Faculty Opinions recommendation of Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses.

Abstract Background: The mitochondrial genomes (mitogenomes) of 12 bothids (Pleuronectiformes) from eight genera have been obtained. From the data, the genomic-scale and various gene rearrangements revealed the high diversity of variation in these mitogenomes. Results: A total of 18170 bp of Grammatobothus polyophthalmus mitogenome was determined including 37 genes and two control regions (CRs). Genes encoded by L-strand were grouped to an eight-genes cluster (Q-A-C-Y-S1-ND6-E-P) except for the tRNA-N, other genes encoded by H-strand were grouped together (F-12S … CytB-T) except for the tRNA-D that was translocated to inside of the eight-genes cluster. The mitogenome of G. polyophthalmus and that of 12 known bothids possessed the similar genomic-scale rearrangements with the only differences in the various combinations of CR, tRNA-D and eight-genes cluster, and the shuffling of tRNA-V. Based on the structure character of all 13 bothid mitogenomes, the Dimer-Mitogenome and Non-Random Loss (DMNR) model was fitted to account for all these rearrangements. And the translocation of tRNA-D occurring after the DMNR process in 10 of 13 bothid mitogenomes was confirmed. The striking finding was that each of degenerated genes existing in the gene rearrangement process in 13 bothids had their counterparts of intergenic spaces. Conclusions: The result of corresponding relationship between degenerated genes and intergenic spaces provided the significant evidence to support the possibility of the DMNR model, as well as, the existing of dimeric mitogenome in mitochondrion. The findings of this study were rare phenomenona in teleost fish, which not only promoted the understanding of mitogenome structural diversity, but also shed light on studying of mitochondrial rearrangement and replication.

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Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC

BMC Evolutionary Biology ◽

10.1186/s12862-017-0924-0 ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 8

Author(s):

Maciej Chyleński ◽

Anna Juras ◽

Edvard Ehler ◽

Helena Malmström ◽

Janusz Piontek ◽

...

Keyword(s):

Central Europe ◽

Mitochondrial Genomes ◽

Shed Light

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Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids

Nucleic Acids Research ◽

10.1093/nar/gkz1215 ◽

2020 ◽

Vol 48 (5) ◽

pp. 2694-2708 ◽

Cited By ~ 4

Author(s):

Binnypreet Kaur ◽

Kristína Záhonová ◽

Matus Valach ◽

Drahomíra Faktorová ◽

Galina Prokopchuk ◽

...

Keyword(s):

Mitochondrial Genome ◽

Comparative Study ◽

Rna Editing ◽

Gene Structure ◽

Mitochondrial Gene ◽

Mitochondrial Genomes ◽

Genome Architecture ◽

High Complexity ◽

Coding Regions ◽

Marine Protists

Abstract Diplonemids are highly abundant heterotrophic marine protists. Previous studies showed that their strikingly bloated mitochondrial genome is unique because of systematic gene fragmentation and manifold RNA editing. Here we report a comparative study of mitochondrial genome architecture, gene structure and RNA editing of six recently isolated, phylogenetically diverse diplonemid species. Mitochondrial gene fragmentation and modes of RNA editing, which include cytidine-to-uridine (C-to-U) and adenosine-to-inosine (A-to-I) substitutions and 3′ uridine additions (U-appendage), are conserved across diplonemids. Yet as we show here, all these features have been pushed to their extremes in the Hemistasiidae lineage. For example, Namystynia karyoxenos has its genes fragmented into more than twice as many modules than other diplonemids, with modules as short as four nucleotides. Furthermore, we detected in this group multiple A-appendage and guanosine-to-adenosine (G-to-A) substitution editing events not observed before in diplonemids and found very rarely elsewhere. With >1,000 sites, C-to-U and A-to-I editing in Namystynia is nearly 10 times more frequent than in other diplonemids. The editing density of 12% in coding regions makes Namystynia’s the most extensively edited transcriptome described so far. Diplonemid mitochondrial genome architecture, gene structure and post-transcriptional processes display such high complexity that they challenge all other currently known systems.

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Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications

Insects ◽

10.3390/insects12080757 ◽

2021 ◽

Vol 12 (8) ◽

pp. 757

Author(s):

Qi Sun ◽

Yumeng Yang ◽

Xiangyu Hao ◽

Jintian Xiao ◽

Jiaqi Liu ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Strong Support ◽

Mitochondrial Genomes ◽

Structural Elements ◽

Protein Coding ◽

Circular Dna ◽

Phylogenetic Implications ◽

Rna Genes ◽

Shed Light ◽

Complete Mitochondrial Genomes

To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).

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Elucidating cyclic AMP signaling in subcellular domains with optogenetic tools and fluorescent biosensors

Biochemical Society Transactions ◽

10.1042/bst20190246 ◽

2019 ◽

Vol 47 (6) ◽

pp. 1733-1747 ◽

Cited By ~ 3

Author(s):

Christina Klausen ◽

Fabian Kaiser ◽

Birthe Stüven ◽

Jan N. Hansen ◽

Dagmar Wachten

Keyword(s):

Cyclic Amp ◽

Adenosine Monophosphate ◽

Adenylyl Cyclases ◽

Temporal Precision ◽

Fluorescent Biosensors ◽

Subcellular Domains ◽

Spatio Temporal ◽

Hydrolysis Of ◽

Shed Light ◽

Cyclic Amp Signaling

The second messenger 3′,5′-cyclic nucleoside adenosine monophosphate (cAMP) plays a key role in signal transduction across prokaryotes and eukaryotes. Cyclic AMP signaling is compartmentalized into microdomains to fulfil specific functions. To define the function of cAMP within these microdomains, signaling needs to be analyzed with spatio-temporal precision. To this end, optogenetic approaches and genetically encoded fluorescent biosensors are particularly well suited. Synthesis and hydrolysis of cAMP can be directly manipulated by photoactivated adenylyl cyclases (PACs) and light-regulated phosphodiesterases (PDEs), respectively. In addition, many biosensors have been designed to spatially and temporarily resolve cAMP dynamics in the cell. This review provides an overview about optogenetic tools and biosensors to shed light on the subcellular organization of cAMP signaling.

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Sentence-Based Experience Logging in New Hearing Aid Users

American Journal of Audiology ◽

10.1044/2020_aja-19-00077 ◽

2020 ◽

Vol 29 (3S) ◽

pp. 631-637

Author(s):

Katja Lund ◽

Rodrigo Ordoñez ◽

Jens Bo Nielsen ◽

Dorte Hammershøi

Keyword(s):

Hearing Aid ◽

Patient Experiences ◽

Online Tool ◽

Rehabilitation Process ◽

Hearing Rehabilitation ◽

Clinical Observations ◽

Hearing Aid Use ◽

Wide Range ◽

Insight Into ◽

Shed Light

Purpose The aim of this study was to develop a tool to gain insight into the daily experiences of new hearing aid users and to shed light on aspects of aided performance that may not be unveiled through standard questionnaires. Method The tool is developed based on clinical observations, patient experiences, expert involvement, and existing validated hearing rehabilitation questionnaires. Results An online tool for collecting data related to hearing aid use was developed. The tool is based on 453 prefabricated sentences representing experiences within 13 categories related to hearing aid use. Conclusions The tool has the potential to reflect a wide range of individual experiences with hearing aid use, including auditory and nonauditory aspects. These experiences may hold important knowledge for both the patient and the professional in the hearing rehabilitation process.

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