scholarly journals Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Eva Šatović ◽  
Andrea Luchetti ◽  
Juan J. Pasantes ◽  
Daniel García-Souto ◽  
Andrea Cedilak ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Mytilus Galloprovincialis ◽  
Terminal Repeat ◽  
Ruditapes Decussatus ◽  
Direct Repeats ◽  
First Finding ◽  
Genomic Studies ◽  
Clustering Pattern ◽  
Internal Domain

AbstractTerminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this element.

Occurrence, Seasonal Distribution, and Molecular Characterization of Vibrio vulnificus, Vibrio cholerae, and Vibrio parahaemolyticus in Shellfish (Mytilus galloprovincialis and Ruditapes decussatus) Collected in Sardinia (Italy)

2019 ◽  
Vol 82 (11) ◽  
pp. 1851-1856 ◽  
Author(s):  
SONIA LAMON ◽  
SIMONETTA G. CONSOLATI ◽  
FEDERICA FOIS ◽  
MARIA G. CAMBULA ◽  
MARGHERITA PES ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Molecular Characterization ◽  
Vibrio Parahaemolyticus ◽  
Mytilus Galloprovincialis ◽  
Vibrio Vulnificus ◽  
Seasonal Distribution ◽  
Ruditapes Decussatus ◽  
Pathogenic Vibrios ◽  
Vibrio Spp

ABSTRACT In this study, we investigated the occurrence, seasonal distribution, and molecular characterization of pathogenic vibrios in Mediterranean mussels (Mytilus galloprovincialis) and grooved carpet shells (Ruditapes decussatus) from two harvesting areas of Sardinia (Italy). Samples collected before and after depuration were submitted for qualitative and quantitative determination of Vibrio spp. Vibrio spp. isolates were presumptively identified by means of biochemical methods. Identification and virulence profile of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus were performed by molecular methods. The prevalence of Vibrio spp. in M. galloprovincialis and R. decussatus was, respectively, 96 and 77%. The averaged enumeration (mean ± standard deviation) of Vibrio spp. in samples of M. galloprovincialis and R. decussatus collected at the harvesting time was 2.04 ± 0.45 and 2.51 ± 0.65 log CFU/g, respectively. The average contamination levels in samples collected after purification were 2.28 ± 0.58 log CFU/g (M. galloprovincialis) and 2.12 ± 0.67 log CFU/g (R. decussatus). Four potentially pathogenic V. parahaemolyticus isolates (tdh+ or trh+) were recovered from grooved carpet shells samples. No isolate was tdh+/trh+. The presence of potentially pathogenic vibrios in Sardinian waters strengthens the need for rational purification practices under controlled conditions to guarantee the protection of consumers.

scholarly journals Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

2021 ◽  
Vol 22 (9) ◽  
pp. 4707
Author(s):  
Mariana Lopes ◽  
Sandra Louzada ◽  
Margarida Gama-Carvalho ◽  
Raquel Chaves
Keyword(s):  
Human Genome ◽  
Satellite Dna ◽  
Repetitive Sequences ◽  
Nucleotide Composition ◽  
Genomic Component ◽  
Genomic Studies ◽  
Human Genomic ◽  
Definition Of ◽  
High Degree

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

scholarly journals Genome-wide binding potential and regulatory activity of the glucocorticoid receptor’s monomeric and dimeric forms

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Thomas A. Johnson ◽  
Ville Paakinaho ◽  
Sohyoung Kim ◽  
Gordon L. Hager ◽  
Diego M. Presman
Keyword(s):  
Receptor Binding ◽  
Site Response ◽  
Physiological Role ◽  
Binding Potential ◽  
Open Chromatin ◽  
Imaging Data ◽  
Response Elements ◽  
Genome Wide ◽  
Genomic Studies

AbstractA widely regarded model for glucocorticoid receptor (GR) action postulates that dimeric binding to DNA regulates unfavorable metabolic pathways while monomeric receptor binding promotes repressive gene responses related to its anti-inflammatory effects. This model has been built upon the characterization of the GRdim mutant, reported to be incapable of DNA binding and dimerization. Although quantitative live-cell imaging data shows GRdim as mostly dimeric, genomic studies based on recovery of enriched half-site response elements suggest monomeric engagement on DNA. Here, we perform genome-wide studies on GRdim and a constitutively monomeric mutant. Our results show that impairing dimerization affects binding even to open chromatin. We also find that GRdim does not exclusively bind half-response elements. Our results do not support a physiological role for monomeric GR and are consistent with a common mode of receptor binding via higher order structures that drives both the activating and repressive actions of glucocorticoids.

scholarly journals Characterization of the Genomic Xist Locus in Rodents Reveals Conservation of Overall Gene Structure and Tandem Repeats but Rapid Evolution of Unique Sequence

2001 ◽  
Vol 11 (5) ◽  
pp. 833-849 ◽  
Author(s):  
T. B. Nesterova ◽  
S. Ya. Slobodyanyuk ◽  
E. A. Elisaphenko ◽  
A. I. Shevchenko ◽  
C. Johnston ◽  
...  
Keyword(s):  
Gene Structure ◽  
Tandem Repeats ◽  
Rapid Evolution ◽  
Unique Sequence ◽  
Xist Locus

scholarly journals Characterization of the Domoic Acid Uptake Mechanism of the Mussel (Mytilus galloprovincialis) Digestive Gland

Toxins ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 458
Author(s):  
Juan Blanco ◽  
Carmen Mariño ◽  
Helena Martín ◽  
Gonzalo Álvarez ◽  
Araceli E. Rossignoli
Keyword(s):  
Digestive Gland ◽  
Domoic Acid ◽  
Mytilus Galloprovincialis ◽  
Metabolic Inhibitor ◽  
Acid Uptake ◽  
Free Medium ◽  
Shellfish Poisoning ◽  
Uptake Mechanism ◽  
Amnesic Shellfish Poisoning

Cultures of the mussel Mytilus galloprovincialis are frequently affected by accumulation of the amnesic shellfish poisoning toxin domoic acid (DA). This species is characterized by a fast uptake and release of the toxin. In this work, the main characteristics of the uptake mechanism have been studied by incubation of digestive gland thin slices in media with different composition and DA concentration. DA uptake seems to follow Michaelis–Menten kinetics, with a very high estimated KM (1722 µg DA mL−1) and a Vmax of 71.9 µg DA g−1 h−1, which is similar to those found for other amino acids in invertebrates. Replacement of NaCl from the incubation media by Cl-choline (Na+-free medium) did not significantly reduce the uptake, but replacement by sorbitol (Na+-free and Cl−-depleted medium) did. A new experiment replacing all chlorides with their equivalent gluconates (Na+- and Cl−-free medium) showed an important reduction in the uptake that should be attributed to the absence of chloride, pointing to a Na+-independent, Cl− (or anion-) dependent transporter. In media with Na+ and Cl−, neither decreasing the pH nor adding cyanide (a metabolic inhibitor) had significant effect on DA uptake, suggesting that the transport mechanism is not H+- or ATP-dependent. In a chloride depleted medium, lowering pH or adding CN increased the uptake, suggesting that other anions could, at least partially, substitute chloride.

scholarly journals Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

2021 ◽  
Vol 22 (10) ◽  
pp. 5373
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer
Keyword(s):  
Tandem Repeats ◽  
Bacterial Species ◽  
Individual Species ◽  
Large Set ◽  
Bacterial Genomes ◽  
Rna Molecules ◽  
Variable Sequence ◽  
Repeat Size ◽  
Genomic Studies ◽  
Dna Tandem Repeats

Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.

scholarly journals Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1313-1320 ◽  
Author(s):  
John S Taylor ◽  
Felix Breden
Keyword(s):  
Tandem Repeat ◽  
Poecilia Reticulata ◽  
Tandem Repeats ◽  
Phylogenetic Reconstruction ◽  
Variable Number ◽  
Repeat Motif ◽  
Raw Material ◽  
Direct Repeats ◽  
Mt Dna ◽  
Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

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