scholarly journals A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

2022 ◽  
Vol 23 (2) ◽  
pp. 684
Author(s):  
Maria Maldonado ◽  
Kaitlyn Madison Abe ◽  
James Anthony Letts
Keyword(s):  
Rna Editing ◽  
Structural Information ◽  
Plant Mitochondria ◽  
Inner Mitochondrial Membrane ◽  
Respiratory Complexes ◽  
Core Energy ◽  
Harvesting Process ◽  
A Chain ◽  
The Impact ◽  
Structural Perspective

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

scholarly journals Effective Demand Forecasting in Health Supply Chains: Emerging Trend, Enablers, and Blockers

Logistics ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 12
Author(s):  
Lakshmy Subramanian
Keyword(s):  
Supply Chains ◽  
Demand Forecasting ◽  
Weak Links ◽  
Key Factors ◽  
Scarce Resources ◽  
Weakest Link ◽  
Emerging Trends ◽  
A Chain ◽  
Health Commodities ◽  
The Impact

Health supply chains aim to improve access to healthcare, and this can be attained only when health commodities appropriate to the health needs of the global population are developed, manufactured, and made available when and where needed. The weak links in the health supply chains are hindering the access of essential healthcare resulting in inefficient use of scarce resources and loss of lives. A chain is only as strong as its weakest link, and demand forecasting is one of the weakest links of health supply chains. Also, many of the existing bottlenecks in supply chains and health systems impede the accurate forecasting of demand, and without the ability to forecast demand with certainty, the stakeholders cannot plan and make commitments for the future. Forecasts are an important feeder for budgeting and logistics planning. Under this backdrop, the study examines how improved forecasting can lead to better short-term and long-term access to health commodities and outlines market-related risks. It explores further how incentives are misaligned creating an uneven distribution of risks, leading to the inability to match demand and supply. For this purpose, a systematic literature review was performed, analyzing 71 articles from a descriptive and content approach. Findings indicate the emerging trends in global health and the consequences of inaccurate demand forecasting for health supply chains. The content analysis identifies key factors that can pose a varying degree of risks for the health supply chain stakeholders. The study highlights how the key factors emerge as enablers and blockers, depending on the impact on the overall health supply chains. The study also provides recommendations for actions for reducing these risks. Consequently, limitations of this work are presented, and opportunities are identified for future lines of research. Finally, the conclusion confirms that by adopting a combination of approaches, stakeholders can ensure better information sharing, identify avenues of diversifying risks, and understand the implications.

scholarly journals Mitochondrial O-GlcNAc Transferase Interacts with and Modifies Many Proteins and Its Up-Regulation Affects Mitochondrial Function and Cellular Energy Homeostasis

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2956
Author(s):  
Paweł Jóźwiak ◽  
Piotr Ciesielski ◽  
Piotr K. Zakrzewski ◽  
Karolina Kozal ◽  
Joanna Oracz ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Energy Homeostasis ◽  
Glucose Sensor ◽  
Single Gene ◽  
Mitochondrial Proteins ◽  
Mitochondrial Activity ◽  
Ros Generation ◽  
Inner Mitochondrial Membrane ◽  
Glcnac Transferase ◽  
The Impact

O-GlcNAcylation is a cell glucose sensor. The addition of O-GlcNAc moieties to target protein is catalyzed by the O-Linked N-acetylglucosamine transferase (OGT). OGT is encoded by a single gene that yields differentially spliced OGT isoforms. One of them is targeted to mitochondria (mOGT). Although the impact of O-GlcNAcylation on cancer cells biology is well documented, mOGT’s role remains poorly investigated. We performed studies using breast cancer cells with up-regulated mOGT or its catalytic inactive mutant to identify proteins specifically modified by mOGT. Proteomic approaches included isolation of mOGT protein partners and O-GlcNAcylated proteins from mitochondria-enriched fraction followed by their analysis by mass spectrometry. Moreover, we analyzed the impact of mOGT dysregulation on mitochondrial activity and cellular metabolism using a variety of biochemical assays. We found that mitochondrial OGT expression is glucose-dependent. Elevated mOGT expression affected the mitochondrial transmembrane potential and increased intramitochondrial ROS generation. Moreover, mOGT up-regulation caused a decrease in cellular ATP level. We identified many mitochondrial proteins as mOGT substrates. Most of these proteins are localized in the mitochondrial matrix and the inner mitochondrial membrane and participate in mitochondrial respiration, fatty acid metabolism, transport, translation, apoptosis, and mtDNA processes. Our findings suggest that mOGT interacts with and modifies many mitochondrial proteins, and its dysregulation affects cellular bioenergetics and mitochondria function.

Deepred-Mt: Deep representation learning for predicting C-to-U RNA editing in plant mitochondria

2021 ◽  
pp. 104682
Author(s):  
Alejandro A. Edera ◽  
Ian Small ◽  
Diego H. Milone ◽  
M. Virginia Sanchez-Puerta
Keyword(s):  
Rna Editing ◽  
Plant Mitochondria ◽  
Representation Learning

Micro-Scale Flow Simulations and Permeability Estimation of Cleat Networks in Coal

2016 ◽  
Vol 846 ◽  
pp. 42-47
Author(s):  
J. Busse ◽  
S. Galindo Torres ◽  
Alexander Scheuermann ◽  
L. Li ◽  
D. Bringemeier
Keyword(s):  
Gas Flow ◽  
Structural Information ◽  
Porous Matrix ◽  
Groundwater Levels ◽  
Micro Scale ◽  
Wide Range ◽  
Boltzmann Method ◽  
The Impact ◽  
Flow Experiments

Coal mining raises a number of environmental and operational challenges, including the impact of changing groundwater levels and flow patterns on adjacent aquifer and surface water systems. Therefore it is of paramount importance to fully understand the flow of water and gases in the geological system on all scales. Flow in coal seams takes place on a wide range of scales from large faults and fractures to the micro-structure of a porous matrix intersected by a characteristic cleat network. On the micro-scale these cleats provide the principal source of permeability for fluid and gas flow. Description of the behaviour of the flow within the network is challenging due to the variations in number, sizing, orientation, aperture and connectivity at a given site. This paper presents a methodology to simulate flow and investigate the permeability of fractured media. A profound characterization of the geometry of the cleat network in micrometer resolution can be derived by CT-scans. The structural information is fed into a Lattice Boltzmann Method (LBM) based model that allows the implementation of virtual flow experiments. With the application of suitable hydraulic boundary conditions the full permeability tensor can be calculated in 3D.

scholarly journals Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution

2020 ◽  
Author(s):  
Christopher Kay ◽  
Tom A Williams ◽  
Wendy Gibson
Keyword(s):  
Molecular Evolution ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Phylogenetic Trees ◽  
Nucleotide Composition ◽  
Sub Saharan Africa ◽  
African Trypanosomes ◽  
Animal Pathogens ◽  
Recent Emergence ◽  
The Impact

Abstract Background: Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA (mtDNA). African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of trypanosome mtDNA to study the evolutionary history of trypanosomes and the molecular evolution of their mtDNAs.Results: We used long-read sequencing to completely assemble mtDNAs from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome mtDNAs from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. Whole mtDNA coding regions were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense .Conclusions: Our mtDNA data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum , major human and animal pathogens.

scholarly journals Detection of A-to-I RNA Editing in SARS-COV-2

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 41
Author(s):  
Ernesto Picardi ◽  
Luigi Mansi ◽  
Graziano Pesole
Keyword(s):  
Rna Editing ◽  
Time Course ◽  
Vero Cells ◽  
Innate Immune ◽  
Therapeutic Interventions ◽  
Clinical Samples ◽  
Transcriptome Data ◽  
Host Interactions ◽  
Rnaseq Data ◽  
The Impact

ADAR1-mediated deamination of adenosines in long double-stranded RNAs plays an important role in modulating the innate immune response. However, recent investigations based on metatranscriptomic samples of COVID-19 patients and SARS-COV-2-infected Vero cells have recovered contrasting findings. Using RNAseq data from time course experiments of infected human cell lines and transcriptome data from Vero cells and clinical samples, we prove that A-to-G changes observed in SARS-COV-2 genomes represent genuine RNA editing events, likely mediated by ADAR1. While the A-to-I editing rate is generally low, changes are distributed along the entire viral genome, are overrepresented in exonic regions, and are (in the majority of cases) nonsynonymous. The impact of RNA editing on virus–host interactions could be relevant to identify potential targets for therapeutic interventions.

Developing Priority Index for Managing Utility Disruptions in Urban Areas with Focus on Cascading and Interdependent Effects

2018 ◽  
Vol 2672 (1) ◽  
pp. 101-112 ◽  
Author(s):  
Srijith Balakrishnan ◽  
Zhanmin Zhang
Keyword(s):  
Urban Areas ◽  
Cyber Attacks ◽  
Service Networks ◽  
Urban Network ◽  
Agent Based ◽  
Priority Index ◽  
Infrastructure Network ◽  
Relief Operations ◽  
A Chain ◽  
The Impact

Unanticipated events such as natural disasters, terrorist attacks, cyber-attacks, and so forth, could cause prolonged disruptions in major utility service networks including, for example, water and electricity, in urban areas. Owing to the presence of complex interdependencies among infrastructure systems in an urban network, the disruption of one system may trigger a chain of events that degrades the proper functioning of several other dependent systems. Consequently, many parts of the city may not have access to multiple utility services and amenities. Identifying the most vulnerable communities exposed to such utility disruptions is key to performing immediate relief operations. In this paper, the concept of Priority Index, introduced as a measure of the susceptibility of communities to the event, is presented to rank urban regions based on the extent of the impact of disruptions (both cascading and interdependent impacts) caused by an event, as well as the social vulnerability of communities. Agent-based models are employed to simulate the consequences of a disruptive event on a semi-realistic urban infrastructure network. Later, the extent of impact on communities is evaluated using the simulation results and the American Community Survey data. The proposed Priority Index could help city administrations and utility service agencies identify the regions in a city that require immediate attention after a disruptive event occurs in the infrastructure network. A case study based on a semi-realistic infrastructure network in Austin, Texas is presented to demonstrate the implementation of the concept of Priority Index and the methodological framework.

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