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

2016 ◽  
Vol 72 (8) ◽  
pp. 505-510 ◽  
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.

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

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 433 ◽  
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.

Sensitive Detection of Soy (Glycine max) by Real-Time Polymerase Chain Reaction Targeting the Mitochondrial atpA Gene

2011 ◽  
Vol 94 (6) ◽  
pp. 1863-1873 ◽  
Author(s):  
Tobias Bauer ◽  
Katja Kirschbaum ◽  
Silvia Panter ◽  
Marion Kenk ◽  
Jörg Bergemann
Keyword(s):  
Mitochondrial Dna ◽  
Real Time ◽  
Nuclear Dna ◽  
Mitochondrial Gene ◽  
Soy Flour ◽  
Detection Methods ◽  
Minimal Amount ◽  
Food Matrix ◽  
Atpa Gene ◽  
Reporter Probe

Abstract Detection of trace amounts of allergens is essential for correct labeling of food products by the food industry. PCR-based detection methods currently used for this purpose are targeting sequences of DNA present in the cell nucleus. In addition to nuclear DNA, a substantial amount of mitochondrial DNA (mtDNA) copies are present in the cytoplasm of eukaryotic cells. The nuclear DNA usually consists of a set of DNA molecules present in two copies per cell, whereas mitochondrial DNA is present in a few hundred copies per cell. Thus, an increase in sensitivity can be expected when mtDNA is used as the target. In this study, we present a reporter probe-based real-time PCR method amplifying the mitochondrial gene of the alpha chain of adenosine triphosphate synthetase from soy. Increase in sensitivity was examined by determining the minimal amount of soy DNA detectable by mtDNA and nuclear DNA (nDNA) amplification. Additionally, the LOD of soy in a food matrix was determined for mtDNA amplification and compared to the LOD determined by nDNA amplification. As food matrix, a model spice spiked with soy flour was used. Sensitivity of PCR-based soy detection can be increased by using mtDNA as the target.

scholarly journals THE DISTRIBUTION OF DNA AMONG DIVIDING MITOCHONDRIA OF TETRAHYMENA PYRIFORMIS

1968 ◽  
Vol 37 (3) ◽  
pp. 683-693 ◽  
Author(s):  
John A. Parsons ◽  
Ronald C. Rustad
Keyword(s):  
Mitochondrial Dna ◽  
Dna Synthesis ◽  
Genetic Information ◽  
Nuclear Dna ◽  
De Novo ◽  
Genetic Material ◽  
Tetrahymena Pyriformis ◽  
Population Doubling ◽  
Population Doubling Time ◽  
The Stability

A squash technique was developed for log phase Tetrahymena pyriformis which permitted the resolution of over 100 individual mitochondria from a single cell. Mitochondria incorporated thymidine at all stages of the cell cycle, even when nuclear DNA synthesis was not occurring. During the stage of macronuclear DNA synthesis, however, there was a significant increase in the extent of mitochondrial labeling. Low radioautograph background suggests that mitochondrial DNA is synthesized at the mitochondria themselves. All mitochondria incorporated thymidine-3H within one population-doubling time. Grain counts also showed that the amount of mitochondrial label was retained for four generations and that this label remained randomly distributed among all mitochondria during this time. The results are not consistent with any theory of de-novo or "microbody" origin of mitochondria, but do support the hypothesis that mitochondria are produced by the growth and division of preexisting mitochondria. The stability of the mitochondrial DNA and its distribution among daughter mitochondria satisfy two prerequisites for a genetic material. The possibility is discussed that some of the genetic information for the mitochondrion is contained in the DNA associated with this organelle.

scholarly journals Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)

ZooKeys ◽  
2018 ◽  
Vol 763 ◽  
pp. 1-111 ◽  
Author(s):  
Tricia C. Goulding ◽  
Munawar Khalil ◽  
Shau Hwai Tan ◽  
Benoît Dayrat
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Comparative Anatomy ◽  
Morphological Characters ◽  
Integrative Taxonomy ◽  
The Philippines ◽  
Coral Triangle ◽  
Yellow Orange

A new genus of onchidiid slugs,WallaconchisGoulding & Dayrat,gen. n., is described, including ten species. Five species were previously described but known only from the type material:Wallaconchisater(Lesson, 1830),W.graniferum(Semper, 1880),W.nangkauriense(Plate, 1893),W.buetschlii(Stantschinsky, 1907), andW.gracile(Stantschinsky, 1907), all of which were originally classified inOnchidiumBuchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new:WallaconchisachleitneriGoulding,sp. n.,W.comendadoriGoulding & Dayrat,sp. n.,W.melanesiensisGoulding & Dayrat,sp. n.,W.sinanuiGoulding & Dayrat,sp. n., andW.uncinusGoulding & Dayrat,sp. n.Nine of the tenWallaconchisspecies are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia).Wallaconchisis distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify allWallaconchisspecies. The copulatory organs ofWallaconchisspecies are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed,nomina dubiaare discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.

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

2017 ◽  
Vol 23 (1) ◽  
pp. 97-105 ◽  
Author(s):  
Kathryn A. Harper ◽  
Kelly A. Meiklejohn ◽  
Richard T. Merritt ◽  
Jessica Walker ◽  
Constance L. Fisher ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Nuclear Dna ◽  
Genetic Material ◽  
Forensic Analysis ◽  
Proof Of Concept ◽  
Automated Extraction ◽  
Pressure Cycling ◽  
Dna Quality ◽  
Pressure Cycling Technology ◽  
The Ideal

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.

Mitochondrial DNA damage as driver of cellular outcomes

2021 ◽  
Author(s):  
Cristina A Nadalutti ◽  
Sylvette Ayala-Peña ◽  
Janine H. Santos
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Function ◽  
Blood Cells ◽  
Energy Production ◽  
Nuclear Dna ◽  
Genetic Material ◽  
Genetic Alterations ◽  
Mtdna Damage ◽  
Mitochondrial Dna Damage ◽  
Cellular Dysfunction

Mitochondria are primarily involved in energy production through the process of oxidative phosphorylation (OXPHOS). Increasing evidence has shown that mitochondrial function impacts a plethora of different cellular activities, including metabolism, epigenetics and innate immunity. Like the nucleus, mitochondria own their genetic material, which is maternally inherited. The mitochondrial DNA (mtDNA) encodes 37 genes that are solely involved in OXPHOS. Maintenance of mtDNA, through replication and repair, requires the import of nuclear DNA encoded proteins. Thus, mitochondria completely rely on the nucleus to prevent mitochondrial genetic alterations. As every cell contains hundreds to thousands of mitochondria, it follows that the shear number of organelles allow for the buffering of dysfunction - at least to some extent - before tissue homeostasis becomes impaired. Only red blood cells lack mitochondria entirely. Impaired mitochondrial function is a hallmark of aging and is involved in a number of different disorders, including neurodegenerative diseases, diabetes, cancer, and autoimmunity. While alterations in mitochondrial processes unrelated to OXPHOS, such as fusion and fission, contribute to aging and disease, maintenance of mtDNA integrity is critical for proper organellar function. Here, we focus on how mtDNA damage contributes to cellular dysfunction and health outcomes.

scholarly journals Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity

2020 ◽  
Vol 21 (5) ◽  
pp. 1838 ◽  
Author(s):  
Giovanna C. Cavalcante ◽  
Leandro Magalhães ◽  
Ândrea Ribeiro-dos-Santos ◽  
Amanda F. Vidal
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
State Of The Art ◽  
Genetic Material ◽  
Future Perspectives ◽  
Epigenetic Factors ◽  
Mitochondrial Functions ◽  
Non Coding Rnas ◽  
Cellular Pathways

Mitochondria are organelles responsible for several functions involved in cellular balance, including energy generation and apoptosis. For decades now, it has been well-known that mitochondria have their own genetic material (mitochondrial DNA), which is different from nuclear DNA in many ways. More recently, studies indicated that, much like nuclear DNA, mitochondrial DNA is regulated by epigenetic factors, particularly DNA methylation and non-coding RNAs (ncRNAs). This field is now called mitoepigenetics. Additionally, it has also been established that nucleus and mitochondria are constantly communicating to each other to regulate different cellular pathways. However, little is known about the mechanisms underlying mitoepigenetics and nuclei–mitochondria communication, and also about the involvement of the ncRNAs in mitochondrial functions and related diseases. In this context, this review presents the state-of-the-art knowledge, focusing on ncRNAs as new players in mitoepigenetic regulation and discussing future perspectives of these fields.

scholarly journals Fragmented Nuclear DNA is the Predominant Genetic Material in Human Hair Shafts

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 640 ◽  
Author(s):  
Michael D. Brandhagen ◽  
Odile Loreille ◽  
Jodi A. Irwin
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Genetic Material ◽  
Total Content ◽  
Hair Shaft ◽  
Mitochondrial Dna Content ◽  
Hair Samples ◽  
Evidence Type ◽  
Dna Profiles ◽  
Hair Shafts

While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations.

scholarly journals Changes in circulating cell-free nuclear DNA and mitochondrial DNA of patients with adolescent idiopathic scoliosis

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiong Li ◽  
Longjie Wang ◽  
Guanteng Yang ◽  
Yunjia Wang ◽  
Chaofeng Guo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Adolescent Idiopathic Scoliosis ◽  
Idiopathic Scoliosis ◽  
Sensitivity And Specificity ◽  
Dna Analysis ◽  
Nuclear Dna ◽  
Predictive Accuracy ◽  
Lower Sensitivity ◽  
Mt Dna ◽  
Potential Biomarker

Abstract Background Adolescent idiopathic scoliosis (AIS) which characterized by complex three-dimensional deformity of spine has been difficult to cure because of the unknown etiopathology and uncertainty of progression. Nowadays, circulating cell-free (ccf) DNA was found to be a potential biomarker for several benign and malignant diseases. However, whether ccf DNA can be a biomarker for AIS has not been reported yet. In this study, we investigate the circulating cell-free nuclear DNA (ccf n-DNA) and mitochondrial DNA (ccf mt-DNA) concentrations in the plasma of patients with AIS and controls (CT), and the changed plasma ccf n-DNA and ccf mt-DNA levels and their association with clinical parameters were assessed. Methods The plasma of peripheral blood from 69 AIS patients and 21 age-matched CT was collected for ccf DNA analysis. Quantitative PCR was used to detect ccf n-DNA and ccf mt-DNA levels, and correlation analyses between the ccf n-DNA and ccf mt-DNA levels and clinical characteristics were conducted. Receiver operator curves (ROC) were used to analyze the sensitivity and specificity of ccf n-DNA and ccf mt-DNA levels to different characteristics. Results The plasma ccf n-DNA levels of both GAPDH and ACTB were significantly decreased in AIS patients compared with those in controls, while the plasma ccf mt-DNA levels did not changed. According to sex-related analyses, the ccf n-DNA levels in male CT-M was higher than that in female CT and male AIS, but the ccf n-DNA levels in female AIS was not significantly changed when compared with male AIS or female CT. However, the concentration of ccf mt-DNA in female AIS increased significantly when compared with male AIS. Surprisingly, Lenke type-related analyses suggested that Lenke type 1 patients had lower ccf n-DNA levels, whereas Lenke type 5 patients had higher ccf mt-DNA levels compared with those of controls. However, a lower sensitivity and specificity of AIS predicted by ccf n-DNA or ccf mt-DNA levels was observed, whether in total, by sex, or by Lenke type. Conclusion Although with no/little predictive accuracy of AIS/progressed AIS by ccf DNA levels, significantly changed plasma ccf DNA levels were observed in AIS patients compared with those in controls.

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