Phenotype robustness, defined as the average mutational robustness of all the genotypes that map to a given phenotype, plays a key role in facilitating neutral exploration of novel phenotypic variation by an evolving population. By applying results from coding theory, we prove that the maximum phenotype robustness occurs when genotypes are organized as bricklayer's graphs, so-called because they resemble the way in which a bricklayer would fill in a Hamming graph. The value of the maximal robustness is given by a fractal continuous everywhere but differentiable nowhere sums-of-digits function from number theory. Interestingly, genotype-phenotype maps for RNA secondary structure and the hydrophobic-polar (HP) model for protein folding can exhibit phenotype robustness that exactly attains this upper bound. By exploiting properties of the sums-of-digits function, we prove a lower bound on the deviation of the maximum robustness of phenotypes with multiple neutral components from the bricklayer's graph bound, and show that RNA secondary structure phenotypes obey this bound. Finally, we show how robustness changes when phenotypes are coarse-grained and derive a formula and associated bounds for the transition probabilities between such phenotypes.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10369032 | PMC |
http://dx.doi.org/10.1098/rsif.2023.0169 | DOI Listing |
J Virol
January 2025
Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.
The imperative for developing robust tools to detect, analyze, and characterize viruses has become increasingly evident as they continue to threaten human health. In this review, we focus on recent advancements in studying human viruses with flow virometry (FV), an emerging technique that has gained considerable momentum over the past 5 years. These advancements include the application of FV in viral surface phenotyping, viral protein functionality, virus sorting, vaccine development, and diagnostics.
View Article and Find Full Text PDFCurr Opin Organ Transplant
January 2025
Department of Kinesiology and Health Sciences.
Purpose Of Review: Patients that present with a physical frail phenotype have a higher risk of poor kidney transplant outcomes and are therefore less likely to be wait listed for a transplant. The physical frailty phonotype is more prevalent in older adults >65years with chronic and end stage kidney disease, thus partly contributing to inequitable access to transplant. Frailty can potentially be reversed by prehabilitation.
View Article and Find Full Text PDFBackground: Several modifiable risk factors for dementia and related neurodegenerative diseases have been identified including education level, socio-economic status, and environmental exposures - however, how these population-level risks relate to individual risk remains elusive. To address this, we assess over 450 potential risk factors in one deeply clinically and demographically phenotyped cohort using random forest classifiers to determine predictive markers of poor cognitive function. This study aims to understand early risk factors for dementia by identifying predictors of poor cognitive performance amongst a comprehensive battery of imaging, blood, atmospheric pollutant and socio-economic measures.
View Article and Find Full Text PDFZebrafish models of genetic epilepsy benefit from the ability to assess disease-relevant knock-out alleles with numerous tools, including genetically encoded calcium indicators (GECIs) and hypopigmentation alleles to improve visualization. However, there may be unintended effects of these manipulations on the phenotypes under investigation. There is also debate regarding the use of stable loss-of-function (LoF) alleles in zebrafish, due to genetic compensation (GC).
View Article and Find Full Text PDFNOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defense mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self/non-self recognition process that prevents the vegetative fusion of genetically distinct individuals, reducing the risk of parasitism. The and NLRs in are highly polymorphic incompatibility genes ( genes) whose products recognize different alleles of the gene via a sensor domain composed of WD40 repeats.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!