Accurate Genomic Prediction Of Human Height

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, $\sim$40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correlate $\sim$0.65 with actual height; actual heights of most individuals in validation samples are within a few cm of the prediction. The variance captured for height is comparable to the estimated SNP heritability from GCTA (GREML) analysis, and seems to be close to its asymptotic value (i.e., as sample size goes to infinity), suggesting that we have captured most of the heritability for the SNPs used. Thus, our results resolve the common SNP portion of the "missing heritability" problem -- i.e., the gap between prediction R-squared and SNP heritability. The $\sim$20k activated SNPs in our height predictor reveal the genetic architecture of human height, at least for common SNPs. Our primary dataset is the UK Biobank cohort, comprised of almost 500k individual genotypes with multiple phenotypes. We also use other datasets and SNPs found in earlier GWAS for out-of-sample validation of our results.Comment: 17 pages, 10 figure

Untangling the Conceptual Isssues Raised in Reydon and Scholz’s Critique of Organizational Ecology and Darwinian Populations

Reydon and Scholz raise doubts about the Darwinian status of organizational ecology by arguing that Darwinian principles are not applicable to organizational populations. Although their critique of organizational ecology’s typological essentialism is correct, they go on to reject the Darwinian status of organizational populations. This paper claims that the distinction between replicators and interactors, raised in modern philosophy of biology but not discussed by Reydon and Scholz, points the way forward for organizational ecologists. It is possible to conceptualise evolving Darwinian populations providing the inheritance mechanism is appropriately specified. By this approach, adaptation and selection are no longer dichotomised, and the evolutionary significance of knowledge transmission is highlightedPeer reviewe

Prediction of Longitudinal White Matter Change in Healthy Elderly Individuals

Diffusion Tensor Imaging (DTI) studies have shown that significant alteration in white matter (WM) integrity differentiates healthy older adults from persons with Mild Cognitive Impairment (MCI) and Alzheimer\u27s disease (AD). Most studies, however, have been cross-sectional and have not related longitudinal DTI changes to cognitive change. Here we report changes in WM integrity and cognition in healthy older adults over an 18-month interval. Sixty-seven cognitively intact elders underwent neuropsychological testing and DTI at baseline to follow-up on the Rey Auditory Verbal Learning Test (recall sum across trials 1-5, delayed recall) and Mattis Dementia Rating Scale-2. Declining participants (N=21) showed a minimum of 1 SD reduction on at least one cognitive measure, while Stable participants (N=46) showed comparable scores at each time point. WM regions-of-interest were derived from Freesurfer. Hierarchical linear regression was used to predict fractional anisotropy (FA) change in regions frequently identified in DTI studies of MCI and AD including transentorhinal cortex, temporal lobe, and posterior cingulate. Groups did not differ at baseline in age, cognition, FA, or WM volume. After controlling for age and baseline FA, cognitive status (Declining, Stable) predicted the baseline to 18-month reduction in FA in the right hippocampal gyrus (p=.004) and left fusi-form gyrus (p=.01) with a trend in the left middle temporal gyrus (p=.06). Future research should examine WM changes in other brain regions and determine whether DTI diffusivity measures are related to cognitive decline

A network medicine approach to quantify distance between hereditary disease modules on the interactome

We introduce a MeSH-based method that accurately quantifies similarity between heritable diseases at molecular level. This method effectively brings together the existing information about diseases that is scattered across the vast corpus of biomedical literature. We prove that sets of MeSH terms provide a highly descriptive representation of heritable disease and that the structure of MeSH provides a natural way of combining individual MeSH vocabularies. We show that our measure can be used effectively in the prediction of candidate disease genes. We developed a web application to query more than 28.5 million relationships between 7,574 hereditary diseases (96% of OMIM) based on our similarity measure

A common genetic target for environmental and heritable influences on aggressiveness in Drosophila

Environmental and genetic factors can modulate aggressiveness, but the biological mechanisms underlying their influence are largely unknown. Social experience with conspecifics suppresses aggressiveness in both vertebrate and invertebrate species, including Drosophila. We searched for genes whose expression levels correlate with the influence of social experience on aggressiveness in Drosophila by performing microarray analysis of head tissue from socially isolated (aggressive) vs. socially experienced (nonaggressive) male flies. Among {approx}200 differentially expressed genes, only one was also present in a gene set previously identified by profiling Drosophila strains subjected to genetic selection for differences in aggressiveness [Dierick HA, Greenspan RJ (2006) Nat Genet 38:1023–1031]. This gene, Cyp6a20, encodes a cytochrome P450. Social experience increased Cyp6a20 expression and decreased aggressiveness in a reversible manner. In Cyp6a20 mutants, aggressiveness was increased in group-housed but not socially isolated flies. These data identify a common genetic target for environmental and heritable influences on aggressiveness. Cyp6a20 is expressed in a subset of nonneuronal support cells associated with pheromone-sensing olfactory sensilla, suggesting that social experience may influence aggressiveness by regulating pheromone sensitivity

Germline Cas9 expression yields highly efficient genome engineering in a major worldwide disease vector, Aedes aegypti.

The development of CRISPR/Cas9 technologies has dramatically increased the accessibility and efficiency of genome editing in many organisms. In general, in vivo germline expression of Cas9 results in substantially higher activity than embryonic injection. However, no transgenic lines expressing Cas9 have been developed for the major mosquito disease vector Aedes aegypti Here, we describe the generation of multiple stable, transgenic Ae. aegypti strains expressing Cas9 in the germline, resulting in dramatic improvements in both the consistency and efficiency of genome modifications using CRISPR. Using these strains, we disrupted numerous genes important for normal morphological development, and even generated triple mutants from a single injection. We have also managed to increase the rates of homology-directed repair by more than an order of magnitude. Given the exceptional mutagenic efficiency and specificity of the Cas9 strains we engineered, they can be used for high-throughput reverse genetic screens to help functionally annotate the Ae. aegypti genome. Additionally, these strains represent a step toward the development of novel population control technologies targeting Ae. aegypti that rely on Cas9-based gene drives

Twenty years of "Lipid World": a fertile partnership with David Deamer

"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.711473 - Minerva Foundation; 80NSSC17K0295, 80NSSC17K0296, 1724150 - National Science FoundationPublished versio

Degeneracy: a link between evolvability, robustness and complexity in biological systems

A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability) and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability