scholarly journals Heritability of the Structures and 13C Fractionation in Tomato Leaf Wax Alkanes: A Genetic Model System to Inform Paleoenvironmental Reconstructions

2017 ◽  
Vol 5 ◽  
Author(s):  
Amanda L. D. Bender ◽  
Daniel H. Chitwood ◽  
Alexander S. Bradley
Keyword(s):  
Genetic Model ◽  
Model System ◽  
Tomato Leaf ◽  
Leaf Wax ◽  
Paleoenvironmental Reconstructions

scholarly journals The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits

2021 ◽  
Author(s):  
Anthony D Long ◽  
Alan Barbour ◽  
Phillip N Long ◽  
Vanessa J Cook ◽  
Arundhati Majumder
Keyword(s):  
Complex Traits ◽  
Genetic Model ◽  
Peromyscus Leucopus ◽  
False Positive Rate ◽  
Model System ◽  
Sequencing Data ◽  
Power Estimate ◽  
Genome Wide ◽  
Low Pass ◽  
Closed Colony

Although Peromyscus leucopus (deermouse) is not considered a genetic model system, its genus is well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and its ability to serve as a disease vector. Here we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a non-traditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals between 1982 and 1985 and subsequently maintained for 35+ years (~40-60 generations). From 405 low-pass (~1X) short-read sequenced deermice we accurately imputed genotypes at 17,751,882 SNPs. Conditional on observed genotypes for a subset of 297 individuals, simulations were conducted in which a QTL contributes 5% to a complex trait under three different genetic models. The power of either a haplotype- or marker-based statistical test was estimated to be 15-25% to detect the hidden QTL. Although modest, this power estimate is consistent with that of DO/HS mice and rat experiments for an experiment with ~300 individuals. This limitation in QTL detection is mostly associated with the stringent significance threshold required to hold the genome-wide false positive rate low, as in all cases we observe considerable linkage signal at the location of simulated QTL, suggesting a larger panel would exhibit greater power. For the subset of cases where a QTL was detected, localization ability appeared very desirable at ~1-2Mb. We finally carried out a GWAS on a demonstration trait, bleeding time. No tests exceeded the threshold for genome-wide significance, but one of four suggestive regions co-localizes with Von Willebrand factor. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice in much the same manner as founders-known DO/HS mice and rats, with genotypes obtained from low pass sequencing data. Our results further suggest that the DO/HS approach can be powerfully extended to any system in which a founders-unknown closed colony has been maintained for several dozen generations.

scholarly journals The FDA-approved drugs ticlopidine, sertaconazole, and dexlansoprazole can cause morphological changes in C. elegans

2020 ◽  
Author(s):  
Kyle F Galford ◽  
Antony M Jose
Keyword(s):  
Proton Pump Inhibitor ◽  
Genetic Model ◽  
Morphological Changes ◽  
Model System ◽  
Model Organisms ◽  
Regulatory Agencies ◽  
C Elegans ◽  
Therapeutic Drugs ◽  
Approved Drugs ◽  
Fda Approved Drugs

AbstractUrgent need for treatments limit studies of therapeutic drugs before approval by regulatory agencies. Analyses of drugs after approval can therefore improve our understanding of their mechanism of action and enable better therapies. We screened a library of 1443 Food and Drug Administration (FDA)-approved drugs using a simple assay in the nematode C. elegans and found three compounds that caused morphological changes. While the anticoagulant ticlopidine and the antifungal sertaconazole caused morphologically distinct pharyngeal defects upon acute exposure, the proton-pump inhibitor dexlansoprazole caused molting defects and required exposure during larval development. Such easily detectable defects in a powerful genetic model system advocate the continued exploration of current medicines using a variety of model organisms to better understand drugs already prescribed to millions of patients.

scholarly journals The fish watch: Zebrafish: a clock in every cell

2005 ◽  
Vol 27 (6) ◽  
pp. 23-26
Author(s):  
Amanda-Jayne F. Carr ◽  
David Whitmore
Keyword(s):  
Circadian Rhythms ◽  
Danio Rerio ◽  
Biological Process ◽  
Genetic Model ◽  
Model System ◽  
Biological Processes ◽  
Powerful Method ◽  
Dark Cycle ◽  
Environmental Light ◽  
The One

The environmental light–dark cycle is one of the most reliable rhythmic signals, and many organisms have evolved a circadian (circa diem, ‘about a day’) system to co-ordinate biological processes with this predictable environmental change. These rhythms are endogenous and persist even in constant conditions, the light–dark cycle serving to synchronize these rhythms precisely to 24 hours. Genetic approaches have proved invaluable in increasing our understanding of the circadian clock. The ability to isolate a mutant with a defect in a rhythmic process is a very powerful method, which depends on no prior assumptions about the biological process under investigation. Consequently, Drosophila and the mouse have become the most powerful genetic models to study circadian rhythms in animals. The one alternative vertebrate genetic model system to the mouse is the zebrafish (Danio rerio).

scholarly journals Heritability of the structures and 13C fractionation in tomato leaf wax alkanes: a genetic model system to inform paleoenvironmental reconstructions

2017 ◽  
Author(s):  
Amanda L.D. Bender ◽  
Daniel H. Chitwood ◽  
Alexander S. Bradley
Keyword(s):  
Plant Communities ◽  
Genetic Model ◽  
Average Chain Length ◽  
Implicit Assumption ◽  
Tomato Cultivar ◽  
Environmental Variance ◽  
Leaf Wax ◽  
Tomato Species ◽  
Leaf Waxes ◽  
Paleoclimate Proxy

AbstractLeaf wax n-alkanes are broadly used to reconstruct paleoenvironmental information. However, the utility of the n-alkane paleoclimate proxy is modulated by the extent to which genetic as well as environmental factors influence the structural and isotopic variability of leaf waxes. In paleoclimate applications, there is an implicit assumption that most variation of leaf wax traits through a time series can be attributed to environmental change and that biological sources of variability within plant communities are small. For example, changes in hydrology affect the δ2 H of waxes though rainwater and the δ13C of leaf waxes by changing plant communities (i.e., C3 versus C4 input). Here we test the assumption of little genetic control over 5 C variation of leaf wax by presenting the results of an experimental greenhouse growth study in which we estimate the role of genetic variability on structural and isotopic leaf wax traits in a set of 76 introgression lines (ILs) between two interfertile Solanum (tomato) species: S. lycopersicum cv M82 (hereafter cv M82) and S. pennellii. We found that the leaves of S. pennellii, a wild desert tomato relative, produces significantly more iso-alkanes than cv M82, a domesticated tomato cultivar adapted to water-replete conditions; we introduce a methylation index to summarize the ratio of branched (iso- and anteiso-) to total alkanes. Between S. pennellii and cv M82, the iso-alkanes were found to be enriched in 13C by 1.2–1.4%o over n-alkanes. By modeling our results from the ILs, we report the broad-sense heritability values (H2) of leaf wax traits to describe the degree to which genetic variation contributes to variation of these traits. Individual carbon isotope values of alkanes are of low heritability (H2 = 0.13–0.19), suggesting that δ13C of leaf waxes from this study are strongly influenced by environmental variance, which supports the interpretation that variation in the 5 C of wax compounds recorded in sediments reflects paleohydrological changes. Average chain length (ACL) values of n-alkanes are of intermediate heritability (H2 = 0.30), suggesting that ACL values are strongly influenced by genetic cues.

scholarly journals The Intestine of Drosophila melanogaster: An Emerging Versatile Model System to Study Intestinal Epithelial Homeostasis and Host-Microbial Interactions in Humans

2019 ◽  
Vol 7 (9) ◽  
pp. 336 ◽  
Author(s):  
Florence Capo ◽  
Alexa Wilson ◽  
Francesca Di Cara
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Model ◽  
Current Knowledge ◽  
Cell Lineage ◽  
Model Organism ◽  
Model System ◽  
Microbial Interactions ◽  
Stem Cell Lineage ◽  
Bowel Diseases

In all metazoans, the intestinal tract is an essential organ to integrate nutritional signaling, hormonal cues and immunometabolic networks. The dysregulation of intestinal epithelium functions can impact organism physiology and, in humans, leads to devastating and complex diseases, such as inflammatory bowel diseases, intestinal cancers, and obesity. Two decades ago, the discovery of an immune response in the intestine of the genetic model system, Drosophila melanogaster, sparked interest in using this model organism to dissect the mechanisms that govern gut (patho) physiology in humans. In 2007, the finding of the intestinal stem cell lineage, followed by the development of tools available for its manipulation in vivo, helped to elucidate the structural organization and functions of the fly intestine and its similarity with mammalian gastrointestinal systems. To date, studies of the Drosophila gut have already helped to shed light on a broad range of biological questions regarding stem cells and their niches, interorgan communication, immunity and immunometabolism, making the Drosophila a promising model organism for human enteric studies. This review summarizes our current knowledge of the structure and functions of the Drosophila melanogaster intestine, asserting its validity as an emerging model system to study gut physiology, regeneration, immune defenses and host-microbiota interactions.

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