Prediction of the importance of auxiliary traits using computational intelligence and machine learning: A simulation study

The present study evaluated the importance of auxiliary traits of a principal trait based on phenotypic information and previously known genetic structure using computational intelligence and machine learning to develop predictive tools for plant breeding. Data of an F2 population represented by 500 individuals, obtained from a cross between contrasting homozygous parents, were simulated. Phenotypic traits were simulated based on previously established means and heritability estimates (30%, 50%, and 80%); traits were distributed in a genome with 10 linkage groups, considering two alleles per marker. Four different scenarios were considered. For the principal trait, heritability was 50%, and 40 control loci were distributed in five linkage groups. Another phenotypic control trait with the same complexity as the principal trait but without any genetic relationship with it and without pleiotropy or a factorial link between the control loci for both traits was simulated. These traits shared a large number of control loci with the principal trait, but could be distinguished by the differential action of the environment on them, as reflected in heritability estimates (30%, 50%, and 80%). The coefficient of determination were considered to evaluate the proposed methodologies. Multiple regression, computational intelligence, and machine learning were used to predict the importance of the tested traits. Computational intelligence and machine learning were superior in extracting nonlinear information from model inputs and quantifying the relative contributions of phenotypic traits. The R2 values ranged from 44.0% - 83.0% and 79.0% - 94.0%, for computational intelligence and machine learning, respectively. In conclusion, the relative contributions of auxiliary traits in different scenarios in plant breeding programs can be efficiently predicted using computational intelligence and machine learning.

Children do not distinguish efficient from inefficient actions during observation

Observation is a powerful way to learn efficient actions from others. However, the role of observers’ motor skill in assessing efficiency of others is unknown. Preschoolers are notoriously poor at performing multi-step actions like grasping the handle of a tool. Preschoolers (N = 22) and adults (N = 22) watched video-recorded actors perform efficient and inefficient tool use. Eye tracking showed that preschoolers and adults looked equally long at the videos, but adults looked longer than children at how actors grasped the tool. Deep learning analyses of participants’ eye gaze distinguished efficient from inefficient grasps for adults, but not for children. Moreover, only adults showed differential action-related pupil dilation and neural activity (suppressed oscillation power in the mu frequency) while observing efficient vs. inefficient grasps. Thus, children observe multi-step actions without “seeing” whether the initial step is efficient. Findings suggest that observer’s own motor efficiency determines whether they can perceive action efficiency in others.

Differential Action of Connexin Hemichannel and Pannexin Channel Therapeutics for Potential Treatment of Retinal Diseases

Dysregulation of retinal function in the early stages of light-induced retinal degeneration involves pannexins and connexins. These two types of proteins may contribute to channels that release ATP, leading to activation of the inflammasome pathway, spread of inflammation and retinal dysfunction. However, the effect of pannexin channel block alone or block of both pannexin channels and connexin hemichannels in parallel on retinal activity in vivo is unknown. In this study, the pannexin channel blocker probenecid and the connexin hemichannel blocker tonabersat were used in the light-damaged rat retina. Retinal function was evaluated using electroretinography (ERG), retinal structure was analyzed using optical coherence tomography (OCT) imaging and the tissue response to light-induced injury was assessed immunohistochemically with antibodies against glial fibrillary acidic protein (GFAP), Ionized calcium binding adaptor molecule 1 (Iba-1) and Connexin43 (Cx43). Probenecid did not further enhance the therapeutic effect of connexin hemichannel block in this model, but on its own improved activity of certain inner retina neurons. The therapeutic benefit of blocking connexin hemichannels was further evaluated by comparing these data against results from our previously published studies that also used the light-damaged rat retina model. The analysis showed that treatment with tonabersat alone was better than probenecid alone at restoring retinal function in the light-damaged retina model. The results assist in the interpretation of the differential action of connexin hemichannel and pannexin channel therapeutics for potential treatment of retinal diseases.

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories

Mutations of the haematopoietic master regulator RUNX1 are associated with acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend upon the class of the RUNX1 mutation. The biochemical behaviour of these oncoproteins and their ability to cause unique diseases has been well studied, but the genomic basis of their differential action is unknown. To address this question we compared integrated phenotypic, transcriptomic, and genomic data from cells expressing four types of RUNX1 oncoproteins in an inducible fashion during blood development from embryonic stem cells. We show that each class of mutant RUNX1 deregulates endogenous RUNX1 function by a different mechanism, leading to specific alterations in developmentally controlled transcription factor binding and chromatin programming. The result is distinct perturbations in the trajectories of gene regulatory network changes underlying blood cell development which are consistent with the nature of the final disease phenotype. The development of novel treatments for RUNX1-driven diseases will therefore require individual consideration.

Protection Effects of Vernonia Amygdalina Methanolic Extracts Against Hepatocellular Damage Induced by Petroleum Contaminated Diets in Male Rats

Recently, bitter leaf (Vernonia amygdalina) was found to prevent petroleum – induced toxicities on the kidney whereas it potentiates the toxic effect of petroleum adulterated diet on the testes of animal model. This differential action has elicited further inquest into the role of bitter leaf extract in other organs in the midst of petroleum affronts. The hepatoprotective ability of Vernonia amygdalina methanol extract (VAME) is the objective of this investigation. Administration of VAME significantly (P <0.05) reduced serum liver function indices relative to the control. In addition, the activities of liver oxidative enzymes, energy metabolizing enzymes and oxidative stress indices altered by crude oil adulterated diet were significantly (P < 0.05) reversed near control values. Similarly, VAME injection restored the histopathological indices caused by crude oil adulterated diet. It is obvious that all the liver damage indices induced by crude oil contaminated feed were prevented by the intake of VAME, indicating the hepatoprotective ability of bitter leaf

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories

Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platelet disorder and other haematological malignancies whose phenotypes and prognoses depend upon the class of RUNX1 mutation. The biochemical behaviour of these oncoproteins and their ability to cause unique diseases has been well studied, but the genomic basis of their differential action is unknown. To address this question we compared integrated phenotypic, transcriptomic and genomic data from cells expressing four types of RUNX1 oncoproteins in an inducible fashion during blood development from embryonic stem cells. We show that each class of mutated RUNX1 deregulates endogenous RUNX1 function by a different mechanism, leading to specific alterations in developmentally controlled transcription factor binding and chromatin programming. The result is distinct perturbations in the trajectories of gene regulatory network changes underlying blood cell development that are consistent with the nature of the final disease phenotype. The development of novel treatments for RUNX1-driven diseases will therefore require individual consideration.