Quantifying Phenotypic Variation in Isogenic Caenorhabditis elegans Expressing Phsp-16.2::gfp by Clustering 2D Expression Patterns

Seewald, Alexander K.; Cypser, James R.; Mendenhall, Alexander; Johnson, Thomas E.

doi:10.1371/journal.pone.0011426

Cited by 13 publications

(12 citation statements)

References 14 publications

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“…Morphological variation in genetically alike animals, as we have detected in the aortic valve of our hamsters, is not a novelty. There is enough evidence that isogenic populations can show a considerable phenotypic variation between individuals for a given trait (reviewed in Veitia, 2005;Wong et al 2005;Vogt et al 2008;Seewald et al 2010). The phenotype results from the interaction between genotype and environmental factors, along with an additional third component (Gä rtner, 1990) of stochastic nature that causes random variation.…”

Section: Discussionmentioning

confidence: 99%

Genetically alike Syrian hamsters display both bifoliate and trifoliate aortic valves

Sans‐Coma

Fernández

et al. 2011

Journal of Anatomy

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The bifoliate, or bicuspid, aortic valve (BAV) is the most frequent congenital cardiac anomaly in man. It is a heritable defect, but its mode of inheritance remains unclear. Previous studies in Syrian hamsters showed that BAVs with fusion of the right and left coronary leaflets are expressions of a trait, the variation of which takes the form of a phenotypic continuum. It ranges from a trifoliate valve with no fusion of the coronary leaflets to a bifoliate root devoid of any raphe. The intermediate stages are represented by trifoliate valves with fusion of the coronary aortic leaflets, and bifoliate valves with raphes. The aim of this study was to elucidate whether the distinct morphological variants rely on a common genotype, or on different genotypes. We examined the aortic valves from 1 849 Syrian hamsters belonging to a family subjected to systematic inbreeding by full-sib mating. The incidence of the different trifoliate aortic valve (TAV) and bifoliate aortic valve (BAV) morphological variants widely varied in the successive inbred generations. TAVs with extensive fusion of the leaflets, and BAVs, accounted for five-sixths of the patterns found in Syrian hamsters considered to be genetically alike or virtually isogenic, with the probability of homozygosity being 0.999 or higher. The remaining one-sixth hamsters had aortic valves with a tricuspid design, but in most cases the right and left coronary leaflets were slightly fused. Results of crosses between genetically alike hamsters, with the probability of homozygosity being 0.989 or higher, revealed no significant association between the valvar phenotypes in the parents and their offspring. Our findings are consistent with the notion that the BAVs of the Syrian hamster are expressions of a quantitative trait subject to polygenic inheritance. They suggest that the genotype of the virtually isogenic animals produced by systematic inbreeding greatly predisposes to the development of anomalous valves, be they bifoliate, or trifoliate with extensive fusion of the leaflets. We infer that the same underlying genotype may account for the whole range of valvar morphological variants, suggesting that factors other than genetic ones are acting during embryonic life, creating the so-called intangible variation or developmental noise, and playing an important role in the definitive anatomic configuration of the valve. The clinical implication from our study is that congenital aortic valves with a trifoliate design, but with fusion of coronary aortic leaflets, may harbour the same inherent risks as those already recognised for BAVs with fusion of right and left coronary leaflets.

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Section: Discussionmentioning

confidence: 99%

Genetically alike Syrian hamsters display both bifoliate and trifoliate aortic valves

Sans‐Coma

Fernández

et al. 2011

Journal of Anatomy

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“…Because approximately 90% of the reporter signal in adult animals expressing P hsp-16 . 2 -GFP comes from the 20 cells of the intestine [ 11 , 12 ] (additional details in Results and S1 Text , Section 1), we developed low measurement error methods to measure reporter gene expression in these cells. Both a characterized 530 copy reporter strain and a single copy strain showed consistent patterns of expression.…”

Section: Introductionmentioning

confidence: 99%

Single Cell Quantification of Reporter Gene Expression in Live Adult Caenorhabditis elegans Reveals Reproducible Cell-Specific Expression Patterns and Underlying Biological Variation

et al. 2015

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In multicellular organisms such as Caenorhabditis elegans, differences in complex phenotypes such as lifespan correlate with the level of expression of particular engineered reporter genes. In single celled organisms, quantitative understanding of responses to extracellular signals and of cell-to-cell variation in responses has depended on precise measurement of reporter gene expression. Here, we developed microscope-based methods to quantify reporter gene expression in cells of Caenorhabditis elegans with low measurement error. We then quantified expression in strains that carried different configurations of Phsp-16.2-fluorescent-protein reporters, in whole animals, and in all 20 cells of the intestine tissue, which is responsible for most of the fluorescent signal. Some animals bore more recently developed single copy Phsp-16.2 reporters integrated at defined chromosomal sites, others, “classical” multicopy reporter gene arrays integrated at random sites. At the level of whole animals, variation in gene expression was similar: strains with single copy reporters showed the same amount of animal-to-animal variation as strains with multicopy reporters. At the level of cells, in animals with single copy reporters, the pattern of expression in cells within the tissue was highly stereotyped. In animals with multicopy reporters, the cell-specific expression pattern was also stereotyped, but distinct, and somewhat more variable. Our methods are rapid and gentle enough to allow quantification of expression in the same cells of an animal at different times during adult life. They should allow investigators to use changes in reporter expression in single cells in tissues as quantitative phenotypes, and link those to molecular differences. Moreover, by diminishing measurement error, they should make possible dissection of the causes of the remaining, real, variation in expression. Understanding such variation should help reveal its contribution to differences in complex phenotypic outcomes in multicellular organisms.

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“…Our subsequent studies showed that the bulk of the fluorescent signal came from the 20 individual cells (Seewald et al ., ). Subsequent work to develop low measurement error methods for single cells showed that the reporter signal could be quantified in individual cells in anesthetized live animals (Mendenhall et al ., ; Fig.…”

Section: Quantification Of Reporter Outputs In Living Single Cells Camentioning

confidence: 97%

Using measures of single‐cell physiology and physiological state to understand organismic aging

2015

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SummaryGenetically identical organisms in homogeneous environments have different lifespans and healthspans. These differences are often attributed to stochastic events, such as mutations and 'epimutations', changes in DNA methylation and chromatin that change gene function and expression. But work in the last 10 years has revealed differences in lifespan-and health-related phenotypes that are not caused by lasting changes in DNA or identified by modifications to DNA or chromatin. This work has demonstrated persistent differences in single-cell and wholeorganism physiological states operationally defined by values of reporter gene signals in living cells. While some single-cell states, for example, responses to oxygen deprivation, were defined previously, others, such as a generally heightened ability to make proteins, were, revealed by direct experiment only recently, and are not well understood. Here, we review technical progress that promises to greatly increase the number of these measurable single-cell physiological variables and measureable states. We discuss concepts that facilitate use of single-cell measurements to provide insight into physiological states and state transitions. We assert that researchers will use this information to relate cell level physiological readouts to whole-organism outcomes, to stratify aging populations into groups based on different physiologies, to define biomarkers predictive of outcomes, and to shed light on the molecular processes that bring about different individual physiologies. For these reasons, quantitative study of single-cell physiological variables and state transitions should provide a valuable complement to genetic and molecular explanations of how organisms age.

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Quantifying Phenotypic Variation in Isogenic Caenorhabditis elegans Expressing Phsp-16.2::gfp by Clustering 2D Expression Patterns

Cited by 13 publications

References 14 publications

Genetically alike Syrian hamsters display both bifoliate and trifoliate aortic valves

Genetically alike Syrian hamsters display both bifoliate and trifoliate aortic valves

Single Cell Quantification of Reporter Gene Expression in Live Adult Caenorhabditis elegans Reveals Reproducible Cell-Specific Expression Patterns and Underlying Biological Variation

Using measures of single‐cell physiology and physiological state to understand organismic aging

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