scholarly journals Genomic Balance: Two Genomes Establishing Synchrony to Modulate Cellular Fate and Function

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1306 ◽  
Author(s):  
St. John
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Genome ◽  
Cell Fate ◽  
Nuclear Genome ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Epigenetic Regulators ◽  
And Function ◽  
Effective Function

It is becoming increasingly apparent that cells require cooperation between the nuclear and mitochondrial genomes to promote effective function. However, it was long thought that the mitochondrial genome was under the strict control of the nuclear genome and the mitochondrial genome had little influence on cell fate unless it was extensively mutated, as in the case of the mitochondrial DNA diseases. However, as our understanding of the roles that epigenetic regulators, including DNA methylation, and metabolism play in cell fate and function, the role of the mitochondrial genome appears to have a greater influence than previously thought. In this review, I draw on examples from tumorigenesis, stem cells, and oocyte pre- and post-fertilisation events to discuss how modulating one genome affects the other and that this results in a compromise to produce functional mature cells. I propose that, during development, both of the genomes interact with each other through intermediaries to establish genomic balance and that establishing genomic balance is a key facet in determining cell fate and viability.

scholarly journals A battle for transmission: the cooperative and selfish animal mitochondrial genomes

Open Biology ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 180267 ◽  
Author(s):  
Anna Klucnika ◽  
Hansong Ma
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Energy Production ◽  
Nuclear Genome ◽  
The Other ◽  
Mitochondrial Genomes ◽  
Cellular Processes ◽  
Mitochondrial Replacement Therapy ◽  
Mtdna Evolution ◽  
Organismal Fitness

The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

PIN-FORMED 1 regulates cell fate at the periphery of the shoot apical meristem

Development ◽  
2000 ◽  
Vol 127 (23) ◽  
pp. 5157-5165 ◽  
Author(s):  
T. Vernoux ◽  
J. Kronenberger ◽  
O. Grandjean ◽  
P. Laufs ◽  
J. Traas
Keyword(s):  
Cell Fate ◽  
Apical Meristem ◽  
Transmembrane Protein ◽  
Loss Of Function ◽  
Hybrid Identity ◽  
Hormone Transport ◽  
Early Markers ◽  
Ideal Tool ◽  
And Function

The process of organ positioning has been addressed, using the pin-formed 1 (pin1) mutant as a tool. PIN1 is a transmembrane protein involved in auxin transport in Arabidopsis. Loss of function severely affects organ initiation, and pin1 mutants are characterised by an inflorescence meristem that does not initiate any flowers, resulting in the formation of a naked inflorescence stem. This phenotype, combined with the proposed role of PIN1 in hormone transport, makes the mutant an ideal tool to study organ formation and phyllotaxis, and here we present a detailed analysis of the molecular modifications at the shoot apex caused by the mutation. We show that meristem structure and function are not severely affected in the mutant. Major alterations, however, are observed at the periphery of the pin1 meristem, where organ initiation should occur. Although two very early markers of organ initiation, LEAFY and AINTEGUMENTA, are expressed at the periphery of the mutant meristem, the cells are not recruited into distinct primordia. Instead a ring-like domain expressing those primordium specific genes is observed around the meristem. This ring-like domain also expresses a boundary marker, CUP-SHAPED COTYLEDON 2, involved in organ separation, showing that the zone at the meristem periphery has a hybrid identity. This implies that PIN1 is not only involved in organ outgrowth, but that it is also necessary for organ separation and positioning. A model is presented in which PIN1 and the local distribution of auxin control phyllotaxis.

scholarly journals The influence of mitochondria in epigenetics revealed through naturally occurring fish cybrids

2012 ◽  
Vol 58 (1) ◽  
pp. 138-145 ◽  
Author(s):  
Bernard Angers ◽  
Antoine Dallaire ◽  
Simon Vervaet ◽  
Francis Vallières ◽  
Annie Angers
Keyword(s):  
Dna Methylation ◽  
Strong Influence ◽  
Nuclear Genome ◽  
Genome Comparison ◽  
Mitochondrial Genomes ◽  
Wild Type ◽  
Ideal Model ◽  
Naturally Occurring ◽  
Cytoplasmic Hybrids ◽  
Epigenetic Processes

Abstract Epigenetic processes are important mechanisms for phenotypic changes that occur in response to the environment. As such, it is expected that the alteration of cytoplasmic composition (the immediate environment of nuclei) results in the modification of the methylome and the expression of the nuclear genome. Cytoplasmic hybrids (or cybrids) are an ideal model to study the influence of mitochondria on gene expression. In this study, we take advantage of the natural co-occurrence of two biotypes that have a similar nuclear genome type Chrosomus eos, but harbor mitochondria from different species (C. eos in wild type or C. neogaeus in cybrids) to assess the effects of mitochondria on DNA methylation profiles and protein expression of the nuclear genome. Comparison between these biotypes is particularly relevant given their recent divergence and their low level of genetic differentiation. Variations of DNA methylation assessed on tissues from different embryonic origins revealed the distinct profiles of cybrid and wild type populations. Differences are more pronounced between wild type and cybrids than between populations of a given biotype. The proteome is also more different between biotypes than within a given biotype. These results indicate a strong influence of mitochondria on the nuclear genome, which remains detectable in different genetic and environmental contexts. These changes in the methylome and proteome of cybrids are expected to reflect the adjustments imposed by the coexistence of nuclear and mitochondrial genomes from different species.

Indigenous approaches to the past: ‘Creative histories’ at the Hyde Park Barracks, Sydney

2020 ◽  
Vol 9 (1) ◽  
pp. 83-102 ◽  
Author(s):  
Kiera Lindsey
Keyword(s):  
Visual Art ◽  
The Other ◽  
Cultural Relations ◽  
Form And Function ◽  
The Past ◽  
Cultural Responses ◽  
And Function ◽  
The Way

This article discusses a recent art project created by the Wiradjuri and Kamilaroi artist Jonathon Jones, which was commissioned to commemorate the opening of the revitalized Hyde Park Barracks in Sydney in early 2020. Jones’ work involves a dramatic installation of red and white crushed stones laid throughout the grounds of the barracks, merging the image of the emu footprint with that of the English broad convict arrow to ‘consider Australia’s layered history and contemporary cultural relations’. This work was accompanied by a ‘specially-curated programme’ of performances, workshops, storytelling and Artist Talks. Together, these elements were designed to unpack how certain ‘stories determine the ways we came together as a nation’. As one of the speakers of the Artist Talk’s programme, I had a unique opportunity to experiment with what colleagues and I have been calling ‘Creative histories’ in reference to the way some artists and historians are choosing to communicate their research about the past in ways that experiment with form and function and push disciplinary or generic boundaries. This article reflects upon how these two distinct creative history projects – one visual art, the other performative – renegotiate the complex and contested pasts of the Hyde Park Barracks. I suggest that both examples speak to the role of memory and creativity in shaping cultural responses to Australia’s colonial past, while Jones' programme illustrates how Indigenous artists and academics are making a profound intervention into contemporary understandings of how history is ‘done’ in Australia.

scholarly journals Characterization of DNA methylation as a function of biological complexity via dinucleotide inter-distances

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150227 ◽  
Author(s):  
Giulia Paci ◽  
Giampaolo Cristadoro ◽  
Barbara Monti ◽  
Marco Lenci ◽  
Mirko Degli Esposti ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Statistical Study ◽  
The Other ◽  
Biological Complexity ◽  
Functional Roles ◽  
Exponential Tails ◽  
Cg Dinucleotide ◽  
Cg Dinucleotides

We perform a statistical study of the distances between successive occurrences of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the CG dinucleotide distribution in mammalian DNA, pointing towards a connection with the role of such dinucleotide in DNA methylation. While the CG distributions of mammals exhibit exponential tails with comparable parameters, the picture for the other organisms studied (e.g. fish, insects, bacteria and viruses) is more heterogeneous, possibly because in these organisms DNA methylation has different functional roles. Our analysis suggests that the distribution of the distances between CG dinucleotides provides useful insights into characterizing and classifying organisms in terms of methylation functionalities.

scholarly journals Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

2018 ◽  
Author(s):  
Xin-Yan Gao ◽  
Yin-Yin Cai ◽  
Dan-Na Yu ◽  
Kenneth B. Storey ◽  
Jia-Yong Zhang
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Nucleotide Composition ◽  
The Other ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Duplicated Genes ◽  
Sister Clade ◽  
Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae). The total length of the S.longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr(CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S.longialata mitogenome was as follows: A=41.0%, T=33.8%, C=15.5%, G=9.7%. Both BI and ML analyse strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

scholarly journals The Polyphony of the Silent: The Specifics of Dostoevsky’s Philosophical Discourse

2021 ◽  
Vol 26 (3) ◽  
pp. 375-391
Author(s):  
Alexandr B. Krinitsyn
Keyword(s):  
Psychological Aspects ◽  
The Other ◽  
Philosophical Discourse ◽  
And Function

The article describes the phenomenon of silence in Dostoevskys later prose. Philosophical, plot-forming and psychological aspects of silence are looked at. A confessional type of monologue is defined as a discursive genre, with specific roles of the speaker and his silent listeners, whose predominance in Dostoevskys prose lets the author of the article adjust the notion of polyphony and dialogue within the context of Dostoevskys poetics. The conventionality of the other in the confessional type of monologue is proved by the absence of the completing functions in listeners. In most cases Dostoevskys later works retain some rudimental forms of frantic dialogue while the role of specific monologue discourse, caused and conditioned by silence, is increasing. By semantics and function types of silence in Dostoevsky fall into three groups: 1) the underground silence as expression of human disunity in the epoch of universal solitude; 2) role silence of listeners in the discursive genre of confessional monologue; 3) sacred silence of Christ indicating transition to a new higher level of communication

scholarly journals Bacterial Diversity and Community in Regional Water Microbiota between Different Towns in World’s Longevity Township Jiaoling, China

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 361
Author(s):  
Lei Wu ◽  
Xinqiang Xie ◽  
Jumei Zhang ◽  
Yu Ding ◽  
Qingping Wu
Keyword(s):  
16S Rrna ◽  
High Throughput Sequencing ◽  
The Other ◽  
Rrna Gene ◽  
Metabolic Characteristics ◽  
Kegg Pathways ◽  
Healthy Longevity ◽  
And Function ◽  
Regional Water

Healthy longevity is associated with many factors, however, the potential correlation between longevity and microbiota remains elusive. To address this, we explored environmental microbiota from one of the world’s longevity townships in China. We used 16S rRNA gene high-throughput sequencing to analyze the composition and function of water microbiota. The composition and diversity of water microbiota significantly differed between the towns. Lactobacillus, Streptococcus, Bacteroides, Faecalibacterium, and Stenotrophomonas were only dominant in Xinpu, a town with an exceptionally high centenarian population. Several biomarkers were identified, including Flavobacterium, Acinetobacter, Paracoccus, Lactobacillales, Psychrobacter, Bacteroides, Ruminococcaceae, and Faecalibacterium, and these shown to be responsible for the significant differences between towns. The main species contributing to the differences between towns were Cyanobacteria, Cupriavidus and Ralstonia. Based on KEGG pathways showed that the predicted metabolic characteristics of the water microbiota in Xinpu towns were significantly different to those of the other towns. The results revealed significant differences in the composition and diversity of water microbiota in the longevity township. These findings provide a foundation for further research on the role of water microbiota in healthy longevity.

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