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The Human Mitochondrial Genome

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The Human Mitochondrial Genome

The Human Mitochondrial Genome Book
Author : Giuseppe Gasparre,Anna Maria Porcelli
Publisher : Academic Press
Release : 2020-08-19
ISBN : 0128196564
Language : En, Es, Fr & De

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Book Description :

The Human Mitochondrial Genome: From Basic Biology to Disease offers a comprehensive, up-to-date examination of human mitochondrial genomics, connecting basic research to translational medicine across a range of disease types. Here, international experts discuss the essential biology of human mitochondrial DNA (mtDNA), including its maintenance, repair, segregation, and heredity. Furthermore, mtDNA evolution and exploitation, mutations, methods, and models for functional studies of mtDNA are dealt with. Disease discussion is accompanied by approaches for treatment strategies, with disease areas discussed including cancer, neurodegenerative, age-related, mtDNA depletion, deletion, and point mutation diseases. Nucleosides supplementation, mitoTALENs, and mitoZNF nucleases are among the therapeutic approaches examined in-depth. With increasing funding for mtDNA studies, many clinicians and clinician scientists are turning their attention to mtDNA disease association. This book provides the tools and background knowledge required to perform new, impactful research in this exciting space, from distinguishing a haplogroup-defining variant or disease-related mutation to exploring emerging therapeutic pathways. Fully examines recent advances and technological innovations in the field, enabling new mtDNA studies, variant and mutation identification, pathogenic assessment, and therapies Disease discussion accompanied by diagnostic and therapeutic strategies currently implemented clinically Outlines and discusses essential research protocols and perspectives for young scientists to pick up Features an international team of authoritative contributors from basic biologists to clinician-scientists

High throughput Analysis of the Human Mitochondrial Genome Reveals Its Dynamics Function and Signals of Selection in Cancer

High throughput Analysis of the Human Mitochondrial Genome Reveals Its Dynamics  Function  and Signals of Selection in Cancer Book
Author : Sneha Grandhi
Publisher : Unknown
Release : 2018
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Known as the energy powerhouses of the cell, mitochondria carry their own genomes, and encode for key cellular respiration proteins. Carrying multiple copies per cell, a given mitochondrial DNA (mtDNA) variant can be present at varying proportions, termed heteroplasmy. MtDNA is acquired exclusively through maternal inheritance and becomes stochastically replicated and segregated into dividing mitochondria over an organism's lifespan. An individual's constellation of mtDNA variants and their respective heteroplasmy levels can therefore change in response to selective pressures in somatic cells and/or selection that takes place during germline transmission. MtDNA aberrations are associated with many disorders, including cancer. Although mitochondrial genomes accumulate elevated mutation rates in cancer cells, the origin and functional impact of these mutations remain controversial. Here, we queried whole-genome sequencing data from 1,916 patients across 24 cancer types to characterize patterns of mtDNA mutations and elucidate the selective constraints driving their fate. We also tracked changes in per-cell abundances of mtDNA mutations from normal to tumor cells in the same patient. Tumor mitochondrial genomes show distinct mutational patterns and are disproportionately enriched for protein-altering changes. Moreover, protein-altering mtDNA variants that are initially present at low frequencies in normal cells preferentially expand in the altered tumor environment, suggesting selective advantage. Renal chromophobe and thyroid cancers show strong signals of positive selection with higher proportions and per-cell abundances of truncating mtDNA variants. Dramatic tumor- and tissue-specific variations in selective pressures suggest that cancer cells with advantageous levels of damaged mitochondrial genomes will selectively proliferate to facilitate the tumorigenic process.We also cataloged mitochondrial sequence variants and gene expression across 927 cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE). We used this data to create a novel computational method called DoReMi (Donor, Recipient Mitochondrial DNA matching). DoReMi scores candidate mtDNA donor and recipient cell lines for cybridization experiments, which help identify the role of mtDNA variants in-vitro under a controlled nuclear genetic background. This tool allows researchers to design optimized cybrid experiments for querying the role of mutations in their mitochondrial-encoded gene of interest. Researchers may also apply DoReMi to study their own cell lines of interest.

Normal and Disease related Sequence Variants of the Human Mitochondrial Genome

Normal and Disease related Sequence Variants of the Human Mitochondrial Genome Book
Author : Patcharee Lertrit
Publisher : Unknown
Release : 1992
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Normal and Disease related Sequence Variants of the Human Mitochondrial Genome book written by Patcharee Lertrit, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

The Evolution of Human Mitochondrial DNA

The Evolution of Human Mitochondrial DNA Book
Author : Rebecca Louise Cann
Publisher : Unknown
Release : 1982
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download The Evolution of Human Mitochondrial DNA book written by Rebecca Louise Cann, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

The Role of MGME1 in Maintenance of the Human Mitochondrial Genome

The Role of MGME1 in Maintenance of the Human Mitochondrial Genome Book
Author : Thomas Joseph James Nicholls
Publisher : Unknown
Release : 2014
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download The Role of MGME1 in Maintenance of the Human Mitochondrial Genome book written by Thomas Joseph James Nicholls, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

MITOMAP

MITOMAP Book
Author : Anonim
Publisher : Unknown
Release : 1997
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

MITOMAP uses the mtDNA sequence as the unifying element for bringing together information on mitochondrial genome structure and function, pathogenic mutations, and their clinical characteristics, population associated variation, and gene-gene interactions.

Human Mitochondrial DNA and the Evolution of Homo sapiens

Human Mitochondrial DNA and the Evolution of Homo sapiens Book
Author : Hans-Jürgen Bandelt,Martin Richards,Vincent Macaulay
Publisher : Springer Science & Business Media
Release : 2006-09-05
ISBN : 3540317899
Language : En, Es, Fr & De

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Book Description :

Mitochondrial DNA is one of the most closely explored genetic systems, because it can tell us so much about the human past. This book takes a unique perspective, presenting the disparate strands that must be tied together to exploit this system. From molecular biology to anthropology, statistics to ancient DNA, this first volume of three presents a comprehensive global picture and a critical appraisal of human mitochondrial DNA variation.

Detection of Sequence Variation in the HVII Region of the Human Mitochondrial Genome in 689 Individuals Using Immobilized Sequence Specific Oligonucleotide Probes

Detection of Sequence Variation in the HVII Region of the Human Mitochondrial Genome in 689 Individuals Using Immobilized Sequence Specific Oligonucleotide Probes Book
Author : R. Reynolds,K. Walker,J. Varlaro,M. Alavaren,E. Clark,H. Erlich
Publisher : Unknown
Release : 2000
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

We have developed a rapid, immobilized probe-based assay for the detection of sequence variation in the hyper-variable segment II (HVII) of the mitochondrial DNA (mtDNA) control region. Using a panel of 17 sequence-specific oligonucleotide (SSO) probes immobilized on nylon membrane strips, we typed 689 individuals from four population groups. The genetic diversity value for each population was calculated from the frequency data, and the frequencies of distinct "mitotypes" in each group were determined. We performed DNA sequence analysis of 129 samples to characterize the sequences associated with "blanks" (absence of probe signals) and weak probe signals. Out of 689 samples, we observed five heteroplasmic samples (excluding the variable C-stretch beginning at position 303) using the immobilized SSO probe panel. The SSO probe strips were used for the analysis of shed hairs and bloodstains from several criminal cases in Sweden, one of which is described here. We conclude that this mtDNA typing system is useful for human identification and significantly decreases casework turnaround time.

Restriction Fragment Length Polymorphism Analysis of the Human Mitochondrial Genome in Maternally Transmitted Huntington s Disease

Restriction Fragment Length Polymorphism Analysis of the Human Mitochondrial Genome in Maternally Transmitted Huntington s Disease Book
Author : kathryn Mary Tchorz
Publisher : Unknown
Release : 1989
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Restriction Fragment Length Polymorphism Analysis of the Human Mitochondrial Genome in Maternally Transmitted Huntington s Disease book written by kathryn Mary Tchorz, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Organization and Expression of the Mouse L Cell Mitochondrial DNA Genome

Organization and Expression of the Mouse L Cell Mitochondrial DNA Genome Book
Author : Richard Alfred Van Etten
Publisher : Unknown
Release : 1984
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Organization and Expression of the Mouse L Cell Mitochondrial DNA Genome book written by Richard Alfred Van Etten, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Investigation of Human Mitochondrial DNA Abnormality in Colon Cancer

Investigation of Human Mitochondrial DNA Abnormality in Colon Cancer Book
Author : Mansoureh Akouchekian
Publisher : Cuvillier Verlag
Release : 2008
ISBN : 3867277591
Language : En, Es, Fr & De

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Book Description :

Download Investigation of Human Mitochondrial DNA Abnormality in Colon Cancer book written by Mansoureh Akouchekian, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Human Mitochondrial DNA Evolution in Papua New Guinea

Human Mitochondrial DNA Evolution in Papua New Guinea Book
Author : Mark Allen Stoneking
Publisher : Unknown
Release : 1988
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Human Mitochondrial DNA Evolution in Papua New Guinea book written by Mark Allen Stoneking, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Regulation of Human Mitochondrial Gene Expression

Regulation of Human Mitochondrial Gene Expression Book
Author : Maria Isabel Guadalupe Lopez Sanchez
Publisher : Unknown
Release : 2014
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Human mitochondrial DNA is a distinct, compact genetic system that encodes proteins crucial for energy metabolism in the cell. Due to its reduced size and relatively simple organisation, all the regulatory factors directing the expression of the mitochondrial genome are encoded by nuclear DNA. It is evident that mitochondrial gene expression is regulated at different levels, which is reflected by the numerous diseases associated with mutations in both nuclear and mitochondrial DNA-encoded mitochondrial proteins. Research focusing on the identification and characterisation of RNA-binding proteins as regulators of mitochondrial function is ongoing. However, the components and mechanisms involved in the post-transcriptional regulation of mitochondrial DNA are not well understood. The aim of this research project was to investigate different aspects of the regulation of human mitochondrial gene expression via the direct action of nuclear-encoded mitochondrial proteins on RNA metabolism. First, I validated the proteins responsible for 5' end processing of mitochondrial precursor transcripts and identified the protein responsible for 3' end processing cleavage, showing that they are important for mitochondrial function. Next, I studied a previously uncharacterised mitochondrial ribosomal subunit protein and found that it is an important factor in the regulation of protein synthesis. Finally, I examined a protein that has multiple and independent functions in the organelle and identified it as a new target for the estrogenic modulation of mitochondrial gene expression via the estrogen receptor alpha. Both the nuclear and the mitochondrial genomes contribute to the mitochondrial proteome and hence to mitochondrial function. Because mitochondria possess a genome that is central to multiple cellular functions, understanding the different levels and mechanisms involved in the regulation of mitochondrial gene expression is essential in elucidating the contribution of mitochondrial dysfunction to human disease.

The Human Mitochondrial Genome

The Human Mitochondrial Genome Book
Author : Giuseppe Gasparre,Anna Maria Porcelli
Publisher : Academic Press
Release : 2020-07-23
ISBN : 0128226420
Language : En, Es, Fr & De

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Book Description :

The Human Mitochondrial Genome: From Basic Biology to Disease offers a comprehensive, up-to-date examination of human mitochondrial genomics, connecting basic research to translational medicine across a range of disease types. Here, international experts discuss the essential biology of human mitochondrial DNA (mtDNA), including its maintenance, repair, segregation, and heredity. Furthermore, mtDNA evolution and exploitation, mutations, methods, and models for functional studies of mtDNA are dealt with. Disease discussion is accompanied by approaches for treatment strategies, with disease areas discussed including cancer, neurodegenerative, age-related, mtDNA depletion, deletion, and point mutation diseases. Nucleosides supplementation, mitoTALENs, and mitoZNF nucleases are among the therapeutic approaches examined in-depth. With increasing funding for mtDNA studies, many clinicians and clinician scientists are turning their attention to mtDNA disease association. This book provides the tools and background knowledge required to perform new, impactful research in this exciting space, from distinguishing a haplogroup-defining variant or disease-related mutation to exploring emerging therapeutic pathways. Fully examines recent advances and technological innovations in the field, enabling new mtDNA studies, variant and mutation identification, pathogenic assessment, and therapies Disease discussion accompanied by diagnostic and therapeutic strategies currently implemented clinically Outlines and discusses essential research protocols and perspectives for young scientists to pick up Features an international team of authoritative contributors from basic biologists to clinician-scientists

The Mitochondrial Genome in Forensic Genetics

The Mitochondrial Genome in Forensic Genetics Book
Author : Anonim
Publisher : Unknown
Release : 2015
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download The Mitochondrial Genome in Forensic Genetics book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

DNA Damage Tolerance and Repair Pathways in the Mitochondrial Compartment

DNA Damage Tolerance and Repair Pathways in the Mitochondrial Compartment Book
Author : Lidza Kalifa,Daniel F. Quintana,Gisela Beutner,Naina Phadnis
Publisher : Unknown
Release : 2011
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

"Mitochondria are essential organelles in nearly all eukaryotic cells. Due to their crucial function in respiration, mitochondria are frequently referred to as the powerhouses of the cell. These highly dynamic structures contain their own DNA genome, and the stability of this genome is fundamental in maintaining normal cellular function. Mutations in the human mitochondrial genome have been implicated in many diseases, including neuromuscular disorders, heart disease, and diabetes. Moreover, the accumulation of mutations in the mitochondrial genome has been shown to contribute to aging and aging-related disorders. Mutations in DNA occur as a result of errors in DNA synthesis and repair processes acting on damaged DNA. Although nuclear processes responsible for DNA replication and repair are well studied, pathways involved in mitochondrial DNA replication and repair are comparatively poorly understood. The work presented here describes the identification and characterization of mechanisms involved in DNA damage tolerance and repair in the mitochondrial compartment. In this study, I performed a screen of the Saccharomyces cerevisiae deletion collection to identify novel candidate genes involved in maintaining mitochondrial DNA integrity. Results from this analysis revealed that several proteins required for nuclear nucleotide excision repair function in mitochondrial DNA mutation avoidance after UV-induced damage. Additionally, I have demonstrated that a highly conserved nuclear protein FEN1, and its yeast homolog Rad27p, localize to the mitochondrial compartment in yeast and mice. I have completed a comprehensive genetic analysis of RAD27 mutants and describe the functional relevance in mitochondrial base excision repair as well as mitochondrial DNA maintenance. Furthermore, I have characterized the impact of translesion DNA polymerases on mitochondrial DNA stability and revealed a novel, mitochondrial-specific mechanism of mutagenesis. Lastly, I have critically examined the pathways involved in mitochondrial DNA double-strand break repair. Using novel reporter constructs, I implicate roles for the nuclear double-strand break repair proteins in generating mitochondrial DNA deletions. Moreover, I have generated a system to induce a single, specific mitochondrial double-strand break allowing for the analysis of the kinetics of this type of repair. In summary, these studies have identified novel mechanisms of maintaining mitochondrial DNA integrity, as well as, developed our current understanding of mitochondrial DNA mutagenesis."--Leaves v-vi.

Preparing Whole Genome Human Mitochondrial DNA Libraries for Next Generation Sequencing Using Illumina Nextera XT

Preparing Whole Genome Human Mitochondrial DNA Libraries for Next Generation Sequencing Using Illumina Nextera XT Book
Author : Hilde Stawski
Publisher : Unknown
Release : 2013
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Preparing Whole Genome Human Mitochondrial DNA Libraries for Next Generation Sequencing Using Illumina Nextera XT book written by Hilde Stawski, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Functional Genomic Studies of the Structure and Regulation of Eukaryotic Transcriptomes

Functional Genomic Studies of the Structure and Regulation of Eukaryotic Transcriptomes Book
Author : Georgi Kolev Marinov,California Institute of Technology. Division of Biology and Biological Engineering,ENCODE Project
Publisher : Unknown
Release : 2014
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

The main focus of this thesis is the use of high-throughput sequencing technologies in functional genomics (in particular in the form of ChIP-seq, chromatin immunoprecipitation coupled with sequencing, and RNA-seq) and the study of the structure and regulation of transcriptomes. Some parts of it are of a more methodological nature while others describe the application of these functional genomic tools to address various biological problems. A significant part of the research presented here was conducted as part of the ENCODE (ENCyclopedia Of DNA Elements) Project. The first part of the thesis focuses on the structure and diversity of the human transcriptome. Chapter 1 contains an analysis of the diversity of the human polyadenylated transcriptome based on RNA-seq data generated for the ENCODE Project. Chapter 2 presents a simulation-based examination of the performance of some of the most popular computational tools used to assemble and quantify transcriptomes. Chapter 3 includes a study of variation in gene expression, alternative splicing and allelic expression bias on the single-cell level and on a genome-wide scale in human lymphoblastoid cells; it also brings forward a number of critical to the practice of single-cell RNA-seq measurements methodological considerations. The second part presents several studies applying functional genomic tools to the study of the regulatory biology of organellar genomes, primarily in mammals but also in plants. Chapter 5 contains an analysis of the occupancy of the human mitochondrial genome by TFAM, an important structural and regulatory protein in mitochondria, using ChIP-seq. In Chapter 6, the mitochondrial DNA occupancy of the TFB2M transcriptional regulator, the MTERF termination factor, and the mitochondrial RNA and DNA polymerases is characterized. Chapter 7 consists of an investigation into the curious phenomenon of the physical association of nuclear transcription factors with mitochondrial DNA, based on the diverse collections of transcription factor ChIP-seq datasets generated by the ENCODE, mouseENCODE and modENCODE consortia. In Chapter 8 this line of research is further extended to existing publicly available ChIP-seq datasets in plants and their mitochondrial and plastid genomes. The third part is dedicated to the analytical and experimental practice of ChIP-seq. As part of the ENCODE Project, a set of metrics for assessing the quality of ChIP-seq experiments was developed, and the results of this activity are presented in Chapter 9. These metrics were later used to carry out a global analysis of ChIP-seq quality in the published literature (Chapter 10). In Chapter 11, the development and initial application of an automated robotic ChIP-seq (in which these metrics also played a major role) is presented. The fourth part presents the results of some additional projects the author has been involved in, including the study of the role of the Piwi protein in the transcriptional regulation of transposon expression in Drosophila (Chapter 12), and the use of single-cell RNA-seq to characterize the heterogeneity of gene expression during cellular reprogramming (Chapter 13). The last part of the thesis provides a review of the results of the ENCODE Project and the interpretation of the complexity of the biochemical activity exhibited by mammalian genomes that they have revealed (Chapters 15 and 16), an overview of the expected in the near future technical developments and their impact on the field of functional genomics (Chapter 14), and a discussion of some so far insufficiently explored research areas, the future study of which will, in the opinion of the author, provide deep insights into many fundamental but not yet completely answered questions about the transcriptional biology of eukaryotes and its regulation.