scholarly journals Engines of change: Transposable element mutation rates are high and variable within Daphnia magna

PLoS Genetics ◽  
2021 ◽  
Vol 17 (11) ◽  
pp. e1009827
Author(s):  
Eddie K. H. Ho ◽  
Emily S. Bellis ◽  
Jaclyn Calkins ◽  
Jeffrey R. Adrion ◽  
Leigh C. Latta IV ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Insertion Site ◽  
Low Frequency ◽  
Interspecific Variation ◽  
Mutation Rates ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Short And Long Term ◽  
Powerful Mechanism

Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10−5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.

scholarly journals Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

2020 ◽  
Author(s):  
Eddie K. H. Ho ◽  
E.S. Bellis ◽  
Jaclyn Calkins ◽  
Jeffrey R. Adrion ◽  
Leigh C. Latta ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Latitudinal Gradient ◽  
Mutation Rates ◽  
Base Substitution ◽  
Genome Wide ◽  
Microsatellite Mutation ◽  
Underlying Mechanisms ◽  
Short Time ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) represent a large and dynamic portion of most eukaryotic genomes, yet little is known about their mutation rates or the correspondence between rates and long-term patterns of accrual. We compare TE activity over long and short time periods by quantifying TE profiles and mutation rates (with and without minimizing selection) among 9 genotypes from three populations of Daphnia magna sampled along a latitudinal gradient. The patterns of genome-wide variation observed in nature mirror direct estimates of rates and spectra observed in a multi-year laboratory mutation accumulation experiment, where net rates range from -11.98 to 12.79 x 10-5 per copy per generation across genotypes. Overall, gains outnumber losses and both types of events are highly deleterious based on comparing lines with and without selection minimized. The rate and spectrum of TE mutations vary widely among genotypes and across TE families/types, even within the same population. We compare TE mutation rates to previously published rates of base substitution, microsatellite mutation, and gene conversion for the same genotypes, and show a correlation only with the latter. Our study provides strong evidence for the notion that TEs represent a highly mutagenic force in the genome. Furthermore, the variation we observe underscores the need to expand the repertoire of mutations studied to include a wider array of mutation types with different underlying mechanisms in order to better understand the evolution of the mutation rate and the ways in which genetic variation is generated genome wide.

scholarly journals Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

2019 ◽  
Author(s):  
Eddie K. H. Ho ◽  
Fenner Macrae ◽  
Leigh C. Latta ◽  
Maia J. Benner ◽  
Cheng Sun ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Tandem Repeats ◽  
Mutation Accumulation ◽  
Mutation Rates ◽  
Evolutionary Forces ◽  
Repeat Content ◽  
Long Time ◽  
Order Of Magnitude ◽  
Time Periods ◽  
Microsatellite Mutation

AbstractMicrosatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and are often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species and have rarely been compared across genotypes and populations and intraspecific differences in overall microsatellite content have rarely been explored. To investigate the accumulation of microsatellite DNA over long-and short-time periods, we quantified the abundance and genome-wide mutation rates in whole-genome sequences of 47 mutation accumulation (MA) lines and 12 non-MA lines derived from six different genotypes of the crustacean Daphnia magna collected from three populations (Finland, Germany, and Israel). Each genotype possessed a distinctive microsatellite profile and clustered according to their population of origin. During the period of mutation accumulation, we observed very high microsatellite mutation rates (a net change of −0.19 to 0.33 per copy per generation), which surpass rates reported from a closely-related congener, D. pulex, by an order of magnitude. Rates vary between microsatellite motifs and among genotypes, with those starting with high microsatellite content exhibiting greater losses and those with low microsatellite content exhibiting greater gains. Our results show that microsatellite mutation rates depend both on characteristics of the microsatellites and the genomic background. These context-dependent mutation dynamics may, in conjunction with other evolutionary forces that may differ among populations, explain the differential accumulation of repeat content in the genome over long time periods.

Dictionary-unsanctioned Anglicisms

2017 ◽  
Author(s):  
Valérie Saugera
Keyword(s):  
Life Cycle ◽  
Low Frequency ◽  
Short Life ◽  
Global English ◽  
Very Low Frequency ◽  
Short And Long Term

This core chapter reports on the findings from the investigation of the Libération corpus. Systematic tracking of dictionary-unattested Anglicisms occurring over a year of press language reveals that contact with global English has resulted in new patterns of borrowing and processes for extending the French lexicon, for the short and long term. A major finding is that the database includes many types of Anglicisms with very few tokens: global English is a robust supplier of transient words (nonce borrowings and very low-frequency items) which complement the more durable lexicon. Diachronic comparisons show that these Anglicisms typically have a short life cycle in the French lexicon, though some Anglicisms from the corpus entered subsequent editions of the dictionary. The data also reveal the less common borrowing of items from closed classes, including pronoun himself, stressed article the, and the preposition-like series starring/featuring/including.

Transcatheter Pulmonary Valve Replacement in Patients With Congenital Heart Disease

2018 ◽  
Vol 38 (1) ◽  
pp. 30-36
Author(s):  
Shantelle Bartra
Keyword(s):  
Valve Replacement ◽  
Pulmonary Valve ◽  
Insertion Site ◽  
Pulmonary Valve Replacement ◽  
Long Term Outcomes ◽  
Transcatheter Pulmonary Valve Replacement ◽  
Feasible Alternative ◽  
Short And Long Term ◽  
Infection Monitoring

Transcatheter pulmonary valve replacement is now a feasible alternative to surgical pulmonary valve replacement in children and adults with dysfunctional right ventricular outflow conduits. Currently, 2 types of valves can be used for this application. This article provides an overview of the procedure and how it is performed, indications and contraindications for transcatheter pulmonary valve replacement, and short- and long-term outcomes. Nursing considerations mainly focus on educating patients, preventing bleeding and infection, monitoring renal function, and preventing injury to the catheter insertion site. This article enhances the knowledge of nurses working in cardiac catheterization laboratories and post-procedure recovery and cardiac units so that the nurses can anticipate interventions and understand the management of patients who have transcatheter pulmonary valve replacement.

scholarly journals An accurate genetic clock

2015 ◽  
Author(s):  
David H Hamilton
Keyword(s):  
Stochastic Process ◽  
Kin Selection ◽  
Common Ancestor ◽  
Mutation Rates ◽  
Recent Common Ancestor ◽  
Molecular Clocks ◽  
Most Recent Common Ancestor ◽  
Wide Range ◽  
Short And Long Term

Molecular clocks give ``Time to most recent common ancestor'' TMRCA} of genetic trees. By Watson-Galton most lineages terminate, with a few overrepresented singular lineages generated by W. Hamilton's ``kin selection''. Applying current methods to this non-uniform branching produces greatly exaggerated TMRCA. We introduce an inhomogenous stochastic process which detects singular lineages by asymmetries, whose reduction gives true TMRCA. This implies a new method for computing mutation rates. Despite low rates similar to mitosis data, reduction implies younger TMRCA, with smaller errors. We establish accuracy by a comparison across a wide range of time, indeed this is only clock giving consistent results for both short and long term times. In particular we show that the dominant European y-haplotypes R1a1a & R1b1a2, expand from c3700BC, not reaching Anatolia before c3300BC. While this contradicts current clocks which date R1b1a2 to either the Neolithic Near East$ or Paleo-Europe, our dates support recent genetic analysis of ancient skeletons by Reich.

scholarly journals Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

2019 ◽  
Vol 36 (9) ◽  
pp. 1942-1954 ◽  
Author(s):  
Eddie K H Ho ◽  
Fenner Macrae ◽  
Leigh C Latta ◽  
Maia J Benner ◽  
Cheng Sun ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Tandem Repeats ◽  
Large Population ◽  
Daphnia Pulex ◽  
Mutation Rates ◽  
Evolutionary Forces ◽  
Repeat Content ◽  
Order Of Magnitude ◽  
Microsatellite Mutation ◽  
Short Time

Abstract Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.

scholarly journals Activity-Dependent Plasticity of Astroglial Potassium and Glutamate Clearance

2015 ◽  
Vol 2015 ◽  
pp. 1-16 ◽  
Author(s):  
Giselle Cheung ◽  
Jérémie Sibille ◽  
Jonathan Zapata ◽  
Nathalie Rouach
Keyword(s):  
Synaptic Transmission ◽  
Neuronal Activity ◽  
Hippocampal Slices ◽  
Low Frequency ◽  
Extracellular Potassium ◽  
Inward Currents ◽  
Frequency Stimulation ◽  
Short And Long Term ◽  
Acute Hippocampal Slices

Recent evidence has shown that astrocytes play essential roles in synaptic transmission and plasticity. Nevertheless, how neuronal activity alters astroglial functional properties and whether such properties also display specific forms of plasticity still remain elusive. Here, we review research findings supporting this aspect of astrocytes, focusing on their roles in the clearance of extracellular potassium and glutamate, two neuroactive substances promptly released during excitatory synaptic transmission. Their subsequent removal, which is primarily carried out by glial potassium channels and glutamate transporters, is essential for proper functioning of the brain. Similar to neurons, different forms of short- and long-term plasticity in astroglial uptake have been reported. In addition, we also present novel findings showing robust potentiation of astrocytic inward currents in response to repetitive stimulations at mild frequencies, as low as 0.75 Hz, in acute hippocampal slices. Interestingly, neurotransmission was hardly affected at this frequency range, suggesting that astrocytes may be more sensitive to low frequency stimulation and may exhibit stronger plasticity than neurons to prevent hyperexcitability. Taken together, these important findings strongly indicate that astrocytes display both short- and long-term plasticity in their clearance of excess neuroactive substances from the extracellular space, thereby regulating neuronal activity and brain homeostasis.

Effect of low frequency electrical stimulation on seizure-induced short- and long-term impairments in learning and memory in rats

2017 ◽  
Vol 168 ◽  
pp. 112-121 ◽  
Author(s):  
Khadijeh Esmaeilpour ◽  
Vahid Sheibani ◽  
Mohammad Shabani ◽  
Javad Mirnajafi-Zadeh
Keyword(s):  
Electrical Stimulation ◽  
Learning And Memory ◽  
Low Frequency ◽  
Short And Long Term

scholarly journals Genome-Wide Analysis of HAK/KUP/KT Potassium Transporter Genes in Banana (Musa Acuminata L.) and Their Tissue-Specific Expression Profiles Under Potassium Stress

2021 ◽  
Author(s):  
Siwen Liu ◽  
Bangting Wu ◽  
Yanling Xie ◽  
Sijun Zheng ◽  
Jianghui Xie ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Expression ◽  
Genome Wide ◽  
Low Potassium ◽  
Duplication Events ◽  
Osmotic Balance ◽  
Short And Long Term ◽  
Low K

Abstract Potassium is one of the most essential inorganic cations for plant growth and development. The high affinity K+ (HAK)/K+ uptake (KUP)/K+ transporter (KT) family plays essential roles in the regulation of cellular K+ levels and the maintenance of osmotic balance. However, the roles of these genes in the responses of bananas to low-potassium stress are unclear. In this study, 24 HAK/KUP/KT (MaHAK) genes were identified from banana genomic data. These genes were further classified into four groups based on phylogenetic analysis, gene structure and conserved domain analysis. Segmental duplication events played an important role in the expansion of the MaHAK gene family. Transcriptome analysis revealed the expression patterns of MaHAKs in various tissues under different K+ conditions. MaHAK14b was upregulated under both short- and long-term K+-deficient conditions, suggesting that it plays crucial roles in K+ uptake at low K+ concentrations. Furthermore, MaHAK14b mediated K+ uptake when it was heterologously expressed in the yeast mutant R5421 on low K+ medium. Collectively, these findings provide a foundation for further functional analysis of MaHAK genes, which may be used to improve stress resistance in bananas.

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