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"Francis, C."
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Epigenetics : how environment shapes our genes
\"The burgeoning new science of epigenetics offers a cornucopia of insights - some comforting, some frightening. For example, the male fetus may be especially vulnerable to certain common chemicals in our environment, in ways that damage not only his own sperm but also the sperm of his sons. And it's epigenetics that causes identical twins to vary widely in their susceptibility to dementia and cancer. But here's the good news: unlike mutations, epigenetic effects are reversible. Indeed, epigenetic engineering is the future of medicine. \" - Publishers description
Book
Genome-Wide Association Mapping for Seedling and Adult Plant Resistance to Stripe Rust in Synthetic Hexaploid Wheat
Use of genetic diversity from related wild and domesticated species has made a significant contribution to improving wheat productivity. Synthetic hexaploid wheats (SHWs) exhibit natural genetic variation for resistance and/or tolerance to biotic and abiotic stresses. Stripe rust caused by (Puccinia striiformis f. sp. tritici; Pst), is an important disease of wheat worldwide. To characterise loci conferring resistance to stripe rust in SHWs, we conducted a genome-wide association study (GWAS) with a panel of 181 SHWs using the wheat 9K SNP iSelect array. The SHWs were evaluated for their response to the prevailing races of Pst at the seedling and adult plant stages, the latter in replicated field trials at two sites in Ethiopia in 2011. About 28% of the SHWs exhibited immunity at the seedling stage while 56% and 83% were resistant to Pst at the adult plant stage at Meraro and Arsi Robe, respectively. A total of 27 SNPs in nine genomic regions (1BS, 2AS, 2BL, 3BL, 3DL, 5A, 5BL, 6DS and 7A) were linked with resistance to Pst at the seedling stage, while 38 SNPs on 18 genomic regions were associated with resistance at the adult plant stage. Six genomic regions were commonly detected at both locations using a mixed linear model corrected for population structure, kinship relatedness and adjusted for false discovery rate (FDR). The loci on chromosome regions 1AS, 3DL, 6DS and 7AL appeared to be novel QTL; our results confirm that resynthesized wheat involving its progenitor species is a rich source of new stripe (yellow) rust resistance that may be useful in choosing SHWs and incorporating diverse yellow rust (YR) resistance loci into locally adapted wheat cultivars.
Journal Article
Experimental ocean acidification alters the allocation of metabolic energy
Energy is required to maintain physiological homeostasis in response to environmental change. Although responses to environmental stressors frequently are assumed to involve high metabolic costs, the biochemical bases of actual energy demands are rarely quantified. We studied the impact of a near-future scenario of ocean acidification [800 µatm partial pressure of CO ₂ ( p CO ₂)] during the development and growth of an important model organism in developmental and environmental biology, the sea urchin Strongylocentrotus purpuratus . Size, metabolic rate, biochemical content, and gene expression were not different in larvae growing under control and seawater acidification treatments. Measurements limited to those levels of biological analysis did not reveal the biochemical mechanisms of response to ocean acidification that occurred at the cellular level. In vivo rates of protein synthesis and ion transport increased ∼50% under acidification. Importantly, the in vivo physiological increases in ion transport were not predicted from total enzyme activity or gene expression. Under acidification, the increased rates of protein synthesis and ion transport that were sustained in growing larvae collectively accounted for the majority of available ATP (84%). In contrast, embryos and prefeeding and unfed larvae in control treatments allocated on average only 40% of ATP to these same two processes. Understanding the biochemical strategies for accommodating increases in metabolic energy demand and their biological limitations can serve as a quantitative basis for assessing sublethal effects of global change. Variation in the ability to allocate ATP differentially among essential functions may be a key basis of resilience to ocean acidification and other compounding environmental stressors.
Significance Anthropogenic emission of CO ₂ is causing global ocean acidification. For many species, biological responses to acidification often show limited impact at the level of the whole animal. Our integrative studies of whole-organism growth and metabolic rates, rates of protein synthesis and ion transport, enzyme activity, and gene expression show that although the organismal-level impact of acidification on developing sea urchins was minimal, dramatic compensation occurred at the cellular level. Increased rates of synthesis and ion transport resulted in 84% of available energy being allocated to those processes under acidification. Defining the limits of differential energy allocation for the maintenance of critical physiological functions in response to compounding stressors will help provide a mechanistic understanding of resilience potential to environmental change.
Journal Article
The origins and history of consciousness
'The Origins and History of Consciousness' draws on a full range of world mythology to show how individual consciousness undergoes the same archetypal stages of development as human consciousness as a whole.
Book
Cover crop mixture diversity, biomass productivity, weed suppression, and stability
The diversity-productivity, diversity-invasibility, and diversity-stability hypotheses propose that increasing species diversity should lead, respectively, to increased average biomass productivity, invasion resistance, and stability. We tested these three hypotheses in the context of cover crop mixtures, evaluating the effects of increasing cover crop mixture diversity on aboveground biomass, weed suppression, and biomass stability. Twenty to forty cover crop treatments were replicated three or four times at eleven sites using eighteen species representing three cover crop species each from six pre-defined functional groups: cool-season grasses, cool-season legumes, cool-season brassicas, warm-season grasses, warm-season legumes, and warm-season broadleaves. Each species was seeded as a pure stand, and the most diverse treatment contained all eighteen species. Remaining treatments included treatments representing intermediate levels of cover crop species and functional richness and a no cover crop control. Cover crop seeding dates ranged from late July to late September with both cover crop and weed aboveground biomass being sampled prior to winterkill. Stability was assessed by evaluating the variability in cover crop biomass for each treatment across plots within each site. While increasing cover crop mixture diversity was associated with increased average aboveground biomass, we assert that this was the result of the average biomass of the pure stands being drawn down by low biomass species rather than due to niche complementarity or increased resource use efficiency. At no site did the highest biomass mixture produce more than the highest biomass pure stand. Furthermore, while increases in cover crop mixture diversity were correlated with increases in weed suppression and biomass stability, we argue that this was largely the result of diversity co-varying with aboveground biomass, and that differences in aboveground biomass rather than differences in diversity drove the differences observed in weed suppression and stability.
Journal Article
The arcsine is asinine: the analysis of proportions in ecology
The arcsine square root transformation has long been standard procedure when analyzing proportional data in ecology, with applications in data sets containing binomial and non-binomial response variables. Here, we argue that the arcsine transform should not be used in either circumstance. For binomial data, logistic regression has greater interpretability and higher power than analyses of transformed data. However, it is important to check the data for additional unexplained variation, i.e., overdispersion, and to account for it via the inclusion of random effects in the model if found. For non-binomial data, the arcsine transform is undesirable on the grounds of interpretability, and because it can produce nonsensical predictions. The logit transformation is proposed as an alternative approach to address these issues. Examples are presented in both cases to illustrate these advantages, comparing various methods of analyzing proportions including untransformed, arcsine- and logit-transformed linear models and logistic regression (with or without random effects). Simulations demonstrate that logistic regression usually provides a gain in power over other methods.
Journal Article
Lipid-based Nanoparticles for Nucleic Acid Delivery
Lipid-based colloidal particles have been extensively studied as systemic gene delivery carriers. The topic that we would like to emphasize is the formulation/assembly of lipid-based nanoparticles (NP) with diameter under 100 nm for delivering nucleic acid in vivo. NP are different from cationic lipid-nucleic acid complexes (lipoplexes) and are vesicles composed of lipids and encapsulated nucleic acids with a diameter less than 100 nm. The diameter of the NP is an important attribute to enable NP to overcome the various in vivo barriers for systemic gene delivery such as: the blood components, reticuloendothelial system (RES) uptake, tumor access, extracellular matrix components, and intracellular barriers. The major formulation factors that impact the diameter and encapsulation efficiency of DNA-containing NP include the lipid composition, nucleic acid to lipid ratio and formulation method. The particle assembly step is a critical one to make NP suitable for in vivo gene delivery. NP are often prepared using a dialysis method either from an aqueous-detergent or aqueous-organic solvent mixture. The resulting particles have diameters about 100 nm and nucleic acid encapsulation ratios are >80%. Additional components can then be added to the particle after it is formed. This ordered assembly strategy enables one to optimize the particle physico-chemical attributes to devise a biocompatible particle with increased gene transfer efficacy in vivo. The components included in the sequentially assembled NP include: poly(ethylene glycol) (PEG)-shielding to improve the particle pharmacokinetic behavior, a targeting ligand to facilitate the particle-cell recognition and in some case a bioresponsive lipid or pH-triggered polymer to enhance nucleic acid release and intracellular trafficking. A number of groups have observed that a PEG-shielded NP is a robust and modestly effective system for systemic gene or small interfering RNA (siRNA) delivery.
Journal Article