scholarly journals Truncated Non-Nuclear Transposable Elements in Grapevine: A Mini Review

2019 ◽  
Vol 50 (4) ◽  
pp. 219-227
Author(s):  
A.V. Milovanov ◽  
J. Tello ◽  
U.C.M. Anhalt ◽  
A. Forneck
Keyword(s):  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Transposable Elements ◽  
Vitis Vinifera ◽  
In Silico ◽  
Gene Evolution ◽  
High Rate ◽  
Miniature Inverted Transposable Elements ◽  
High Level ◽  
Inner Region

Abstract In this mini-review we present insight to the non-nuclear transposable elements and in silico analysis of miniature inverted transposable elements (MITEs) in the grapevine mitochondrial genome. Here we report the identification of 17 truncated sequences in grapevine (Vitis vinifera L.) mitochondrial genome which expectedly belongs to the four ancient transposon families (hAT, Tc1Mariner, Mutator and PIF/Harbinger). Some sequences with a high rate of homology in chloroplast and nuclear genomes were also identified. Thus, it suggests the intercellular gene transfer between these three organelles. These partial sequences showed a high level of similitude with full MITE sequences, and they were found in their inner region, supporting their MITE origin. Further analysis revealed these sequences in other life kingdoms (including eubacteria and archaea), which indicates their ancient origin. Further research showed that 13 out of the 17 sequences are conserved domains of the genes where they are located, suggesting their contribution to gene evolution. Therefore, we suppose that more studies of nature, origin and functional meaning of these sequences and their fusion with genes are necessary. In the light of our observations it will be useful for further studies of V. vinifera genome organizing and systematics, as well as for other species.

scholarly journals Transposable elements promote the evolution of genome streamlining

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Bram van Dijk ◽  
Frederic Bertels ◽  
Lianne Stolk ◽  
Nobuto Takeuchi ◽  
Paul B. Rainey
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Transposable Elements ◽  
Genome Size ◽  
In Silico ◽  
Mobile Genetic Elements ◽  
Theme Issue ◽  
Local Interactions ◽  
Genetic Elements ◽  
Genome Expansion

Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio of coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes have small, streamlined genomes? Using an in silico model describing the genomes of single-celled asexual organisms that coevolve with TEs, we show that TEs acquired from the environment by horizontal gene transfer can promote the evolution of genome streamlining. The process depends on local interactions and is underpinned by rock–paper–scissors dynamics in which populations of cells with streamlined genomes beat TEs, which beat non-streamlined genomes, which beat streamlined genomes, in continuous and repeating cycles. Streamlining is maladaptive to individual cells, but improves lineage viability by hindering the proliferation of TEs. Streamlining does not evolve in sexually reproducing populations because recombination partially frees TEs from the deleterious effects they cause. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

scholarly journals Bioinformatic identification of Ty1/Copia-like transposable elements in Deschampsia antarctica E. Desv.

2019 ◽  
Vol 24 ◽  
pp. 317-320
Author(s):  
I. O. Andreev ◽  
I. I. Konvalyuk ◽  
V. A. Kunakh
Keyword(s):  
Transposable Elements ◽  
In Silico ◽  
Transcriptional Activity ◽  
Background Level ◽  
Bioinformatic Analysis ◽  
Reference Sequence ◽  
Deschampsia Antarctica ◽  
The Family ◽  
High Level ◽  
Copia Retrotransposons

Aim. Identification of Ty1/Copia-like transposable elements in Deschampsia antarctica E Desv. in silico. Methods. Bioinformatic analysis of sequence read archives of D. antarctica genome and transcriptome contained in the GenBank database was conducted. The search was carried out using the rice Ty1/Copia TE Tos 17 as a reference sequence. Results. The search revealed the sequences of Ty1/Copia retrotransposons in the D. antarctica genome to show a high level of identity (up to 75% in the homologous regions) to Tos 17. The uneven distribution of the found reads along the reference sequence indicates the existence of a group of the sequences in the genome to contain elements typical of the family and have varying degrees of identity to Tos 17, with more conservative ones being represented in correspondingly greater numbers among the found reads. The presence of the reads identical to Tos 17 in transcriptome indicates that the TE sequences identified in genome have a certain background level of transcriptional activity. Conclusions. Transcriptionally active Ty1/Copia-like transposable elements were identified in silico in D. antarctica genome using methods of bioinformatics. The sequences found can be used to construct primers for PCR and to analyze the activity of the TE of this family in D. antarctica in further studies. Keywords: bioinformatic analysis, Deschampsia antarctica E Desv., transposable elements, Ty1/Copia.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

scholarly journals High-Intensity Focused Ultrasound Circular Cyclocoagulation in Glaucoma: A Step Forward for Cyclodestruction?

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Rodolfo Mastropasqua ◽  
Vincenzo Fasanella ◽  
Alessandra Mastropasqua ◽  
Marco Ciancaglini ◽  
Luca Agnifili
Keyword(s):  
High Intensity ◽  
Ciliary Body ◽  
Focused Ultrasound ◽  
Current Knowledge ◽  
High Intensity Focused Ultrasound ◽  
High Rate ◽  
Dose Effect ◽  
Computer Assisted ◽  
Refractory Glaucoma ◽  
High Level

The ciliary body ablation is still considered as a last resort treatment to reduce the intraocular pressure (IOP) in uncontrolled glaucoma. Several ablation techniques have been proposed over the years, all presenting a high rate of complications, nonselectivity for the target organ, and unpredictable dose-effect relationship. These drawbacks limited the application of cyclodestructive procedures almost exclusively to refractory glaucoma. High-intensity focused ultrasound (HIFU), proposed in the early 1980s and later abandoned because of the complexity and side effects of the procedure, was recently reconsidered in a new approach to destroy the ciliary body. Ultrasound circular cyclocoagulation (UC3), by using miniaturized transducers embedded in a dedicated circular-shaped device, permits to selectively treat the ciliary body in a one-step, computer-assisted, and non-operator-dependent procedure. UC3 shows a high level of safety along with a predictable and sustained IOP reduction in patients with refractory glaucoma. Because of this, the indication of UC3 was recently extended also to naïve-to-surgery patients, thus reconsidering the role and timing of ciliary body ablation in the surgical management of glaucoma. This article provides a review of the most used cycloablative techniques with particular attention to UC3, summarizing the current knowledge about this procedure and future possible developments.

scholarly journals Mitochondrial DNA Toxicity in Forebrain Neurons Causes Apoptosis, Neurodegeneration, and Impaired Behavior

2010 ◽  
Vol 30 (6) ◽  
pp. 1357-1367 ◽  
Author(s):  
Knut H. Lauritzen ◽  
Olve Moldestad ◽  
Lars Eide ◽  
Harald Carlsen ◽  
Gaute Nesse ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Cognitive Abilities ◽  
Natural Aging ◽  
Base Substitution ◽  
Behavioral Alterations ◽  
Adult Mice ◽  
Progressive Loss ◽  
Forebrain Neurons ◽  
High Level

ABSTRACT Mitochondrial dysfunction underlying changes in neurodegenerative diseases is often associated with apoptosis and a progressive loss of neurons, and damage to the mitochondrial genome is proposed to be involved in such pathologies. In the present study we designed a mouse model that allows us to specifically induce mitochondrial DNA toxicity in the forebrain neurons of adult mice. This is achieved by CaMKIIα-regulated inducible expression of a mutated version of the mitochondrial UNG DNA repair enzyme (mutUNG1). This enzyme is capable of removing thymine from the mitochondrial genome. We demonstrate that a continual generation of apyrimidinic sites causes apoptosis and neuronal death. These defects are associated with behavioral alterations characterized by increased locomotor activity, impaired cognitive abilities, and lack of anxietylike responses. In summary, whereas mitochondrial base substitution and deletions previously have been shown to correlate with premature and natural aging, respectively, we show that a high level of apyrimidinic sites lead to mitochondrial DNA cytotoxicity, which causes apoptosis, followed by neurodegeneration.

scholarly journals In silico Phylogenetic Analysis of hAT Transposable Elements in Plants

Genes ◽  
2018 ◽  
Vol 9 (6) ◽  
pp. 284 ◽  
Author(s):  
Gökhan Karakülah ◽  
Athanasia Pavlopoulou
Keyword(s):  
Phylogenetic Analysis ◽  
Transposable Elements ◽  
In Silico

708 A NEW DIAGNOSTIC PARADIGM FOR LARYNGOPHARYNGEAL REFLUX DISEASE: CORRELATION OF IMPEDANCE-PH MONITORING AND DIGITAL REFLUX SCINTIGRAPHY RESULTS

2021 ◽  
Vol 34 (Supplement_1) ◽  
Author(s):  
Jin-soo Park ◽  
Oleksandr Khoma ◽  
Hans Van Der Wall ◽  
Gregory Falk
Keyword(s):  
Laryngopharyngeal Reflux ◽  
Ph Monitoring ◽  
Acid Reflux ◽  
High Rate ◽  
High Yield ◽  
Time Activity ◽  
Proximal Esophagus ◽  
Laryngopharyngeal Reflux Disease ◽  
High Level ◽  
No Gold Standard

Abstract   No gold-standard investigation exists for laryngopharyngeal reflux (LPR). Multichannel intraluminal impedance (MII)-pH testing has uncertain utility in LPR. Meanwhile, reflux scintigraphy allows immediate and delayed visualisation of tracer reflux in the esophagus, pharynx, and lungs. The present study aimed to correlate MII-pH and scintigraphic reflux results in patients with primary LPR. Methods Consecutive patients with LPR underwent MII-pH and scintigraphic reflux studies. Abnormal values for MII-pH results were defined from existing literature. MII-pH and scintigraphic data were correlated. Results 105 patients with LPR (31 males (29.5%), median age 60 years (range: 20–87)) were studied. Scintigraphic reflux was seen in the pharynx in 94 (90.4%), and in the proximal esophagus in 94 (90.4%). Delayed scintigraphic contamination of the pharynx was seen in 101 patients (96.2%) and in the lungs of 56 patients (53.3%). Abnormal reflux was seen in the distal esophagus in 12.4%, proximal esophagus in 25.7%, and in the pharynx in 82.9%. Patients with poor scintigraphic clearance had higher Demeester scores (p = 0.043), more proximal reflux episodes (p = 0.046), more distal acid reflux episodes (p = 0.023), and longer bolus clearance times (p = 0.002). Conclusion Reflux scintigraphy has a high yield in LPR patients. Scintigraphic time-activity curves correlated with validated MII-pH results. A high rate of pulmonary microaspiration was found in LPR patients. This study demonstrated a high level of pharyngeal contamination by scintigraphy and MII-pH, which supports the use of digital reflux scintigraphy in diagnosing LPR.

Comparative assessment of the dynamics of the incidence of pulmonary and etraulmonary tuberculosis in St. Petersburg for half a century of observation

MedAlliance ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 6-14
Keyword(s):  
Control System ◽  
Incidence Rate ◽  
Extrapulmonary Tuberculosis ◽  
High Rate ◽  
Tb Control ◽  
Complete Restoration ◽  
Third Stage ◽  
High Level ◽  
Clinical Awareness ◽  
Positive Effect

This article describes the results of comparative analysis of the dynamics of incidence of pulmonary tuberculo-sis (TBP), extrapulmonary extrarespiratory tuberculo-sis (TBER) and respiratory extrapulmonary tuberculosis (TBREP) in St. Petersburg (Leningrad) from 1970 to 2019. Throughout the 50 years of observation, epidemiological situation for TBP, especially for TBER, hasmuch improved, with incidence of the latter going down 30 times. Five stages (decades) were identified, within which the factors demonstrate practically the same impact, the growth rate of indicators was calculated for each stage (the value of indicators at the beginning of each stage taken as 100%).The first stage was a simultaneous reduction in the inci-dence rate in all categories of TB localization against the background of socio-economic factors positive effect and organization of effective and comprehensive an-ti-TB measures. In the second stage (1980ies, a period of growing socio-economic problems), the positive dynam-ics of TB incidence stopped and switched to stabilization at a low level. Indicators became more volatile, while TB dynamics by localization more and more desynchro-nized. Тhe third stage (1990iеs, a period of social and economic crisis) was char-acterised by a sharp increase of TB incidence, especially TBREP, with a switch to stabi-lization at a high level. The fourth stage (2000 through 2009, the beginning of TB control system restoration) demonstrated the indicators’ dynamics desynchroniza-tion: the incidence of TBP and TBREP has stabilized, and TBER continued to decline. The fifth stage (2009 through 2019, complete restoration of TB control system) showed a steady trend of incidence rate reduction and return of uniformity in incidence rate of various localizations.There is no increase in the proportion of extrapulmonary TB expected for the incidence decline. TBER incidence had been declining in most stages, with the exception of the 90ies, which could be explained by substandard work in identifying patients, and the rarity of TBER etiological verification. It is necessary to raise the clinical awareness of narrow specialists and general practitioners in the di-agnostic problems associated with TBER.The coincidence of the rate of TB incidence decrease in main localizations in the 1970ies and 2010s proves that a comprehensive state strategy to combat tuberculosis can provide a high rate of TB incidence decrease in various social layers with positive social and economic conditions of life of the population.

scholarly journals Podophyllotoxin and Quercetin in Silico Derivatives Docking Analysis with Cyclooxygenase-2 and Aminopeptidase-N

2021 ◽  
Author(s):  
A.E. Manukyan ◽  
A.A. Hovhannisyan
Keyword(s):  
In Silico ◽  
Biological Activities ◽  
Three Dimensional ◽  
Aminopeptidase N ◽  
Docking Analysis ◽  
Quercetin Derivatives ◽  
Pubchem Database ◽  
A Cell ◽  
Cox 2 ◽  
High Level

ABSTRACTThe cyclooxygenase (COX) enzymes are tumor markers, the inhibition of which can be used in the prevention and therapy of carcinogenesis. It was found that COX-2 IS considered as targets for tumor inhibition. Aminopeptidase N (APN) is a type II membrane-bound metalloprotease associated with cancer, being identified as a cell marker on the surface of malignant myeloid cells and reached a high level of expression in progressive tumors. In anticancer therapy, plant compounds are considered that can inhibit their activity. Modeling of the COX-2 and APN enzymes was carried out on the basis of molecular models of three-dimensional structures from the PDB database [PDB ID: 5f19, 4fyq] RCSB. For docking analysis, 3D ligand models were created using MarvinSketch based on the PubChem database [CID: 5280343, 5281654]. In silico experiments, for the first time, revealed the possible interaction and inhibition of COX-2 and APN by quercetin and quercetin derivatives. Aspirin and Marimastat were taken to compare the results. Possible biological activities and possible side effects of the ligands have been identified.

scholarly journals In silico analysis of GATA4 variants demonstrates main contribution to congenital heart disease

2021 ◽  
Author(s):  
Shiva Abbasi ◽  
Neda Mohsen-Pour ◽  
Niloofar Naderi ◽  
Shahin Rahimi ◽  
Majid Maleki ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
In Silico ◽  
Structure Prediction ◽  
Congenital Heart ◽  
In Silico Analysis ◽  
Different Types ◽  
Frequent Variant ◽  
High Level ◽  
Silico Analysis

Introduction: Congenital heart disease (CHD) is the most common congenital abnormality and the main cause of infant mortality worldwide. Some of the mutations that occur in the GATA4 gene region may result in different types of CHD. Here, we report our in silico analysis of gene variants to determine the effects of the GATA4 gene on the development of CHD. Methods: Online 1000 Genomes Project, ExAC, gnomAD, GO-ESP, TOPMed, Iranome, GME, ClinVar, and HGMD databases were drawn upon to collect information on all the reported GATA4 variations.The functional importance of the genetic variants was assessed by using SIFT, MutationTaster, CADD,PolyPhen-2, PROVEAN, and GERP prediction tools. Thereafter, network analysis of the GATA4protein via STRING, normal/mutant protein structure prediction via HOPE and I-TASSER, and phylogenetic assessment of the GATA4 sequence alignment via ClustalW were performed. Results: The most frequent variant was c.874T>C (45.58%), which was reported in Germany.Ventricular septal defect was the most frequent type of CHD. Out of all the reported variants of GATA4,38 variants were pathogenic. A high level of pathogenicity was shown for p.Gly221Arg (CADD score=31), which was further analyzed. Conclusion: The GATA4 gene plays a significant role in CHD; we, therefore, suggest that it be accorded priority in CHD genetic screening.

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