scholarly journals Evolution of ribosomal internal transcribed spacers in Deuterostomia

2017 ◽  
Author(s):  
Alexandr Dyomin ◽  
Valeria Volodkina ◽  
Elena Koshel ◽  
Svetlana Galkina ◽  
Alsu Saifitdinova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Mobile Genetic Element ◽  
Gc Content ◽  
Internal Transcribed Spacers ◽  
General Tendency ◽  
Ltr Retrotransposon ◽  
Content Increase ◽  
Evolutionary Changes

AbstractSequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITSs sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown. A possible role of GC-based gene conversion in Deuterostomia ITSs evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra. The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well.

scholarly journals Inclusion of Kickxia abhaica D.A. Sutton in the genus Nanorrhinum (Plantaginaceae): Evidence from its nuclear ribosomal DNA sequences

2018 ◽  
Vol 25 (2) ◽  
pp. 209-214
Author(s):  
M. Ajmal Ali
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Taxonomic Status ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Universal Primers ◽  
Discrimination Power ◽  
Molecular Phylogenetic ◽  
Endemic Taxon

The nuclear ribosomal DNA (nrDNA) internal transcribed spacers (ITS) sequences is extensively used in the plant molecular phylogenetics for plant taxonomic identification and DNA barcoding purposes because the nrDNA ITS gene is easy to amplify by using the universal primers, its length is shorter and thus easy to sequence, and has strong discrimination power to distinguish the taxon at the species level. The present molecular phylogenetic analysis of ITS nrDNA sequences focuses to determine the taxonomic status of an unresolved endemic taxon Kickxia abhaica D.A. Sutton (Family Plantaginaceae, tribe Antirrhineae) reported from Saudi Arabia. The analysis supports the transfer of K. abhaica under the genus Nanorrhinum.

scholarly journals Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

2020 ◽  
Vol 2020 ◽  
pp. 1-17 ◽  
Author(s):  
Xin Yang ◽  
Deng-Feng Xie ◽  
Jun-Pei Chen ◽  
Song-Dong Zhou ◽  
Yan Yu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Relationship ◽  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Gc Content ◽  
Intergenic Spacer ◽  
Living Environment ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
Relationship Of

Recent advances in molecular phylogenetics provide us with information of Allium L. taxonomy and evolution, such as the subgenus Cyathophora, which is monophyletic and contains five species. However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved. In our study, we newly assembled the whole chloroplast genome of four species in subgenus Cyathophora and two allied Allium species. The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp. Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content. Seven hotspot regions (infA, rps16, rps15, ndhF, trnG-UCC, trnC-GCA, and trnK-UUU) with nucleotide diversity greater than 0.02 were discovered. The selection analysis showed that some genes have elevated Ka/Ks ratios. Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus Cyathophora was a monophyletic group, containing four species, and A. cyathophorum var. farreri was sister to A. spicatum with 100% bootstrap value. Our study revealed selective pressure may exert effect on several genes of the six Allium species, which may be useful for them to adapt to their specific living environment. We have well resolved the phylogenetic relationship of species in the subgenus Cyathophora, which will contribute to future evolutionary studies or phylogeographic analysis of Allium.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Acta Naturae ◽  
2016 ◽  
Vol 8 (2) ◽  
pp. 79-86 ◽  
Author(s):  
P. V. Elizar’ev ◽  
D. V. Lomaev ◽  
D. A. Chetverina ◽  
P. G. Georgiev ◽  
M. M. Erokhin
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Transcription Terminator ◽  
Response Elements ◽  
Polycomb Response Elements ◽  
The Individual ◽  
Multicellular Organisms ◽  
Different Cell Types ◽  
Main Factor

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesnt prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.

Parasites in Antarctic krill guts inferred from DNA sequences

2019 ◽  
Vol 31 (1) ◽  
pp. 16-22 ◽  
Author(s):  
Alison C. Cleary ◽  
Maria C. Casas ◽  
Edward G. Durbin ◽  
Jaime Gómez-Gutiérrez
Keyword(s):  
Dna Sequences ◽  
High Frequency ◽  
Dna Analysis ◽  
Antarctic Krill ◽  
Euphausia Superba ◽  
Gut Contents ◽  
The West ◽  
West Antarctic ◽  
Wide Range

AbstractThe keystone role of Antarctic krill,Euphausia superbaDana, in Southern Ocean ecosystems, means it is essential to understand the factors controlling their abundance and secondary production. One such factor that remains poorly known is the role of parasites. A recent study of krill diet using DNA analysis of gut contents provided a snapshot of the parasites present within 170E. superbaguts in a small area along the West Antarctic Peninsula. These parasites includedMetschnikowiaspp. fungi,Haptoglossasp. peronosporomycetes,LankesteriaandParalecudinaspp. apicomplexa,Stegophorussp. nematodes, andPseudocolliniaspp. ciliates. Of these parasites,Metschnikowiaspp. fungi andPseudocolliniaspp. ciliates had previously been observed inE. superba, as had other genera of apicomplexans, though notLankesteriaandParalecudina.In contrast, nematodes had previously only been observed in eggs ofE. superba, and there are no literature reports of peronosporomycetes in euphausiids.Pseudocolliniaspp., parasitoids which obligately kill their host, were the most frequently observed infection, with a prevalence of 12%. The wide range of observed parasites and the relatively high frequency of infections suggest parasites may play a more important role than previously acknowledged inE. superbaecology and population dynamics.

Risk as Value: A Switch of Set Hypothesis

1976 ◽  
Vol 38 (2) ◽  
pp. 655-658 ◽  
Author(s):  
George W. Kelling ◽  
Rhea Zirkes ◽  
Deena Myerowitz
Keyword(s):  
High School ◽  
Sex Differences ◽  
High School Students ◽  
General Tendency ◽  
Age Group ◽  
School Students ◽  
Risky Shift

Advisers are expected to be cautious. Typical instructions in research on risky shift induce the adviser role. However, subjects may take the role of the story's hero when they can identify with the hero. It is acceptable for people to be daring when acting for themselves. This hypothesis of a switch of set predicts that subjects should consider themselves more risky than the majority of their peers, a way of expressing the value of risk, when they are similar to the story's hero. High school students rated themselves and the majority on stories dealing with situations common to their age group and on stories dealing with adult problems. Sex of hero was also manipulated. Results supported the hypothesis of a switch of set. Subjects displaced themselves more when the situation was similar to those they might face; in addition, subjects displaced themselves more when the story's hero was of their sex. No sex differences in general tendency to risky displacement were found.

scholarly journals Assessment of the Role of Activator Protein-1 on Transcription of the Mouse Steroidogenic Acute Regulatory Protein Gene

2004 ◽  
Vol 18 (3) ◽  
pp. 558-573 ◽  
Author(s):  
Pulak R. Manna ◽  
Darrell W. Eubank ◽  
Douglas M. Stocco
Keyword(s):  
Binding Site ◽  
Gene Transcription ◽  
Dna Sequences ◽  
Regulatory Protein ◽  
Activator Protein 1 ◽  
Transcriptional Responses ◽  
Activator Protein ◽  
Steroidogenic Acute Regulatory ◽  
Star Gene

Abstract cAMP-dependent mechanisms regulate the steroidogenic acute regulatory (StAR) protein even though its promoter lacks a consensus cAMP response-element (CRE, TGACGTCA). Transcriptional regulation of the StAR gene has been demonstrated to involve combinations of DNA sequences that provide recognition motifs for sequence-specific transcription factors. We recently identified and characterized three canonical 5′-CRE half-sites within the cAMP-responsive region (−151/−1 bp) of the mouse StAR gene. Among these CRE elements, the CRE2 half-site is analogous (TGACTGA) to an activator protein-1 (AP-1) sequence [TGA(C/G)TCA]; therefore, the role of the AP-1 transcription factor was explored in StAR gene transcription. Mutation in the AP-1 element demonstrated an approximately 50% decrease in StAR reporter activity. Using EMSA, oligonucleotide probes containing an AP-1 binding site were found to specifically bind to nuclear proteins obtained from mouse MA-10 Leydig and Y-1 adrenocortical tumor cells. The integrity of the sequence-specific AP-1 element in StAR gene transcription was assessed using the AP-1 family members, Fos (c-Fos, Fra-1, Fra-2, and Fos B) and Jun (c-Jun, Jun B, and Jun D), which demonstrated the involvement of Fos and Jun in StAR gene transcription to varying degrees. Disruption of the AP-1 binding site reversed the transcriptional responses seen with Fos and Jun. EMSA studies utilizing antibodies specific to Fos and Jun demonstrated the involvement of several AP-1 family proteins. Functional assessment of Fos and Jun was further demonstrated by transfecting antisense c-Fos, Fra-1, and dominant negative forms of Fos (A-Fos) and c-Jun (TAM-67) into MA-10 cells, which significantly (P < 0.01) repressed transcription of the StAR gene. Mutation of the AP-1 site in combination with mutations in other cis-elements resulted in a further decrease of StAR promoter activity, demonstrating a functional cooperation between these factors. Mammalian two-hybrid assays revealed high-affinity protein-protein interactions between c-Fos and c-Jun with steroidogenic factor 1, GATA-4, and CCAAT/enhancer binding protein-β. These findings demonstrate that Fos and Jun can bind to the TGACTGA element in the StAR promoter and provide novel insights into the mechanisms regulating StAR gene transcription.

scholarly journals The cultural and economic power of advertisers in the business press

Journalism ◽  
2017 ◽  
Vol 19 (8) ◽  
pp. 1078-1095 ◽  
Author(s):  
Maha Rafi Atal
Keyword(s):  
Economic Analysis ◽  
Financial Analysis ◽  
Cultural Analysis ◽  
Content Increase ◽  
Organizational Mission ◽  
Media Companies ◽  
Business Press ◽  
Business Journalism ◽  
The Impact

Media studies scholarship on advertising has traditionally fallen into two camps. Cultural analysis emphasizes the signals advertisements send to consumers, focusing primarily on the role of advertising creatives. Economic analysis emphasizes advertising’s impact on media companies’ financial performance, focusing on the role of sales managers and proprietors. Both approaches minimize the role of reporters, against whose work advertisers place their messages. This article draws on interviews, as well as financial analysis, at six newsrooms to examine the impact of advertising practices on the editorial independence of reporters. Combining cultural and economic analysis, the article highlights the unique threat advertiser influence poses to critical business reporting, which takes as its subject the very firms who must choose to advertise against it. The article argues that the new forms of advertising, where branded content is presented alongside, and intended to mimic, reported content, increase the threat of advertiser capture. At four legacy outlets studied, investigative business coverage has declined as media organizations react to the changed operating environment with practices that compromise the divide between news and advertising staff. At two online startups studied, where new advertising formats have always been part of strategy, news and sales staff remain separate. Yet there is limited appetite at these outlets for conducting critical business journalism, which is not seen as key to organizational mission. The article concludes with policy recommendations to safeguard the viability of critical business journalism.

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