterynaryjna ◽

10.21521/mw.5544 ◽

2016 ◽

Vol 72 (8) ◽

pp. 505-510 ◽

Cited By ~ 1

Author(s):

Sylwia Nisztuk-Pacek

Keyword(s):

Mitochondrial Dna ◽

Dna Analysis ◽

Nuclear Dna ◽

Mitochondrial Gene ◽

Genetic Material ◽

Cox1 Gene ◽

Phylogenetic Distance ◽

Raccoon Dog ◽

Study Results ◽

Fur Animals

The aim of the study was to assess the biodiversity of farmed fur animals from the Canidae family (common fox, polar fox, and raccoon dog) using nuclear and mitochondrial markers. The study involved 434 animals. The biological material included whole peripheral blood or skin tissue. The isolated genetic material was subjected to qualitative and quantitative analyses. Mitochondrial DNA (mtDNA) gene fragments (COX1, COX2, CYTB) and nuclear DNA (nDNA) gene fragments (MSTN1, MSTN2, MSTN3, IGF1, GHR) were amplified with the PCR (polymerase chain reaction) technique. The amplicons obtained were sequenced or subjected to PCR-RFLP (restriction fragment length polymorphism) reaction, and bioinformatics analyses were performed. The interspecific analysis of the nDNA sequences revealed a total of 25 polymorphisms. On the other hand, the interspecific analysis of the mtDNA gene fragments identified 277 polymorphisms. The COX1 gene fragment exhibited the greatest variability. It was shown that the frequency of polymorphisms within the mitochondrial genome was almost 20-fold higher than that in the nuclear genome of the raccoon dog. It was found that the genetic distances revealed by the analysis of the mitochondrial gene fragments were similar to the results obtained by the nDNA analysis. The genetic distance between the raccoon and common fox was the greatest. The smallest phylogenetic distance was revealed between the two fox species. The study results indicate mitochondrial and nuclear genes may be alternatively used for determining the phylogenetic relationships between fur animals from the Canidae family.

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Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases

Cells ◽

10.3390/cells8050433 ◽

2019 ◽

Vol 8 (5) ◽

pp. 433 ◽

Cited By ~ 3

Author(s):

Maxime Merheb ◽

Rachel Matar ◽

Rawad Hodeify ◽

Shoib Sarwar Siddiqui ◽

Cijo George Vazhappilly ◽

...

Keyword(s):

Mitochondrial Dna ◽

Dna Analysis ◽

Nuclear Dna ◽

Genetic Material ◽

Modern Science ◽

Criminal Cases ◽

Trade Routes ◽

Ancient Trade ◽

Degraded Samples ◽

Mtdna Sequence

Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.

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Genetic structure in Atlantic brown trout (Salmo truttaL.) populations in the Iberian peninsula: evidence from mitochondrial and nuclear DNA analysis

Journal of Animal Breeding and Genetics ◽

10.1046/j.1439-0388.2000.00240.x ◽

2000 ◽

Vol 117 (3) ◽

pp. 105-120 ◽

Cited By ~ 1

Author(s):

S. Dunner ◽

L. Royo ◽

J. Cañon

Keyword(s):

Genetic Structure ◽

Iberian Peninsula ◽

Brown Trout ◽

Dna Analysis ◽

Nuclear Dna

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Analysis of ancient DNA from a prehistoric Amerindian cemetery

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1999.0368 ◽

1999 ◽

Vol 354 (1379) ◽

pp. 153-159 ◽

Cited By ~ 41

Author(s):

Anne C. Stone ◽

Mark Stoneking

Keyword(s):

Ancient Dna ◽

Dna Analysis ◽

Nuclear Dna ◽

Genetic Research ◽

Hypervariable Region ◽

Dna Preservation ◽

European Contact ◽

Novel Method ◽

High Level ◽

Central Illinois

The Norris Farms No. 36 cemetery in central Illinois has been the subject of considerable archaeological and genetic research. Both mitochondrial DNA (mtDNA) and nuclear DNA have been examined in this 700–year–old population. DNA preservation at the site was good, with about 70% of the samples producing mtDNA results and approximately 15% yielding nuclear DNA data. All four of the major Amerindian mtDNA haplogroups were found, in addition to a fifth haplogroup. Sequences of the first hypervariable region of the mtDNA control region revealed a high level of diversity in the Norris Farms population and confirmed that the fifth haplogroup associates with Mongolian sequences and hence is probably authentic. Other than a possible reduction in the number of rare mtDNA lineages in many populations, it does not appear as if European contact significantly altered patterns of Amerindian mtDNA variation, despite the large decrease in population size that occurred. For nuclear DNA analysis, a novel method for DNA–based sex identification that uses nucleotide differences between the X and Y copies of the amelogenin gene was developed and applied successfully in approximately 20 individuals. Despite the well–known problems of poor DNA preservation and the ever–present possibility of contamination with modern DNA, genetic analysis of the Norris Farms No. 36 population demonstrates that ancient DNA can be a fruitful source of new insights into prehistoric populations.

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Isolation of serum nucleic acids for fetal DNA analysis: comparison of manual and automated extraction methods

Prenatal Diagnosis ◽

10.1002/pd.2154 ◽

2008 ◽

Vol 28 (13) ◽

pp. 1227-1231 ◽

Cited By ~ 7

Author(s):

Irina Banzola ◽

Inès Kaufmann ◽

Olav Lapaire ◽

Sinuhe Hahn ◽

Wolfgang Holzgreve ◽

...

Keyword(s):

Nucleic Acids ◽

Dna Analysis ◽

Extraction Methods ◽

Automated Extraction ◽

Fetal Dna

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Multiplexed Detection of COVID-19 with Single-Molecule Technology

10.1101/2021.05.25.21257501 ◽

2021 ◽

Author(s):

Noa Furth ◽

Shay Shilo ◽

Niv Cohen ◽

Nir Erez ◽

Vadim Fedyuk ◽

...

Keyword(s):

Immune Response ◽

Viral Infection ◽

Single Molecule ◽

Direct Detection ◽

Genetic Material ◽

Diagnostic Tools ◽

Proof Of Concept ◽

Multiplexed Detection ◽

Diagnostic Approaches ◽

Quantitative Nature

The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for multiplexed detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients' samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.

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Discordance between Mitochondrial and Nuclear DNA Genes Suggests the Possibility of Hybridization of Indian and Southeast Asian Types of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh

Indian Journal of Agricultural Research ◽

10.18805/ijare.a-540 ◽

2020 ◽

Author(s):

M. M. Rahman ◽

S. Hosoishi ◽

K. Ogata

Keyword(s):

Dna Analysis ◽

Nuclear Dna ◽

Nuclear Gene ◽

Southeast Asian ◽

Phylogenetic Study ◽

Tropical Islands ◽

Oecophylla Smaragdina ◽

Mtdna Sequences ◽

Mitochondrial Dna Analysis ◽

Shed Light

Background: Oecophylla smaragdina is distributed from India, SE Asia and Australia including many tropical Islands. A recent phylogenetic study based on mitochondrial DNA analysis reveals that Bangladesh is the overlapping zone of both Indian and Southeast Asian type of O. smaragdina. These two different lineages of Indian and SE Asian type have the opportunities of creating the zone of contacts, but no such data was found. In this study, shed light was given to reveal the chance of hybridized colony of O. smaragdina in Bangladesh. Methods: To asses the hybridization scenario, 28 O. smaragdina colony from 27 localities in Bangladesh were analyzed using Longwave length Rhodopsin (LWRh) nuclear gene sequences and was compared with the mtDNA sequences, which was collected from the same localities and deposited into NCBI GenBank. Results: The inconsistency between mitochondrial and nuclear gene types was observed from two colonies of the overlapped zone of contact. These two colonies were identified as SE Asian type by mtDNA analysis however, by nuclear DNA analysis; it was identified as Indian type. These significant discrepancies within the colony suggested the possibility of hybridization of weaver ant in Bangladesh.

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