Synthesis of oleyl oleate wax esters in Arabidopsis thaliana and Camelina sativa seed oil

Seed oil composed of wax esters with long‐chain monoenoic acyl moieties represents a high‐value commodity for industry. Such plant‐derived sperm oil‐like liquid wax esters are biodegradable and can have excellent properties for lubrication. In addition, wax ester oil may represent a superior substrate for biodiesel production. In this study, we demonstrate that the low‐input oil seed crop Camelina sativa can serve as a biotechnological platform for environmentally benign wax ester production. Two biosynthetic steps catalysed by a fatty alcohol‐forming acyl‐CoA reductase (FAR) and a wax ester synthase (WS) are sufficient to achieve wax ester accumulation from acyl‐CoA substrates. To produce plant‐derived sperm oil‐like liquid wax esters, the WS from Mus musculus (MmWS) or Simmondsia chinensis (ScWS) were expressed in combination with the FAR from Mus musculus (MmFAR1) or Marinobacter aquaeolei (MaFAR) in seeds of Arabidopsis thaliana and Camelina sativa. The three analysed enzyme combinations Oleo3:mCherry:MmFAR1?c/Oleo3:EYFP:MmWS, Oleo3:mCherry:MmFAR1?c/ScWS and MaFAR/ScWS showed differences in the wax ester molecular species profiles and overall biosynthetic performance. By expressing MaFAR/ScWS in Arabidopsis or Camelina up to 59% or 21% of the seed oil TAGs were replaced by wax esters, respectively. This combination also yielded wax ester molecular species with highest content of monounsaturated acyl moieties. Expression of the enzyme combinations in the Arabidopsis fae1 fad2 mutant background high in oleic acid resulted in wax ester accumulation enriched in oleyl oleate (18:1/18:1 > 60%), suggesting that similar values may be obtained with a Camelina high oleic acid line.     

Priming and memory of stress responses in organisms lacking a nervous system

Experience and memory of environmental stimuli that indicate future stress can prepare (prime) organismic stress responses even in species lacking a nervous system. The process through which such organisms prepare their phenotype for an improved response to future stress has been termed ‘priming’. However, other terms are also used for this phenomenon, especially when considering priming in different types of organisms and when referring to different stressors. Here we propose a conceptual framework for priming of stress responses in bacteria, fungi and plants which allows comparison of priming with other terms, e.g. adaptation, acclimation, induction, acquired resistance and cross protection. We address spatial and temporal aspects of priming and highlight current knowledge about the mechanisms necessary for information storage which range from epigenetic marks to the accumulation of (dormant) signalling molecules. Furthermore, we outline possible patterns of primed stress responses. Finally, we link the ability of organisms to become primed for stress responses (their ‘primability’) with evolutionary ecology aspects and discuss which properties of an organism and its environment may favour the evolution of priming of stress responses.     

Family-based approaches: design,imputation, analysis,and beyond

Participants in the family-based analysis group at Genetic Analysis Workshop 19 addressed diverse topics, all of which used the family data. Topics addressed included questions of study design and data quality control (QC), genotype imputation to augment available sequence data, and linkage and/or association analyses. Results show that pedigree-based tests that are sensitive to genotype error may be useful for QC. Imputation quality improved with inclusion of small amounts of pedigree information used to phase the data in evaluation of 5 commonly used approaches for imputation in samples of (typically) unrelated subjects. It improved still further when pedigree-based imputation using larger pedigrees was also added. An important distinction was made between methods that do versus do not make use of Mendelian transmission in pedigrees, because this serves as a key difference between underlying models and assumptions. Methods that model relatedness generally had higher power in association testing than did analyses that carry out testing in the presence of a transmission model, but this may reflect details of implementation and/or ability of more general methods to jointly include data from larger pedigrees. In either case, for single nucleotide polymorphism–set approaches, weights that incorporate information on functional effects may be more useful than those that are based only on allele frequencies. The overall results demonstrate that family data continue to provide important information in the search for trait loci.     

Imputation of missing covariate values in epigenome-wide analysis of DNA methylation data

DNA methylation is a widely studied epigenetic mechanism and alterations in methylation patterns may be involved in the development of common diseases. Unlike inherited changes in genetic sequence, variation in site-specific methylation varies by tissue, developmental stage, and disease status, and may be impacted by aging and exposure to environmental factors, such as diet or smoking. These non-genetic factors are typically included in epigenome-wide association studies (EWAS) because they may be confounding factors to the association between methylation and disease. However, missing values in these variables can lead to reduced sample size and decrease the statistical power of EWAS. We propose a site selection and multiple imputation (MI) method to impute missing covariate values and to perform association tests in EWAS. Then, we compare this method to an alternative projection-based method. Through simulations, we show that the MI-based method is slightly conservative, but provides consistent estimates for effect size. We also illustrate these methods with data from the Atherosclerosis Risk in Communities (ARIC) study to carry out an EWAS between methylation levels and smoking status, in which missing cell type compositions and white blood cell counts are imputed.     

Response to strigolactone treatment in chrysanthemum axillary buds is influenced by auxin transport inhibition and sucrose availability

Axillary bud outgrowth is regulated by both environmental cues and internal plant hormone signaling. Central to this regulation is the balance between auxins, cytokinins, and strigolactones. Auxins are transported basipetally and inhibit the axillary bud outgrowth indirectly by either restricting auxin export from the axillary buds to the stem (canalization model) or inducing strigolactone biosynthesis and limiting cytokinin levels (second messenger model). Both models have supporting evidence and are not mutually exclusive. In this study, we used a modified split-plate bioassay to apply different plant growth regulators to isolated stem segments of chrysanthemum and measure their effect on axillary bud growth. Results showed axillary bud outgrowth in the bioassay within 5 days after nodal stem excision. Treatments with apical auxin (IAA) inhibited bud outgrowth which was counteracted by treatments with basal cytokinins (TDZ, zeatin, 2-ip). Treatments with basal strigolactone (GR24) could inhibit axillary bud growth without an apical auxin treatment. GR24 inhibition of axillary buds could be counteracted with auxin transport inhibitors (TIBA and NPA). Treatments with sucrose in the medium resulted in stronger axillary bud growth, which could be inhibited with apical auxin treatment but not with basal strigolactone treatment. These observations provide support for both the canalization model and the second messenger model with, on the one hand, the influence of auxin transport on strigolactone inhibition of axillary buds and, on the other hand, the inhibition of axillary bud growth by strigolactone without an apical auxin source. The inability of GR24 to inhibit bud growth in a sucrose treatment raises an interesting question about the role of strigolactone and sucrose in axillary bud outgrowth and calls for further investigation.     

Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli

A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10⁻⁴ insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10⁻⁵ recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186. Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5′-GGGG(N6/N7)CCCC-3′. We also detected 48 long deletions not involving IS elements.     

Life Cycle Impacts of Natural Fiber Composites for Automotive Applications: Effects of Renewable Energy Content and Lightweighting

This study examines the life cycle energy demand and greenhouse gas (GHG) emissions associated with substituting natural cellulose and kenaf in place of glass fibers in automotive components. Specifically, a 30 wt% glass‐fiber composite component weighing 3 kilograms (kg) was compared to a 30 wt% cellulose fiber composite component (2.65 kg) and 40 wt% kenaf fiber composite component (2.79 kg) for six cars, crossovers, and sport utility vehicles. The use‐phase fuel consumption of the baseline and substitute components, with and without powertrain resizing, were determined using a mass‐induced fuel consumption model based on U.S. Environmental Protection Agency test records. For all vehicles, compared to the baseline glass fiber component, using the cellulose composite material reduced life cycle energy demand by 9.2% with powertrain resizing (7.2% without) and reduced life cycle GHG emissions by 18.6% with powertrain resizing (16.3% without), whereas the kenaf composite component reduced energy demand by 6.0% with powertrain resizing (4.8% without) and GHG emissions by 10.7% with powertrain resizing (9.2% without). For both natural fiber components, the majority of the life cycle energy savings is realized in the use‐phase fuel consumption as a result of the reduced weight of the component.     

Preparation of Extracellular Matrix Protein Fibers for Brillouin Spectroscopy

Brillouin spectroscopy is an emerging technique in the biomedical field. It probes the mechanical properties of a sample through the interaction of visible light with thermally induced acoustic waves or phonons propagating at a speed of a few km/sec. Information on the elasticity and structure of the material is obtained in a nondestructive contactless manner, hence opening the way to in vivo applications and potential diagnosis of pathology. This work describes the application of Brillouin spectroscopy to the study of biomechanics in elastin and trypsin-digested type I collagen fibers of the extracellular matrix. Fibrous proteins of the extracellular matrix are the building blocks of biological tissues and investigating their mechanical and physical behavior is key to establishing structure-function relationships in normal tissues and the changes which occur in disease. The procedures of sample preparation followed by measurement of Brillouin spectra using a reflective substrate are presented together with details of the optical system and methods of spectral data analysis.     

Understory Plant Community Composition Is Associated with Fine-Scale Above- and Below-Ground Resource Heterogeneity in Mature Lodgepole Pine (Pinus contorta) Forests

Understory plant communities play critical ecological roles in forest ecosystems. Both above- and below-ground ecosystem properties and processes influence these communities but relatively little is known about such effects at fine (i.e., one to several meters within-stand) scales, particularly for forests in which the canopy is dominated by a single species. An improved understanding of these effects is critical for understanding how understory biodiversity is regulated in such forests and for anticipating impacts of changing disturbance regimes. Our primary objective was to examine the patterns of fine-scale variation in understory plant communities and their relationships to above- and below-ground resource and environmental heterogeneity within mature lodgepole pine forests. We assessed composition and diversity of understory vegetation in relation to heterogeneity of both the above-ground (canopy tree density, canopy and tall shrub basal area and cover, downed wood biomass, litter cover) and below-ground (soil nutrient availability, decomposition, forest floor thickness, pH, and phospholipid fatty acids (PLFAs) and multiple carbon-source substrate-induced respiration (MSIR) of the forest floor microbial community) environment. There was notable variation in fine-scale plant community composition; cluster and indicator species analyses of the 24 most commonly occurring understory species distinguished four assemblages, one for which a pioneer forb species had the highest cover levels, and three others that were characterized by different bryophyte species having the highest cover. Constrained ordination (distance-based redundancy analysis) showed that two above-ground (mean tree diameter, litter cover) and eight below-ground (forest floor pH, plant available boron, microbial community composition and function as indicated by MSIR and PLFAs) properties were associated with variation in understory plant community composition. These results provide novel insights into the important ecological associations between understory plant community composition and heterogeneity in ecosystem properties and processes within forests dominated by a single canopy species.