scholarly journals Promoter architecture links gene duplication with transcriptional divergence

2021 ◽  
Author(s):  
Tzachi Hagai ◽  
Evgeny Fraimovitch
Keyword(s):  
Gene Duplication ◽  
Regulatory Element ◽  
Cpg Islands ◽  
Gene Families ◽  
Gene Expansion ◽  
Promoter Architecture ◽  
Duplication Events ◽  
Long Term Retention

Gene duplication is thought to be a central mechanism in evolution to gain new functions, but gene families vary greatly in their rates of gene duplication and long-term retention. Here, we discover a link between the promoter architecture of vertebrate genes and their rate of duplication: Genes that harbor CpG Islands in their promoters (CGI genes) - nearly 60% of our genes - have rarely duplicated in recent evolutionary times, and most CGI gene duplication events predate the emergence of CGI as a major regulatory element of vertebrate genes. In contrast, CGI-less genes predominate duplications that have occurred since the divergence of vertebrates. Furthermore, CGI-less paralogs are transcriptionally more divergent than CGI paralogs, even when comparing CGI and CGI-less paralogs that have duplicated at similar evolutionary times - suggesting greater capacity of CGI-less promoters to enable divergence in expression. This higher divergence between CGI-less paralogs is also reflected in lower similarity of transcription factors that bind to the promoters of CGI-less paralog pairs in comparison with CGI paralogs. Finally, CGI-less paralogs have a greater tendency to sub- and neo-functionalize, and they transcriptionally diversify faster following duplication. Our results highlight the links between promoter architecture, gene expression plasticity and their impact on gene expansion, and unravel an unappreciated role of CGI elements in shaping genome evolution.

The role of retrieval practice in memory and analogical problem-solving

2018 ◽  
Vol 72 (4) ◽  
pp. 858-871 ◽  
Author(s):  
Autumn B Hostetter ◽  
Elizabeth A Penix ◽  
Mackenzie Z Norman ◽  
W Robert Batsell ◽  
Thomas H Carr
Keyword(s):  
Problem Solving ◽  
Retrieval Practice ◽  
Analogous Problem ◽  
Sources Of Information ◽  
Term Retention ◽  
Analogical Problem ◽  
Long Term Retention ◽  
Do So

Retrieval practice (e.g., testing) has been shown to facilitate long-term retention of information. In two experiments, we examine whether retrieval practice also facilitates use of the practised information when it is needed to solve analogous problems. When retrieval practice was not limited to the information most relevant to the problems (Experiment 1), it improved memory for the information a week later compared with copying or rereading the information, although we found no evidence that it improved participants’ ability to apply the information to the problems. In contrast, when retrieval practice was limited to only the information most relevant to the problems (Experiment 2), we found that retrieval practice enhanced memory for the critical information, the ability to identify the schematic similarities between the two sources of information, and the ability to apply that information to solve an analogous problem after a hint was given to do so. These results suggest that retrieval practice, through its effect on memory, can facilitate application of information to solve novel problems but has minimal effects on spontaneous realisation that the information is relevant.

scholarly journals On the Role of Homework in the Learning Process

2020 ◽  
pp. 18-19
Author(s):  
Sofia Fedorovna Usmanova ◽  
Natalia Nikolaevna Kholina
Keyword(s):  
Independent Study ◽  
Quality Information ◽  
High Quality ◽  
Knowledge And Skills ◽  
Term Retention ◽  
High Quality Information ◽  
Cognitive Activities ◽  
Long Term Retention

A complete, long-term retention of material learned during the lesson should be supplemented by independent study at home, as it is a method of reinforcing knowledge and skills; it forms independence in educational and cognitive activities in children as well as develops their thinking and self-discipline skills. This article deals with different approaches to creating a highly effective homework organization system, which allows to get complete and high-quality information about the level of studied material.

scholarly journals GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

2016 ◽  
Author(s):  
Anil S. Thanki ◽  
Nicola Soranzo ◽  
Wilfried Haerty ◽  
Robert P. Davey
Keyword(s):  
Gene Duplication ◽  
Structural Changes ◽  
Gene Families ◽  
Vital Role ◽  
Software Project ◽  
Command Line ◽  
Gene Trees ◽  
Ancestral Gene ◽  
The Galaxy ◽  
Duplication Events

AbstractBackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.FindingsA certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.ConclusionsGeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy’s user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

Individual differences in factors that modulate storage and retrieval of traumatic memories

1998 ◽  
Vol 10 (4) ◽  
pp. 681-698 ◽  
Author(s):  
MARK L. HOWE
Keyword(s):  
Individual Differences ◽  
Social Cognitive ◽  
Traumatic Events ◽  
Storage And Retrieval ◽  
Traumatic Memories ◽  
Significant Events ◽  
Term Retention ◽  
Long Term Retention

It is argued that memory for traumatic events is similar to that for other distinctive, personally significant events regardless of whether they are affectively positive or negative. Examined in this light, the focus now shifts to the role of individual differences in neurobiological, social, cognitive, and constitutional factors that conspire to determine long-term retention of significant autobiographical experiences. What is known about these factors in determining memorability is reviewed, issues of measurement inadequacies discussed, and recommendations for further research outlined.

scholarly journals The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer

Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 143
Author(s):  
Giuseppe Zardo
Keyword(s):  
Cpg Islands ◽  
Alternative Promoters ◽  
Cpg Dinucleotides ◽  
H3k4 Trimethylation ◽  
Mammalian Embryogenesis ◽  
Intergenic Regions ◽  
Methylation Patterns ◽  
Unmethylated State

CpG methylation in transposons, exons, introns and intergenic regions is important for long-term silencing, silencing of parasitic sequences and alternative promoters, regulating imprinted gene expression and determining X chromosome inactivation. Promoter CpG islands, although rich in CpG dinucleotides, are unmethylated and remain so during all phases of mammalian embryogenesis and development, except in specific cases. The biological mechanisms that contribute to the maintenance of the unmethylated state of CpG islands remain elusive, but the modification of established DNA methylation patterns is a common feature in all types of tumors and is considered as an event that intrinsically, or in association with genetic lesions, feeds carcinogenesis. In this review, we focus on the latest results describing the role that the levels of H3K4 trimethylation may have in determining the aberrant hypermethylation of CpG islands in tumors.

The role of motor affordances in immediate and long-term retention of objects

2015 ◽  
Vol 162 ◽  
pp. 69-75 ◽  
Author(s):  
Katherine Guérard ◽  
Marie-Claude Guerrette ◽  
Vanessa P. Rowe
Keyword(s):  
Term Retention ◽  
Long Term Retention

scholarly journals Transposable Elements in the Genome of Human Parasite Schistosoma mansoni: A Review

2021 ◽  
Vol 6 (3) ◽  
pp. 126
Author(s):  
Gisele Strieder Philippsen
Keyword(s):  
Gene Duplication ◽  
Transposable Elements ◽  
Schistosoma Mansoni ◽  
Dna Sequences ◽  
Current Knowledge ◽  
Coding Sequences ◽  
Human Parasite ◽  
Relevant Role ◽  
Duplication Events

Transposable elements (TEs) are DNA sequences able to transpose within the host genome and, consequently, influence the dynamics of evolution in the species. Among the possible effects, TEs insertions may alter the expression and coding patterns of genes, leading to genomic innovations. Gene-duplication events, resulting from DNA segmental duplication induced by TEs transposition, constitute another important mechanism that contributes to the plasticity of genomes. This review aims to cover the current knowledge regarding TEs in the genome of the parasite Schistosoma mansoni, an agent of schistosomiasis—a neglected tropical disease affecting at least 250 million people worldwide. In this context, the literature concerning TEs description and TEs impact on the genomic architecture for S. mansoni was revisited, displaying evidence of TEs influence on schistosome speciation—mediated by bursts of transposition—and in gene-duplication events related to schistosome–host coevolution processes, as well several instances of TEs contribution into the coding sequences of genes. These findings indicate the relevant role of TEs in the evolution of the S. mansoni genome.

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