scholarly journals Structural Mutations in the Organellar Genomes of Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara Show Dynamic Gene Transfer

2021 ◽  
Vol 22 (7) ◽  
pp. 3770
Author(s):  
Hyoung Tae Kim ◽  
Jung Sung Kim
Keyword(s):  
Gene Transfer ◽  
Hot Spot ◽  
Bony Fish ◽  
Terrestrial Plants ◽  
Endemic Plant ◽  
Organellar Genomes ◽  
Mitogenome Sequence ◽  
Plant Remains ◽  
Different Types ◽  
Structural Mutations

Valeriana sambucifolia f. dageletiana (Nakai. ex Maekawa) Hara is a broad-leaved valerian endemic to Ulleung Island, a noted hot spot of endemism in Korea. However, despite its widespread pharmacological use, this plant remains comparatively understudied. Plant cells generally contain two types of organellar genomes (the plastome and the mitogenome) that have undergone independent evolution, which accordingly can provide valuable information for elucidating the phylogenetic relationships and evolutionary histories of terrestrial plants. Moreover, the extensive mega-data available for plant genomes, particularly those of plastomes, can enable researchers to gain an in-depth understanding of the transfer of genes between different types of genomes. In this study, we analyzed two organellar genomes (the 155,179 bp plastome and the 1,187,459 bp mitogenome) of V. sambucifolia f. dageletiana and detected extensive changes throughout the plastome sequence, including rapid structural mutations associated with inverted repeat (IR) contraction and genetic variation. We also described features characterizing the first reported mitogenome sequence obtained for a plant in the order Dipsacales and confirmed frequent gene transfer in this mitogenome. We identified eight non-plastome-originated regions (NPRs) distributed within the plastome of this endemic plant, for six of which there were no corresponding sequences in the current nucleotide sequence databases. Indeed, one of these unidentified NPRs unexpectedly showed certain similarities to sequences from bony fish. Although this is ostensibly difficult to explain, we suggest that this surprising association may conceivably reflect the occurrence of gene transfer from a bony fish to the plastome of an ancestor of V. sambucifolia f. dageletiana mediated by either fungi or bacteria.

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae)

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 634-641 ◽  
Author(s):  
T HM Mes ◽  
P Kuperus ◽  
J Kirschner ◽  
J Stepanek ◽  
P Oosterveld ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Hot Spot ◽  
Phylogenetic Signal ◽  
Direct Repeats ◽  
Nucleotide Substitutions ◽  
Replication Slippage ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Structural Mutations

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.Key words: Taraxacum, indel, non-coding chloroplast DNA, hairpin, evolution.

scholarly journals The economics of endosymbiotic gene transfer and the evolution of organellar genomes

2020 ◽  
Author(s):  
Steven Kelly
Keyword(s):  
Gene Transfer ◽  
Host Cell ◽  
Protein Import ◽  
Nuclear Genome ◽  
Selective Advantage ◽  
Endosymbiotic Gene Transfer ◽  
Organellar Genomes ◽  
Evolution Of Life ◽  
A Cell ◽  
Life On Earth

AbstractThe endosymbiosis of the bacterial progenitors of mitochondrion and the chloroplast are landmark events in the evolution of life on earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of genes found in living relatives of their ancestors. While some of the 95% of missing organellar genes have been discarded, many have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. Here we demonstrate that the energy liberated or consumed by a cell as a result of endosymbiotic gene transfer can be sufficient to provide a selectable advantage for retention or nuclear-transfer of organellar genes in eukaryotic cells. We further demonstrate that for realistic estimates of protein abundances, organellar protein import costs, host cell sizes, and cellular investment in organelles that it is energetically favourable to transfer the majority of organellar genes to the nuclear genome. Moreover, we show that the selective advantage of such transfers is sufficiently large to enable such events to rapidly reach fixation. Thus, endosymbiotic gene transfer can be advantageous in the absence of any additional benefit to the host cell, providing new insight into the processes that have shaped eukaryotic genome evolution.One sentence summaryThe high copy number of organellar genomes renders endosymbiotic gene transfer energetically favourable for the vast majority of organellar genes.

scholarly journals Trichomes of Satureja horvatii Silic (Lamiaceae): Micromorphology and histochemistry

2012 ◽  
Vol 64 (3) ◽  
pp. 995-1000 ◽  
Author(s):  
Marija Marin ◽  
Lia Ascensao ◽  
Branislava Lakusic
Keyword(s):  
Electron Microscopy ◽  
Leaf Surface ◽  
Glandular Trichomes ◽  
Secondary Compounds ◽  
Endemic Plant ◽  
Histochemical Analysis ◽  
Different Types ◽  
Histochemical Tests ◽  
Scanning Electron ◽  
Comprehensive Study

Considering the importance of Satureja horvatii Silic as an endemic plant, and due to the essential oils produced in its glandular trichomes, we have done a comprehensive study of the micromorphology and a histochemical analysis of the plant?s glandular trichomes. This investigation was carried out using light microscopy and scanning electron microscopy. Non-glandular unbranched and three types of glandular trichomes on the leaf surface - peltate, capitate and digitiform - were investigated. The results of histochemical tests showed a positive reaction to polysaccharides, proteins, pectins, lipids and to some secondary compounds such as terpenes, tannins and phenols in different types of glandular trichomes.

scholarly journals The economics of organellar gene loss and endosymbiotic gene transfer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Steven Kelly
Keyword(s):  
Gene Transfer ◽  
Nuclear Genome ◽  
Energy Budgets ◽  
Net Energy ◽  
Endosymbiotic Gene Transfer ◽  
Organellar Genomes ◽  
Chloroplast Genomes ◽  
Evolution Of Life ◽  
The Difference ◽  
Life On Earth

Abstract Background The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. Results Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell. Conclusion Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.

scholarly journals High Productivity Makes Mangroves Potentially Important Players in the Tropical Silicon Cycle

2021 ◽  
Vol 8 ◽  
Author(s):  
Elani B. Elizondo ◽  
Joanna C. Carey ◽  
Alia N. Al-Haj ◽  
Ariel E. Lugo ◽  
Robinson W. Fulweiler
Keyword(s):  
Salt Marshes ◽  
Plant Biomass ◽  
Net Primary Production ◽  
Hot Spot ◽  
Dry Weight ◽  
Avicennia Germinans ◽  
Terrestrial Plants ◽  
Mangrove Species ◽  
High Productivity ◽  
Nutrient Salt

Over the last two decades, recognition of the important role terrestrial plants play in regulating silicon (Si) cycling has emerged. Si improves plant fitness by protecting them from abiotic (e.g., desiccation) and biotic (e.g., fungal attack) stressors. Once incorporated into plant biomass this biogenic Si is more bio-available than the lithogenic material from which it was ultimately derived. Thus plants play a key function in regulating the amount and timing of Si availability in downstream ecosystems. Recent work has highlighted the importance of salt marshes in the temperate Si cycle. However, the role of their tropical counterparts, mangroves, has largely gone unexplored. Here we report foliar concentrations of plant Si (as %Si by dry weight) for four Caribbean mangrove species: Conocarpus erectus (buttonwood), Laguncularia racemosa (white mangrove), Avicennia germinans (black mangrove), and Rhizophora mangle (red mangrove). Overall, the median Si concentration was low (0.07%) and did not vary among plant part (e.g., foliage, twig, and propagule). There was also little variation in Si among species. Using literature values of aboveground net primary production, and the concentrations reported here, we estimate an aboveground mangrove Si uptake rate of 2–10 kg Si ha–1 year–1. These rates are on par with rates reported for temperate and boreal forests as well as low nutrient salt marshes, but lower than estimates for high nutrient salt marshes. Thus, despite the low Si concentrations observed in mangroves, their high productivity appears to make them a hot spot of Si cycling in tropical coastal systems.

Diversity and habitat segregation of mangrove grapsoid crabs along the west coast of the Malay Peninsula

2020 ◽  
Vol 71 (8) ◽  
pp. 984
Author(s):  
Laura Ribero ◽  
Phaik Eem Lim ◽  
Rosli Ramli ◽  
Gianluca Polgar
Keyword(s):  
Species Composition ◽  
West Coast ◽  
Coastal Wetlands ◽  
Hot Spot ◽  
Malay Peninsula ◽  
The West ◽  
Ecological Traits ◽  
Management Actions ◽  
Different Types ◽  
Local Extinctions

South-East Asia is a biodiversity hot spot for several different animal and plant taxa, and grapsoid crabs are dominant components of its mangrove macrofauna. However, autecological traits of the species and assemblage structures are still largely undescribed. During the period 2012–14, we surveyed six mainland and insular mangrove sites along the west coast of the Malay Peninsula, four of which had not been investigated previously. Species composition differed among sites with different types of substrate and forest area. Small islands, characterised by coarser intertidal substrates, hosted remarkably different assemblages from mainland systems. Most of the species occurred in a small number of sites, suggesting stenotopic ecological traits or patchy distributions, and a marked variation in species composition and environmental conditions among sites was observed. This suggests that management actions assuming that this region’s coastal wetlands have comparable community compositions may likely lead to local extinctions of species, possibly affecting the regional biodiversity of these systems.

Automatic Method for Detecting and Categorizing Train Car Wheel and Bearing Defects

2015 ◽  
Author(s):  
Hanieh Deilamsalehy ◽  
Timothy C. Havens ◽  
Pasi Lautala
Keyword(s):  
Fuzzy Inference ◽  
Hot Spot ◽  
Local Heating ◽  
Severe Damage ◽  
Transportation Services ◽  
Railroad Industry ◽  
Whole Process ◽  
Bearing Defects ◽  
Different Types ◽  
Proper Operation

Worldwide, railways are among the safest transportation services. Nevertheless, every year some serious accidents are reported. A noticeable portion of these accidents are a result of defective wheels, bearings, or brakes. Train wheels are subjected to different types of damage due to their interaction with the brakes and the track and they are required to be periodically inspected to ensure they meet all the safety criteria for proper operation. If the wheel damage remains undetected, it can worsen and result in overheating and severe damage to the wheel and track. There are a variety of wheel damages, classified in different groups based on the type and severity of the defect. The most usual cause of damage is severe braking, which applies directly to the wheel and results in local heating of the wheel. This can stop the wheel from rotating while the train is still moving, producing a defect called a “flat spot” or “hot spot”. Flat-spotted wheels are a serious concern for the railroad industry. Depending on the level of wheel defect, different solutions should be taken. This paper will focus on automatically detecting flat-spotted wheels from thermal imagery using computer vision methods and introduces an algorithm to detect hot bearings. We first extract and segment both the wheel and bearing regions from the whole image, then we introduce a fuzzy inference to categorize the level of wheel damage. The whole process is done automatically and without any need for time consuming and costly manned inspection. Based on the severity of the defect, it can be decided which solution should be taken.

scholarly journals An efficient routing protocol for internet of medical things focusing hot spot node problem

2021 ◽  
Vol 17 (2) ◽  
pp. 155014772199170
Author(s):  
Ghufran Ahmed ◽  
Danish Mehmood ◽  
Khurram Shahzad ◽  
Rauf Ahmed Shams Malick
Keyword(s):  
Internet Of Things ◽  
Ex Vivo ◽  
Hot Spot ◽  
Healthcare Budget ◽  
Care Workers ◽  
Different Types ◽  
Monitoring Performance ◽  
Node Problem ◽  
Day By Day

The healthcare budget is increasing day-by-day as the population of the world increases. The same is the case regarding the workload of health care workers, that is, doctors and other practitioners. Under such a scenario where workload and cost are increasing drastically, there is a dire need of integrating recent technological enhancements with the said domain. Since the last decade, a lot of work is in the process considering the said integration bringing revolutionary changes. For remote monitoring, existing systems use different types of Internet of things devices that measure different health parameters. One of the major problems in such a system is to find an optimum routing approach that can resolve energy and thermal issues that are taking the limelight in the research arena. In this article, a dynamic routing technique is proposed which is keen to connect multiple in vivo/ex vivo Internet of things devices and a sink (focusing thermal and energy problem) and then forwarding data from sink to remote location for monitoring. Performance parameters are kept energy efficiency and thermal awareness and analytical results show that the proposed protocol supersedes existing approaches in said metrics.

scholarly journals Analysis of thermal models to determine the loss of life of mineral oil immersed transformers

2021 ◽  
Vol 10 (5) ◽  
pp. 2327-2336
Author(s):  
Mohammad Tolou Askari ◽  
Mohammad Javad Mohammadi ◽  
Jagadeesh Pasupuleti ◽  
Mehrdad Tahmasebi ◽  
Shangari K. Raveendran ◽  
...  
Keyword(s):  
Distribution Systems ◽  
Residual Life ◽  
Hot Spot ◽  
Mineral Oil ◽  
Effective Parameters ◽  
Loss Of Life ◽  
Thermal Models ◽  
Different Types ◽  
Electrical Transformers ◽  
Transmission And Distribution

Hot spot as well as top oil temperatures have played the most effective parameters on the life of the electrical transformers. The prognostication of these factors is very vital for determining the residual life of the electrical transformers in the transmission and distribution systems. Thus, an accurate mathematical method is required to calculate the critical temperature such as hot spot and top oil temperature based on the different types of thermal models. In this study calculates the service life of the transformers based on an accurate top oil temperature. Accordingly, An approach solution is given for calculating the thermal model. Also, findings are validated with true temperatures. Finally, this method is implemented on 2500 KVA electrical transformer.

Subsoil 14C Dynamics in Different Types of Tropical and Subtropical Soils under Different Crop Management

Radiocarbon ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 1021-1034 ◽  
Author(s):  
Erwin Prastowo ◽  
Pieter M Grootes ◽  
Marie-Josée Nadeau ◽  
Sri R Utami
Keyword(s):  
Organic Carbon ◽  
Climatic Factors ◽  
Soil Column ◽  
Tropical Soils ◽  
Plant Macrofossils ◽  
Plant Materials ◽  
Organic C ◽  
Plant Remains ◽  
Different Types ◽  
Abundance And Distribution

AbstractRadiocarbon has been applied as a tracer to study carbon dynamics in different types of tropical soils, under paddy and non-paddy management on Java, Indonesia. The 14C concentrations were measured in samples of total organic carbon as well as in alkali-soluble humic acids, insoluble humin, and plant remains (roots, seeds, leaves) obtained from three sites with Andosols, Alisols, and Vertisols at different altitudes. In addition, the abundance and distribution of plant macrofossils in the soil column and organic δ13C values were determined. The results obtained so far are compared with those from a chronosequence of Cambisols in China. They indicate the input of fresh plant materials into the subsoil directly via roots and/or by soil cracks and bioturbation of aboveground litter. The total organic C and 14C concentrations show the usual decrease with increasing depth in paddy and non-paddy soils, reflecting the influence of direct input as well as the downward redistribution of organic material as particulates or dissolved organic carbon (DOC) depending on soil type (pedogenesis, plough-pan formation, drying cracks), crop type and management, and climatic factors. A disturbance of the Andosol around 0.4 m depth and a change in profile properties around 0.63 m in the Alisol limit the general conclusions.

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