scholarly journals Repetitive Elements in Humans

2021 ◽  
Vol 22 (4) ◽  
pp. 2072
Author(s):  
Thomas Liehr
Keyword(s):  
Individual Differences ◽  
Repetitive Dna ◽  
Base Pair ◽  
Genetic Background ◽  
Tandem Repeats ◽  
Specific Aspect ◽  
Repetitive Elements ◽  
Small Scale ◽  
Repetitive Dnas ◽  
First Time

Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.

scholarly journals The Pontastacus leptodactylus (Astacidae) Repeatome Provides Insight Into Genome Evolution and Reveals Remarkable Diversity of Satellite DNA

2021 ◽  
Vol 11 ◽  
Author(s):  
Ljudevit Luka Boštjančić ◽  
Lena Bonassin ◽  
Lucija Anušić ◽  
Leona Lovrenčić ◽  
Višnja Besendorfer ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Satellite Dna ◽  
Chromosomal Evolution ◽  
Repetitive Elements ◽  
Centromeric Heterochromatin ◽  
Dna Repeats ◽  
Satellite Repeats ◽  
Interstitial Telomeric Repeats ◽  
Low Coverage ◽  
First Time

Pontastacus leptodactylus is a native European crayfish species found in both freshwater and brackish environments. It has commercial importance for fisheries and aquaculture industries. Up till now, most studies concerning P. leptodactylus have focused onto gaining knowledge about its phylogeny and population genetics. However, little is known about the chromosomal evolution and genome organization of this species. Therefore, we performed clustering analysis of a low coverage genomic dataset to identify and characterize repetitive DNA in the P. leptodactylus genome. In addition, the karyogram of P. leptodactylus (2n = 180) is presented here for the first time consisting of 75 metacentric, 14 submetacentric, and a submetacentric/metacentric heteromorphic chromosome pair. We determined the genome size to be at ~18.7 gigabase pairs. Repetitive DNA represents about 54.85% of the genome. Satellite DNA repeats are the most abundant type of repetitive DNA, making up to ~28% of the total amount of repetitive elements, followed by the Ty3/Gypsy retroelements (~15%). Our study established a surprisingly high diversity of satellite repeats in P. leptodactylus. The genome of P. leptodactylus is by far the most satellite-rich genome discovered to date with 258 satellite families described. Of the five mapped satellite DNA families on chromosomes, PlSAT3-411 co-localizes with the AT-rich DAPI positive probable (peri)centromeric heterochromatin on all chromosomes, while PlSAT14-79 co-localizes with the AT-rich DAPI positive (peri)centromeric heterochromatin on one chromosome and is also located subterminally and intercalary on some chromosomes. PlSAT1-21 is located intercalary in the vicinity of the (peri)centromeric heterochromatin on some chromosomes, while PlSAT6-70 and PlSAT7-134 are located intercalary on some P. leptodactylus chromosomes. The FISH results reveal amplification of interstitial telomeric repeats (ITRs) in P. leptodactylus. The prevalence of repetitive elements, especially the satellite DNA repeats, may have provided a driving force for the evolution of the P. leptodactylus genome.

scholarly journals A resource to explore the discovery of rare diseases and their causative genes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Friederike Ehrhart ◽  
Egon L. Willighagen ◽  
Martina Kutmon ◽  
Max van Hoften ◽  
Leopold M. G. Curfs ◽  
...  
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Genetic Background ◽  
Gene Discovery ◽  
Google Scholar ◽  
Semantic Model ◽  
Causative Gene ◽  
Scientific Publications ◽  
Monogenic Diseases ◽  
First Time

AbstractHere, we describe a dataset with information about monogenic, rare diseases with a known genetic background, supplemented with manually extracted provenance for the disease itself and the discovery of the underlying genetic cause. We assembled a collection of 4166 rare monogenic diseases and linked them to 3163 causative genes, annotated with OMIM and Ensembl identifiers and HGNC symbols. The PubMed identifiers of the scientific publications, which for the first time described the rare diseases, and the publications, which found the genes causing the diseases were added using information from OMIM, PubMed, Wikipedia, whonamedit.com, and Google Scholar. The data are available under CC0 license as spreadsheet and as RDF in a semantic model modified from DisGeNET, and was added to Wikidata. This dataset relies on publicly available data and publications with a PubMed identifier, but by our effort to make the data interoperable and linked, we can now analyse this data. Our analysis revealed the timeline of rare disease and causative gene discovery and links them to developments in methods.

scholarly journals On the Relationship between Low Latitude Scintillation Onset and Sunset Terminator over Africa

2021 ◽  
Vol 13 (11) ◽  
pp. 2087
Author(s):  
Mogese Wassaie Mersha ◽  
Elias Lewi ◽  
Norbert Jakowski ◽  
Volker Wilken ◽  
Jens Berdermann ◽  
...  
Keyword(s):  
Moving Boundary ◽  
Occurrence Rate ◽  
Scintillation Index ◽  
Small Scale ◽  
Bahir Dar ◽  
Remarkable Change ◽  
Equatorial Africa ◽  
Night Side ◽  
Solar Terminator ◽  
First Time

The solar terminator is a moving boundary between day-side and night-side regions on the Earth, which is a substantial source of perturbations in the ionosphere. In the vicinity of the solar terminator, essential parameters like S4 index measurements are widely analyzed in order to monitor and predict perturbations in the ionosphere. The utilization of the scintillation index S4 is a well-accepted approach to describe the amplitude/intensity fluctuation of a received signal, predominantly caused by small-scale irregularities of the ionospheric plasma. We report on the longitudinal daily and seasonal occurrence of GNSS signal scintillations, using the data derived from the GNSS stations in Bahir Dar, Ethiopia, Lomé, Togo and Dakar, Senegal. The observed seasonal climatology of GNSS signal scintillations in equatorial Africa is adequately explained by the alignment of the solar terminator and local geomagnetic declination line. It should be pointed out that the strongest scintillations are most frequently observed during the time when the solar terminator is best aligned with the geomagnetic declination line. At all three stations, the comparison of computational and observational results indicated that the scintillation activity culminated around equinoxes in the years 2014, 2015 and 2016. Comparatively, the western equatorial Africa sector has the most intense, longest-lasting, and highest scintillation occurrence rate in equinoctial seasons in all three years. For the first time, we show that the seasonal variation of the scintillation peaks changes systematically from west to east at equatorial GNSS stations over Africa. A detailed analysis of the solar day–night terminator azimuth at ionospheric heights including the time equation shows that the scintillation intensity has a maximum if the azimuth of the terminator coincides with the declination line of the geomagnetic field. Due to the remarkable change of the declination by about 10° at the considered GNSS stations, the distance between scintillation peaks increases by 46 days when moving westward from the Bahir Dar to the Dakar GNSS station. The observations agree quite well with the computational results, thus confirming Tsunoda’s theory.

Corrosion Testing of Armour Wire in Simulated Annulus Environments of Flexible Pipelines: An Update

2003 ◽  
Author(s):  
Richard Clements ◽  
Andrew D. Ethridge
Keyword(s):  
Deionized Water ◽  
Small Scale ◽  
General Corrosion ◽  
Flexible Pipe ◽  
Scale Test ◽  
Condensed Water ◽  
Test Cells ◽  
Sour Service ◽  
First Time ◽  
Permeation Models

This paper describes further investigations, utilising small scale test cells, into the general corrosion which can occur on wires within the inherent annulus space in a flexible pipe, particularly, and for the first time, in a sour service (H2S containing) environment. The work enhances data presented previously in 2002. Tests have been performed in cells specifically designed to simulate, as closely as possible, the environment and confines of a flexible pipe annulus, using solutions of both deionized water and seawater (to represent seawater flooding and condensed water). The systems were saturated with CO2 and H2S to simulate permeation of gases through the polymer pressure sheath (as predicted by validated permeation models). Weight loss measurements were undertaken in order to quantify the corrosion rate in these simulated annulus environments and metallography was undertaken to characterise the corrosion and check for HIC/SOHIC.

Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1435-1444 ◽  
Author(s):  
Robert M Stupar ◽  
Junqi Song ◽  
Ahmet L Tek ◽  
Zhukuan Cheng ◽  
Fenggao Dong ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Intergenic Spacer ◽  
Pericentromeric Heterochromatin ◽  
Dna Repeats ◽  
Solanum Bulbocastanum ◽  
Origin And Evolution ◽  
Potato Genome ◽  
Dna Elements

Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.

scholarly journals “Audience exchange”: cultivating peer-to-peer dialogue at unfamiliar arts events

2017 ◽  
Vol 7 (1) ◽  
pp. 65-79 ◽  
Author(s):  
Stephanie Pitts ◽  
Jonathan Gross
Keyword(s):  
Peer Learning ◽  
Peer To Peer ◽  
Small Scale ◽  
Exchange Method ◽  
Audience Engagement ◽  
Content Type ◽  
Peer Dialogue ◽  
Targeted Marketing ◽  
Audience Development ◽  
First Time

Purpose The purpose of this paper is to demonstrate the usefulness of the “audience exchange” approach for audience development and research, and to highlight the insights offered by peer-to-peer dialogue in understanding experiences of unfamiliar arts. Design/methodology/approach Using a case study with contemporary arts audiences, and setting this in the wider context of studies with other first-time attenders at a range of arts events, the paper explores the use of the “audience exchange” method, in which facilitated conversations after performance events allow newcomers to reflect upon and deepen their first-time encounters with live arts. Findings The study demonstrates the way in which conversations about arts events can enrich audience experience, and shows how participants use exploratory and emotional language to articulate their understanding of unfamiliar arts events. Peer-to-peer learning occurs through these conversations, in ways that could be further supported by arts organisations as a valuable tool for audience development. The audience exchange discussions also reveal the varieties of participation from “drifting” to full attention that are all part of audience engagement. Research limitations/implications This is a small-scale, qualitative study, and the method has potential to be tested in future studies with a greater variety of participants (e.g. younger or more ethnically diverse groups). Practical implications Use of the audience exchange for enriching experiences of first-time attendance could be adopted by arts organisations as a regular part of their audience engagement. Greater understanding of how new audience members draw on prior cultural experiences in finding the language to articulate their first impressions of an unfamiliar arts event could be valuable for targeted marketing and increasing accessibility. Originality/value The originality of this study lies in its elaboration of the audience exchange method, and its focus on the language and peer-to-peer learning evident in the facilitated post-performance discussions.

scholarly journals Sex differences in virtual navigation influenced by visual factors and individual differences

2019 ◽  
Author(s):  
Lace Padilla
Keyword(s):  
Sex Differences ◽  
Individual Differences ◽  
Mental Rotation ◽  
Morris Water Maze ◽  
Water Maze ◽  
Large Scale ◽  
Small Scale ◽  
Standard Design ◽  
Males And Females ◽  
Virtual Morris Water Maze

The Morris water maze is a task adapted from the animal spatial cognition literature and has been studied in the context of sex differences in humans, particularly because of the standard design, which manipulates proximal (close) and distal (far) cues. However, there are mixed findings with respect to the interaction of cues and sex differences in virtual Morris water maze tasks, which may be attributed to variations in the scale of the space and previously unmeasured individual differences. We explore the question of scale and context by presenting participants with an outdoor virtual Morris water maze that is four times the size of the mazes previously tested. We also measured lifetime mobility and mental rotation skills. Results of this study suggest that for the small-scale environment, males and females performed similarly when asked to navigate with only proximal cues. However, males outperformed females when only distal cues were visible. In the large-scale environment, males outperformed females in both cue conditions. Additionally, greater mental rotation skills predicted better navigation performance with proximal cues only. Finally, we found that highly mobile females and males perform equally well when navigating with proximal cues.

scholarly journals Genome Size Estimation and Full-Length Transcriptome of Sphingonotus tsinlingensis: Genetic Background of a Drought-Adapted Grasshopper

2021 ◽  
Vol 12 ◽  
Author(s):  
Lu Zhao ◽  
Hang Wang ◽  
Ping Li ◽  
Kuo Sun ◽  
De-Long Guan ◽  
...  
Keyword(s):  
Genome Size ◽  
Genetic Background ◽  
Tandem Repeats ◽  
Full Length ◽  
Arid Environments ◽  
Size Estimation ◽  
Sequencing Data ◽  
Protein Coding ◽  
Grasshopper Species ◽  
Hsp Genes

Sphingonotus Fieber, 1852 (Orthoptera: Acrididae), is a grasshopper genus comprising approximately 170 species, all of which prefer dry environments such as deserts, steppes, and stony benchlands. In this study, we aimed to examine the adaptation of grasshopper species to arid environments. The genome size of Sphingonotus tsinlingensis was estimated using flow cytometry, and the first high-quality full-length transcriptome of this species was produced. The genome size of S. tsinlingensis is approximately 12.8 Gb. Based on 146.98 Gb of PacBio sequencing data, 221.47 Mb full-length transcripts were assembled. Among these, 88,693 non-redundant isoforms were identified with an N50 value of 2,726 bp, which was markedly longer than previous grasshopper transcriptome assemblies. In total, 48,502 protein-coding sequences were identified, and 37,569 were annotated using public gene function databases. Moreover, 36,488 simple tandem repeats, 12,765 long non-coding RNAs, and 414 transcription factors were identified. According to gene functions, 61 cytochrome P450 (CYP450) and 66 heat shock protein (HSP) genes, which may be associated with drought adaptation of S. tsinlingensis, were identified. We compared the transcriptomes of S. tsinlingensis and two other grasshopper species which were less tolerant to drought, namely Mongolotettix japonicus and Gomphocerus licenti. We observed the expression of CYP450 and HSP genes in S. tsinlingensis were higher. We produced the first full-length transcriptome of a Sphingonotus species that has an ultra-large genome. The assembly characteristics were better than those of all known grasshopper transcriptomes. This full-length transcriptome may thus be used to understand the genetic background and evolution of grasshoppers.

scholarly journals Transient brightenings in the quiet Sun detected by ALMA at 3 mm

2020 ◽  
Vol 638 ◽  
pp. A62 ◽  
Author(s):  
A. Nindos ◽  
C. E. Alissandrakis ◽  
S. Patsourakos ◽  
T. S. Bastian
Keyword(s):  
Solar Atmosphere ◽  
Power Law ◽  
Small Scale ◽  
Solar Chromosphere ◽  
Average Intensity ◽  
Quiet Sun ◽  
Brightness Temperatures ◽  
Weak Preference ◽  
Thermal Origin ◽  
First Time

Aims. We investigate transient brightenings, that is, weak, small-scale episodes of energy release, in the quiet solar chromosphere; these episodes can provide insights into the heating mechanism of the outer layers of the solar atmosphere. Methods. Using Atacama Large Millimeter/submillimeter Array (ALMA) observations, we performed the first systematic survey for quiet Sun transient brightenings at 3 mm. Our dataset included images of six 87″ × 87″ fields of view of the quiet Sun obtained with angular resolution of a few arcsec at a cadence of 2 s. The transient brightenings were detected as weak enhancements above the average intensity after we removed the effect of the p-mode oscillations. A similar analysis, over the same fields of view, was performed for simultaneous 304 and 1600 Å data obtained with the Atmospheric Imaging Assembly. Results. We detected 184 3 mm transient brightening events with brightness temperatures from 70 K to more than 500 K above backgrounds of ∼7200 − 7450 K. All events showed light curves with a gradual rise and fall, strongly suggesting a thermal origin. Their mean duration and maximum area were 51.1 s and 12.3 Mm2, respectively, with a weak preference of appearing at network boundaries rather than in cell interiors. Both parameters exhibited power-law behavior with indices of 2.35 and 2.71, respectively. Only a small fraction of ALMA events had either 304 or 1600 Å counterparts but the properties of these events were not significantly different from those of the general population except that they lacked their low-end energy values. The total thermal energies of the ALMA transient brightenings were between 1.5 × 1024 and 9.9 × 1025 erg and their frequency distribution versus energy was a power law with an index of 1.67 ± 0.05. We found that the power per unit area provided by the ALMA events could account for only 1% of the chromospheric radiative losses (10% of the coronal ones). Conclusions. We were able to detect, for the first time, a significant number of weak 3 mm quiet Sun transient brightenings. However, their energy budget falls short of meeting the requirements for the heating of the upper layers of the solar atmosphere and this conclusion does not change even if we use the least restrictive criteria possible for the detection of transient brightenings.

Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.)

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 716-728 ◽  
Author(s):  
Pavel Neumann ◽  
Marcela Nouzová ◽  
Jirí Macas
Keyword(s):  
Pisum Sativum ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Genomic Library ◽  
Chromosome Morphology ◽  
Plant Genome ◽  
Genomic Repeats ◽  
Dispersed Repeats

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211–212 bp long, their abundance is 2 × 104 copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104 copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.

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