Tos17 rice element: incomplete but effective.
Ontology highlight
ABSTRACT: Background
Tos17 was the first LTR retrotransposon (Copia) described as active in cultivated rice, and is present in two copies in the genome of the sequenced Nipponbare variety. Only the chromosome 7 copy is active and able to retrotranspose, at least during in vitro culture, and this ability was widely used in insertional mutagenesis assays.Results
Here the structure of the active Tos17 was thoroughly annotated using a set of bioinformatic analyses.Conclusions
Unexpectedly, Tos17 appears to be a non-autonomous LTR retrotransposon, lacking the gag sequence and thus unable to transpose by itself.
SUBMITTER: Sabot F
PROVIDER: S-EPMC3977881 | biostudies-literature | 2014 Apr
REPOSITORIES: biostudies-literature
Publications
<h4>Background</h4>Tos17 was the first LTR retrotransposon (Copia) described as active in cultivated rice, and is present in two copies in the genome of the sequenced Nipponbare variety. Only the chromosome 7 copy is active and able to retrotranspose, at least during in vitro culture, and this ability was widely used in insertional mutagenesis assays.<h4>Results</h4>Here the structure of the active Tos17 was thoroughly annotated using a set of bioinformatic analyses.<h4>Conclusions</h4>Unexpecte ...[more]
Similar Datasets
Project description:Childhood cancer survivors (CCSs) who have undergone bone marrow transplantation with systemic chemotherapy and whole-body irradiation often experience impaired glucose tolerance with marked insulin resistance. Incomplete acquired diabetic lipodystrophy should be considered as a late complication of bone marrow transplantation. A 24-year-old Japanese female patient with incomplete acquired lipodystrophy, a CCS of acute lymphocytic leukemia at the age of 3 years, was treated for diabetes mellitus and dyslipidemia at our hospital. Administration of multiple daily insulin injections (70 units/day), and oral administration of 500 mg/day metformin, 15 mg/day pioglitazone, and 200 mg/day bezafibrate had proven ineffective for her metabolic disorders. Subcutaneous administration of metreleptin improved her insulin resistance and hypertriglyceridemia within a month; however, it failed to maintain adequate plasma glucose levels in the long term. When oral administration of 10 mg/day empagliflozin was added to the metreleptin supplementation, her HbA1c value (National Glycohemoglobin Standardization Program) improved from 11% to 8%, which was maintained for an additional 18 months. This is the first case report of incomplete lipodystrophy that shows efficacy of a combination therapy with metreleptin and a sodium glucose cotransporter 2 (SGLT2) inhibitor for the treatment of diabetes and dyslipidemia. An SGLT2 inhibitor attenuates hyperglycemia through urinary glucose excretion and has been suggested to enhance lipid catabolism in the extra-adipose tissues, especially in the liver and skeletal muscles. Furthermore, metreleptin supplementation could enhance the action of the SGLT2 inhibitor by promoting satiety and lipolysis through the central nervous system. Combination therapy with metreleptin and an SGLT2 inhibitor was suggested to recover the volume of adipose tissue, possibly through improvement of insulin resistance in the adipose tissue. This report highlights the pathophysiological mechanism of an SGLT2 inhibitor in the improvement of glucose metabolism in non-healthy lean CCSs with insulin resistance. Administration of SGLT2 inhibitor, along with metreleptin supplementation, could be a good alternative therapy for diabetic lipodystrophy observed in CCSs.
| S-EPMC8201990 | biostudies-literature
Project description:Spin-orbit coupling (SOC), which is the core of many condensed-matter phenomena such as nontrivial band gap and magnetocrystalline anisotropy, is generally considered appreciable only in heavy elements. This is detrimental to the synthesis and application of functional materials. Therefore, amplifying the SOC effect in light elements is crucial. Herein, focusing on 3d and 4d systems, we demonstrate that the interplay between crystal symmetry and electron correlation can significantly enhance the SOC effect in certain partially occupied orbital multiplets through the self-consistently reinforced orbital polarization as a pivot. Thereafter, we provide design principles and comprehensive databases, where we list all the Wyckoff positions and site symmetries in all two-dimensional (2D) and three-dimensional crystals that could have enhanced SOC effect. Additionally, we predict nine material candidates from our selected 2D material pool as high-temperature quantum anomalous Hall insulators with large nontrivial band gaps of hundreds of meV. Our study provides an efficient and straightforward way for predicting promising SOC-active materials, relieving the use of heavy elements for next-generation spin-orbitronic materials and devices.
| S-EPMC8854432 | biostudies-literature
Project description:Despite the prevalence of transposable elements in the genomes of higher eukaryotes, what is virtually unknown is how they amplify to very high copy numbers without killing their host. Here, we report the discovery of rice strains where a miniature inverted-repeat transposable element (mPing) has amplified from approximately 50 to approximately 1,000 copies in four rice strains. We characterized 280 of the insertions and found that 70% were within 5 kb of coding regions but that insertions into exons and introns were significantly underrepresented. Further analyses of gene expression and transposable-element activity demonstrate that the ability of mPing to attain high copy numbers is because of three factors: (i) the rapid selection against detrimental insertions, (ii) the neutral or minimal effect of the remaining insertions on gene transcription, and (iii) the continued mobility of mPingelements in strains that already have > 1,000 copies. The rapid increase in mPing copy number documented in this study represents a potentially valuable source of population diversity in self-fertilizing plants like rice.
| S-EPMC1693796 | biostudies-literature
Project description:Key messageTransposon insertion polymorphisms can improve prediction of complex agronomic traits in rice compared to using SNPs only, especially when accessions to be predicted are less related to the training set. Transposon insertion polymorphisms (TIPs) are significant sources of genetic variation. Previous work has shown that TIPs can improve detection of causative loci on agronomic traits in rice. Here, we quantify the fraction of variance explained by single nucleotide polymorphisms (SNPs) compared to TIPs, and we explore whether TIPs can improve prediction of traits when compared to using only SNPs. We used eleven traits of agronomic relevance from by five different rice population groups (Aus, Indica, Aromatic, Japonica, and Admixed), 738 accessions in total. We assess prediction by applying data split validation in two scenarios. In the within-population scenario, we predicted performance of improved Indica varieties using the rest of Indica accessions. In the across population scenario, we predicted all Aromatic and Admixed accessions using the rest of populations. In each scenario, Bayes C and a Bayesian reproducible kernel Hilbert space regression were compared. We find that TIPs can explain an important fraction of total genetic variance and that they also improve genomic prediction. In the across population prediction scenario, TIPs outperformed SNPs in nine out of the eleven traits analyzed. In some traits like leaf senescence or grain width, using TIPs increased predictive correlation by 30-50%. Our results evidence, for the first time, that TIPs genotyping can improve prediction on complex agronomic traits in rice, especially when accessions to be predicted are less related to training accessions.
| S-EPMC9482605 | biostudies-literature
Project description:BackgroundGenetically engineered "Golden Rice" contains up to 35 microg beta-carotene per gram of rice. It is important to determine the vitamin A equivalency of Golden Rice beta-carotene to project the potential effect of this biofortified grain in rice-consuming populations that commonly exhibit low vitamin A status.ObjectiveThe objective was to determine the vitamin A value of intrinsically labeled dietary Golden Rice in humans.DesignGolden Rice plants were grown hydroponically with heavy water (deuterium oxide) to generate deuterium-labeled [2H]beta-carotene in the rice grains. Golden Rice servings of 65-98 g (130-200 g cooked rice) containing 0.99-1.53 mg beta-carotene were fed to 5 healthy adult volunteers (3 women and 2 men) with 10 g butter. A reference dose of [13C10]retinyl acetate (0.4-1.0 mg) in oil was given to each volunteer 1 wk before ingestion of the Golden Rice dose. Blood samples were collected over 36 d.ResultsOur results showed that the mean (+/-SD) area under the curve for the total serum response to [2H]retinol was 39.9 +/- 20.7 microg x d after the Golden Rice dose. Compared with that of the [13C10]retinyl acetate reference dose (84.7 +/- 34.6 microg x d), Golden Rice beta-carotene provided 0.24-0.94 mg retinol. Thus, the conversion factor of Golden Rice beta-carotene to retinol is 3.8 +/- 1.7 to 1 with a range of 1.9-6.4 to 1 by weight, or 2.0 +/- 0.9 to 1 with a range of 1.0-3.4 to 1 by moles.ConclusionBeta-carotene derived from Golden Rice is effectively converted to vitamin A in humans. This trial was registered at clinicaltrials.gov as NCT00680355.
| S-EPMC2682994 | biostudies-literature
Project description:The primary objective of acoustic metamaterial research is to design subwavelength systems that behave as effective materials with novel acoustical properties. One such property couples the stress-strain and the momentum-velocity relations. This response is analogous to bianisotropy in electromagnetism, is absent from common materials, and is often referred to as Willis coupling after J.R., Willis, who first described it in the context of the dynamic response of heterogeneous elastic media. This work presents two principal results: first, experimental and theoretical demonstrations, illustrating that Willis properties are required to obtain physically meaningful effective material properties resulting solely from local behaviour of an asymmetric one-dimensional isolated element and, second, an experimental procedure to extract the effective material properties from a one-dimensional isolated element. The measured material properties are in very good agreement with theoretical predictions and thus provide improved understanding of the physical mechanisms leading to Willis coupling in acoustic metamaterials.
| S-EPMC5474687 | biostudies-literature
Project description:Type III secretion system (T3SS) plays important roles in bacteria and host cell interactions by specifically translocating type III effectors into the cytoplasm of the host cells. The N-terminal amino acid sequences of the bacterial type III effectors determine their specific secretion via type III secretion conduits. It is still unclear as to how the N-terminal sequences guide this specificity. In this work, the amino acid composition, secondary structure, and solvent accessibility in the N-termini of type III and non-type III secreted proteins were compared and contrasted. A high-efficacy mathematical model based on these joint features was developed to distinguish the type III proteins from the non-type III ones. The results indicate that secondary structure and solvent accessibility may make important contribution to the specific recognition of type III secretion signals. Analysis also showed that the joint feature of the N-terminal 6(th)-10(th) amino acids are especially important for guiding specific type III secretion. Furthermore, a genome-wide screening was performed to predict Salmonella type III secreted proteins, and 8 new candidates were experimentally validated. Interestingly, type III secretion signals were also predicted in gram-positive bacteria and yeasts. Experimental validation showed that two candidates from yeast can indeed be secreted through Salmonella type III secretion conduit. This research provides the first line of direct evidence that secondary structure and solvent accessibility contain important features for guiding specific type III secretion. The new software based on these joint features ensures a high accuracy (general cross-validation sensitivity of ∼96% at a specificity of ∼98%) in silico identification of new type III secreted proteins, which may facilitate our understanding about the specificity of type III secretion and the evolution of type III secreted proteins.
| S-EPMC3617162 | biostudies-literature
Project description:Rice (Oryza sativa L.) is a staple food for half of the world's population, and its biofortification is a key factor in fighting micronutrient malnutrition. However, harmful heavy metals tend to accumulate in rice grains due to soil and water contamination. Therefore, it is important to improve beneficial micronutrient contents and reduce the accumulation of undesirable metals in rice grain. To better characterize the genetic control of mineral accumulation in rice, we conducted association genetics on the ion contents of white and brown grains using a collection of 184 Vietnamese rice landraces. In total, 27 significant associations were identified and delimited into quantitative trait loci associated with macronutrients such as phosphorus, potassium or calcium; micronutrients such as iron or zinc; or toxic heavy metals such as arsenic and cadmium. Several genes related to ion homeostasis or ion transport were identified in the different quantitative trait loci. LOC_Os10g30610, present in qRAs10-1 associated with arsenic content in brown rice, encodes an ABC transporter (OsABCG25), which is involved in the silicon-induced formation of the Casparian strip in the rice exodermis and could act as a barrier restricting As diffusion within the root cortex. LOC_Os05g04330, present in qRP5-1 and associated with phosphorus content in brown rice, encodes a CHH methylation maintenance protein, and its expression is downregulated in roots in the presence of the phosphorus uptake 1 (Pup1), suggesting a role for epigenetics in the regulation of phosphorus uptake and accumulation in grain. These findings reveal novel quantitative trait loci associated with grain ion content and candidate genes that are potentially valuable for breeding programs aimed at rice grain biofortification and reducing toxic metal accumulation.
| S-EPMC11666011 | biostudies-literature
Project description:BackgroundTransposable element (TE)-related genes comprise a significant portion of the gene catalog of grasses, although their functions are insufficiently characterized. The recent availability of TE-related gene annotation from the complete genome sequence of rice (Oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially mobile elements and their related genes.ResultsWe conducted a genome-wide survey of the transcriptional activity of TE-related genes associated with 15 developmental stages and stress conditions. This dataset was obtained using a microarray encompassing 2,191 unique TE-related rice genes, which were represented by oligonucleotide probes that were free from cross-hybridization. We found that TE-related genes exhibit much lower transcriptional activities than do non-TE-related genes, although representative transcripts were detected from all superfamilies of both type I and II TE-related genes. The strongest transcriptional activities were detected in TE-related genes from among the MULE and CACTA superfamilies. Phylogenetic analyses suggest that domesticated TE-related genes tend to form clades with active transcription. In addition, chromatin-level regulations through histone and DNA modifications, as well as enrichment of certain cis elements in the promoters, appear to contribute to the transcriptional activation of representative TE-related genes.ConclusionOur findings reveal clear, albeit low, general transcription of TE-related genes. In combination with phylogenetic analysis, transcriptional analysis has the potential to lead to the identification of domesticated TEs with adapted host functions.
| S-EPMC1852403 | biostudies-literature
Project description:Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.
| S-EPMC6850418 | biostudies-literature