scholarly journals QTL-based evidence for the role of epistasis in evolution

2005 ◽  
Vol 86 (2) ◽  
pp. 89-95 ◽  
Author(s):  
RUSSELL L. MALMBERG ◽  
RODNEY MAURICIO
Keyword(s):  
Experimental Approach ◽  
Evolutionary Genetics ◽  
Epistatic Qtls ◽  
Epistatic Interactions ◽  
Natural Genetic Variation ◽  
Software Packages ◽  
Controversial Topic ◽  
Trait Locus ◽  
Additive Qtls

The extent to which epistasis contributes to adaptation and speciation has been a controversial topic in evolutionary genetics. One experimental approach to study epistasis is based on quantitative trait locus (QTL) mapping using molecular markers. Comparisons can be made among all possible pair-wise combinations of the markers, irrespective of whether an additive QTL is associated with a marker; several software packages have been developed that facilitate this. We review several examples of using this approach to identify epistatic QTLs for traits of evolutionary or ecological interest. While there is variability in the results, the number of epistatic QTL interactions is often greater than or equal to the number of additive QTLs. The magnitude of epistatic effects can be larger than the additive effects. Thus, epistatic interactions seem to be an important part of natural genetic variation. Future studies of epistatic QTLs could lead to descriptions of the genetic networks underlying variation for fitness-related traits.

scholarly journals Evidence of the Role of QTL Epistatic Interactions in the Increase of Melon Fruit Flesh Content during Domestication

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1064
Author(s):  
Chaymaa Riahi ◽  
Juan Luis Reig-Valiente ◽  
Belén Picó ◽  
Aurora Díaz ◽  
Maria José Gonzalo ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Introgression Line ◽  
Primary Objective ◽  
Chromosome 11 ◽  
Epistatic Interactions ◽  
Fruit Flesh ◽  
F2 Population ◽  
History Of ◽  
Trait Locus

Cultivated melon was domesticated from wild melons, which produce small fruits with non-edible fruit flesh. The increase in fruit flesh is one of the major domestication achievements in this species. In previous work, a quantitative trait locus (QTL) on chromosome 6 (paqt6.1) linked to fruit flesh content was detected in a cross between cultivated (“Piel de Sapo”, PS) and wild (Ames 24294, TRI) accessions. The QTL was introgressed into the PS background, generating the TRI_6-3 introgression line (IL) that confirmed the effects of paqt6.1. The primary objective of this work was to fine-map paqt6.1 as the first step for the map-based cloning. Two different approaches were carried out; however, the results were not consistent, precluding the fine mapping of paqt6.1. TRI_6-3 and other related ILs were genotyped by genotyping-by-sequencing, finding additional introgressions in other chromosomes. In an F2 population from TRI_6-3-x-PS, we found an epistatic interaction between paqt6.1 and another locus on chromosome 11. The interaction was verified in advanced populations, suggesting that the effects of paqt6.1 are conditioned by the allelic composition at another locus in chromosome 11. Both loci should have TRI alleles to reduce the flesh content in the PS background. The implications on the history of melon domestication are discussed.

A Review of the Role of Cue Processing in Task Switching

2013 ◽  
Vol 221 (1) ◽  
pp. 5-14 ◽  
Author(s):  
Kerstin Jost ◽  
Wouter De Baene ◽  
Iring Koch ◽  
Marcel Brass
Keyword(s):  
Cognitive Control ◽  
Task Switching ◽  
Task Switch ◽  
Task Set ◽  
Switch Costs ◽  
Set Switching ◽  
Controversial Topic ◽  
Cue Encoding ◽  
Cue Processing

The role of cue processing has become a controversial topic in research on cognitive control using task-switching procedures. Some authors suggested a priming account to explain switch costs as a form of encoding benefit when the cue from the previous trial is repeated and hence challenged theories that attribute task-switch costs to task-set (re)configuration. A rich body of empirical evidence has evolved that indeed shows that cue-encoding repetition priming is an important component in task switching. However, these studies also demonstrate that there are usually substantial “true” task-switch costs. Here, we review this behavioral, electrophysiological, and brain imaging evidence. Moreover, we describe alternative approaches to the explicit task-cuing procedure, such as the usage of transition cues or the task-span procedure. In addition, we address issues related to the type of cue, such as cue transparency. We also discuss methodological and theoretical implications and argue that the explicit task-cuing procedure is suitable to address issues of cognitive control and task-set switching.

An experimental approach to communal coping

2021 ◽  
pp. 026540752199246
Author(s):  
Melissa Zajdel ◽  
Vicki S. Helgeson
Keyword(s):  
Health Outcomes ◽  
Positive Relationship ◽  
Experimental Approach ◽  
Positive Mood ◽  
Self Report ◽  
Communal Coping ◽  
Observational Measures ◽  
Relationship Outcomes ◽  
The Individual

Communal coping has been linked to better psychological and physical health across a variety of stressful contexts. However, there has been no experimental work causally linking communal coping to relationship and health outcomes. In addition, research has emphasized the collaboration over the shared appraisal component of communal coping. The present study sought to isolate the role of appraisal by manipulating whether dyads viewed a stressor as shared or individual. Friend dyads (n = 64 dyads; 128 participants) were randomly assigned to view a stressor as either a shared or an individual problem, but both groups were allowed to work together. Across self-report and observational measures dyads reported more collaboration and support, better relationship outcomes, and more positive mood after the stressor in the shared than the individual appraisal group. This is the first laboratory evidence to establish causal links of communal coping—specifically shared appraisal—to positive relationship and health outcomes.

scholarly journals Optimizing expression quantitative trait locus mapping workflows for single-cell studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna S. E. Cuomo ◽  
Giordano Alvari ◽  
Christina B. Azodi ◽  
Davis J. McCarthy ◽  
Marc Jan Bonder ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait Locus ◽  
Single Cell ◽  
Quantitative Trait ◽  
Cell Types ◽  
Expression Quantitative Trait Locus ◽  
Eqtl Mapping ◽  
Trait Locus ◽  
The Impact

Abstract Background Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for sample multiplexing improving, population-scale scRNA-seq, and thus single-cell expression quantitative trait locus (sc-eQTL) mapping, is increasingly feasible. Mapping of sc-eQTL provides additional resolution to study the regulatory role of common genetic variants on gene expression across a plethora of cell types and states and promises to improve our understanding of genetic regulation across tissues in both health and disease. Results While previously established methods for bulk eQTL mapping can, in principle, be applied to sc-eQTL mapping, there are a number of open questions about how best to process scRNA-seq data and adapt bulk methods to optimize sc-eQTL mapping. Here, we evaluate the role of different normalization and aggregation strategies, covariate adjustment techniques, and multiple testing correction methods to establish best practice guidelines. We use both real and simulated datasets across single-cell technologies to systematically assess the impact of these different statistical approaches. Conclusion We provide recommendations for future single-cell eQTL studies that can yield up to twice as many eQTL discoveries as default approaches ported from bulk studies.

scholarly journals Inflated false negative rates undermine reproducibility in task-based fMRI

2017 ◽  
Author(s):  
G. Lohmann ◽  
J. Stelzer ◽  
K. Müller ◽  
E. Lacosse ◽  
T. Buschmann ◽  
...  
Keyword(s):  
False Positive ◽  
False Negative ◽  
Sample Sizes ◽  
Test Statistic ◽  
Scientific Validity ◽  
Full Cohort ◽  
Positive Effects ◽  
Software Packages ◽  
Human Connectome Project

AbstractReproducibility is generally regarded as a hallmark of scientific validity. It can be undermined by two very different factors, namely inflated false positive rates or inflated false negative rates. Here we investigate the role of the second factor, i.e. the degree to which true effects are not detected reliably. The availability of large public databases and also supercomputing allows us to tackle this problem quantitatively. Specifically, we estimated the reproducibility in task-based fMRI data over different samples randomly drawn from a large cohort of subjects obtained from the Human Connectome Project. We use the full cohort as a standard of reference to approximate true positive effects, and compute the fraction of those effects that was detected reliably using standard software packages at various smaller sample sizes. We found that with standard sample sizes this fraction was less than 25 percent. We conclude that inflated false negative rates are a major factor that undermine reproducibility. We introduce a new statistical inference algorithm based on a novel test statistic and show that it improves reproducibility without inflating false positive rates.

scholarly journals Molecular Characterization and Expression of PFT, an FHB Resistance Gene at the Fhb1 QTL in Wheat

2018 ◽  
Vol 108 (6) ◽  
pp. 730-736 ◽  
Author(s):  
Yi He ◽  
Xu Zhang ◽  
Yu Zhang ◽  
Dawood Ahmad ◽  
Lei Wu ◽  
...  
Keyword(s):  
Defense Responses ◽  
Wheat Breeding ◽  
Flanking Sequence ◽  
Head Blight ◽  
Breeding Programs ◽  
Diverse Range ◽  
Fhb Resistance ◽  
Trait Locus ◽  
Sumai 3

Fusarium head blight (FHB) is a destructive fungal disease in wheat worldwide. Efforts have been carried out to combat this disease, and the pore-forming toxin-like (PFT) gene at the quantitative trait locus (QTL) Fhb1 was isolated and found to confer resistance to FHB in Sumai 3. In this study, we characterized PFT in 348 wheat accessions. Four haplotypes of PFT were identified. The wild haplotype of PFT had higher resistance than other haplotypes and explained 13.8% of phenotypic variation in FHB resistance by association analysis. PFT was highly expressed during early flowering and increased after Fusarium graminearum treatment in Sumai 3. Analysis of the 5′ flanking sequence of PFT predicted that the cis elements of the PFT promoter were related to hormones and biological defense responses. However, PFT existed not only in the FHB-resistant accessions but also in some susceptible accessions. These results suggested that FHB resistance in a diverse range of wheat genotypes is partially conditioned by PFT. The profiling of FHB resistance and the PFT locus in this large collection of wheat germplasm may prove helpful for incorporating FHB resistance into wheat breeding programs, although more work is needed to reveal the exact role of the QTL Fhb1 in conferring resistance to fungal spread.

Software Literacy

2018 ◽  
pp. 7539-7548
Author(s):  
Elaine Khoo ◽  
Craig Hight
Keyword(s):  
Knowledge Representation ◽  
Conceptual Model ◽  
Information Literacy ◽  
Digital Literacy ◽  
Field Of Study ◽  
Cultural Assumptions ◽  
Software Packages

Software is not neutral. It comes with social and cultural assumptions that afford particular actions while constraining others. The notion of software literacy is emerging as one way to conceptualise the repertoires of skills and understandings needed for people to be critical and creative users of software packages and systems in a software saturated culture. This conceptual model is a response to current digital literacy frameworks which do not identify the implications of the choice of software on what can be achieved. Studies on information literacy and on ways of mastering software have tended to ignore the role of software itself. The study of software is only now emerging as a field of study. This contribution argues for the relevancy of software literacy as part of understanding the ways people engage with software and how its affordances influences knowledge representation, generation and critique. It will define the term and set out three progressive tiers of development towards software literacy.

Function words and polarity

2021 ◽  
pp. 66-85
Author(s):  
Matteo Greco
Keyword(s):  
Experimental Approach ◽  
The Other ◽  
Function Words ◽  
Closed Class ◽  
Other Hand ◽  
Truth Value ◽  
The One ◽  
Syntactic Derivation

Function words are commonly considered to be a small and closed class of words in which each element is associated with a specific and fixed logical meaning. Unfortunately, this is not always true as witnessed by negation: on the one hand, negation does reverse the truth-value conditions of a proposition, and the other hand, it does not, realizing what is called Expletive Negation. This chapter aims to investigate whether a word that is established on the basis of its function can be ambiguous by discussing the role of the syntactic derivation in some instances of so-called Expletive Negation clauses, a case in which negation seems to lose its capacity to deny the proposition associated with its sentence. Both a theoretical and an experimental approach has been adopted.

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