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      Mitochondrial heteroplasmy profiling in single human oocytes by next-generation sequencing

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          Abstract

          Mitochondrial DNA (mtDNA) plays a key role in the development of a competent oocyte. Mutations of the mitochondrial genome lead to an altered energetic metabolism with negative effects on oocyte developmental competence. In this study, mtDNA heteroplasmy at an intra-oocyte level and between the different analyzed human oocytes ( n = 12) was identified by a next-generation sequencing (NGS) protocol previously developed by this research group and submitted to GenBank. This method highlighted, in particular, variants in the genes involved in the respiratory chain providing a direct indication of the cell-specific damage within the mitochondrial genome as predictor of the oocyte quality.

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          Oxidative stress and ageing of the post-ovulatory oocyte.

          R. Alan Aitken, T Lord (2013)
          With extended periods of time following ovulation, the metaphase II stage oocyte experiences deterioration in quality referred to as post-ovulatory oocyte ageing. Post-ovulatory ageing occurs both in vivo and in vitro and has been associated with reduced fertilization rates, poor embryo quality, post-implantation errors and abnormalities in the offspring. Although the physiological consequences of post-ovulatory oocyte ageing have largely been established, the molecular mechanisms controlling this process are not well defined. This review analyses the relationships between biochemical changes exhibited by the ageing oocyte and the symptoms associated with the ageing phenotype. We also discuss molecular events that are potentially involved in orchestrating post-ovulatory ageing with a particular focus on the role of oxidative stress. We propose that oxidative stress may act as the initiator for a cascade of events that create the aged oocyte phenotype. Specifically, oxidative stress has the capacity to cause a decline in levels of critical cell cycle factors such as maturation-promoting factor, impair calcium homoeostasis, induce mitochondrial dysfunction and directly damage multiple intracellular components of the oocyte such as lipids, proteins and DNA. Finally, this review addresses current strategies for delaying post-ovulatory oocyte ageing with a particular focus on the potential use of compounds such as caffeine or selected antioxidants in the development of more refined media for the preservation of oocyte integrity during IVF procedures.
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            Orione, a web-based framework for NGS analysis in microbiology

            Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna … (2014)
            Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics. Availability and implementation: Orione is available online at http://orione.crs4.it. Contact: gianmauro.cuccuru@crs4.it Supplementary information: Supplementary data are available at Bioinformatics online.
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              Complete sequence of human mitochondrial DNA obtained by combining multiple displacement amplification and next-generation sequencing on a single oocyte.

              Massimo Ancora, Massimiliano Orsini, Alessia Colosimo … (2017)
              Mitochondrial DNA (mtDNA) plays a key role in the development of a competent oocyte. In this study, the complete mtDNA sequence obtained for the first time by multiple displacement amplification approach in combination with next-generation sequencing from a single human oocyte is reported (GenBank accession no. KT364276). The analysis of oocyte mitochondrial mutations could provide a better understanding of the genetic variants correlated with the oocyte quality.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 17 August 2017
                Publication date (Electronic, collection): 2017
                Volume: 2
                Issue: 2
                Pages: 542-543
                Affiliations
                [a ]Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale” , Teramo, Italy;
                [b ]Facoltà di Bioscienze e tecnologie agro-alimentari e ambientali, Università degli Studi di Teramo , Teramo, Italy;
                [c ]Casa di Cura Privata Synergo Pierangeli, Spatocco , Chieti, Italy;
                [d ]Dipartimento di Scienze Psicologiche, della Salute e del Territorio, Università “G. D’Annunzio” Chieti-Pescara , Chieti, Italy
                Author notes
                CONTACT Massimo Ancora m.ancora@ 123456izs.it Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise ‘G. Caporale ,’ Via Campo Boario, Teramo, 64100Italy
                Author information
                https://orcid.org/0000-0002-7121-6373
                https://orcid.org/0000-0003-4368-2534
                Article
                Publisher ID: 1365634
                DOI: 10.1080/23802359.2017.1365634
                PMC ID: 7800564
                SO-VID: 0c0ba8e9-8732-4a80-89fb-0d827d756b8b
                Copyright © © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 0, Pages: 2, Words: 702
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: heteroplasmic mutations,human oocyte,mitochondrial dna,next-generation sequencing
                Data availability:
                Keywords: heteroplasmic mutations, human oocyte, mitochondrial dna, next-generation sequencing

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