Mono- and digalactosyldiacylglycerol composition of dinoflagellates. VIII. Temperature effects and a perspective on the curious case of Karenia mikimotoi as a producer of the unusual, ‘green algal’ fatty acid hexadecatetraenoic acid [16:4(n-3)]

Previous studies have shown that dinoflagellates with different plastid ancestries have distinct differences in the fatty acid compositions and regiochemistries of their chloroplast-associated galactolipids, mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively), thus reflecting plastid origin as a major factor in plastid membrane composition. Specifically, dinoflagellates with aberrant plastids (e.g. Karenia brevis, Kryptoperidinium foliaceum and Lepidodinium chlorophorum) possess certain MGDG- and DGDG-associated fatty acids which are not found in peridinin-containing dinoflagellates (the largest group of photosynthetic dinoflagellates with a red algal plastid ancestry which is thought to be an evolutionary precursor to aberrant plastids), but which are common to other algal groups. For example, hexadecatetraenoic acid (16:4(n-3)) is common to green algae and is found in the MGDG and DGDG of L. chlorophorum, which agrees with its green algal plastid ancestry, while hexadecatrienoic acid (16:3) and hexadecadienoic acid (16:2) are found in the MGDG and DGDG of K. foliaceum, which agrees with its diatom plastid ancestry. Notably, 16:4 has been found by others in the total fatty acids and galactolipids of Karenia mikimotoi, but in no other examined members of the Kareniaceae (all of which have plastids of haptophyte origin). However, these findings lack information as to the regiochemistry of 16:4. We have utilized positive-ion electrospray ionization/mass spectrometry (ESI/MS) and ESI/MS/MS to demonstrate that 16:4, which aside from L. chlorophorum is not found conclusively in the MGDG and DGDG of any other dinoflagellates examined to date irrespective of plastid ancestry, is found in K. mikimotoi as 18:5/16:4 (sn-1/sn-2 regiochemistry) MGDG and DGDG, and that its presence is not modulated (i.e. does not become more saturated) with an increase in growth temperature. Considering an aberrant pigment composition as described by others, we present a perspective where galactolipid-associated 16:4 in K. mikimotoi indicates a plastid ancestry more convoluted than for other members of the Kareniaceae.     

Streamlining the Life Cycle Assessment of Buildings by Structured Under‐Specification and Probabilistic Triage

Life cycle thinking plays an important role in sustainable development in the building sector. However, the complexity of data collection and scope definition limits life cycle assessment (LCA) applications. Even if the inventory data have already been collected, tabulated, and indexed, the method is still time‐consuming, which may be discouraging for designers. This study demonstrates how the LCA of buildings can be robustly streamlined using structured underspecification of impact data combined with an effective and efficient triage of the data collection. Tests were conducted with a series of building typologies that were analyzed with a cradle‐to‐gate approach. The probabilistic triage approach was tested to identify selected activities requiring detailed specification because they contribute most to total impact, thereby reducing data gathering effort. Impacts such as global warming, acidification, eutrophication, and smog creation were assessed, and results showed that 40% to 46% of the bill of materials components represent 75% of total impacts of single‐family houses and multifamily buildings. By specifying only a prioritized subset of the bill of materials to the highest level of specificity, results proved to be reasonably accurate and obtainable with less effort.     

Impact of seasonality,storage of semen,and sperm head‐shape on whole tissue methylation and expression of methylation responsive candidate genes in swine placenta and fetal livers from summer and winter breedings

Epigenetics includes the study of external factors that can influence the expression of genes by altering the accessibility of DNA through methylation. To investigate the epigenetic influence of season, sperm head shape, and semen storage on placental and fetal tissues, pregnancies were generated in the summer or winter using boar semen from either least or most sperm head shape change, collected during cool or warm seasons, and stored as cooled‐extended or cryopreserved. The lowest (p < 0.05) ratios of 5‐methylcytosine to 5‐hydroxymethylcytosine activity (5mC:5hmC) in fetal liver were from summer breedings and in placental tissues from winter breedings. The relative expression of placental CDH1 tended ( p < 0.10) to be greater in placenta generated from cryopreserved semen or semen collected during cool periods. The relative expression of placental GNAS was affected ( p < 0.05) by the interaction of breeding and semen collection seasons. Cryopreserved semen increased ( p < 0.05) the placental relative expression of GNAS. Placental MEST and RHOBTB3 tended ( p < 0.10) to have a greater relative expression from pregnancies generated using semen collected during cool periods used during winter breedings. Within fetal liver, the relative expression of GNAS and HGF was greater ( p < 0.05) from winter breedings. Interaction of winter breedings and least sperm head shape change tended ( p < 0.10) to have the greatest fetal liver expression of CDH1. Seasonality of semen collection, breeding, and the effect on sperm head shape change had an influence on the expression of genes with known differentially methylated regions or response to methylation activity from embryonic and extraembryonic tissues.     

Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice (Onychomys)

Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long‐distance acoustic signals to attract and localize mates; Onychomys arenicola and Onychomys torridus are acoustically similar and morphologically cryptic whereas Onychomys leucogaster is larger and acoustically distinct. We used genotyping‐by‐sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, laboratory crosses between O. torridus and O. arenicola produced litters whereas O. leucogaster and O. arenicola crosses did not. Call fundamental frequency in O. torridus and O. arenicola was indistinguishable in allopatry but significantly differentiated in sympatry, a pattern consistent with reproductive character displacement. These results suggest that assortative mating based on a long‐distance signal is an important isolating mechanism between O. torridus and O. arenicola and highlight the importance of behavioral barriers in determining the permeability of species boundaries.     

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro‐organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber‐rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.     

Peroxisomal metabolism of propionic acid and isobutyric acid in plants

The subcellular sites of branched-chain amino acid metabolism in plants have been controversial, particularly with respect to valine catabolism. Potential enzymes for some steps in the valine catabolic pathway are clearly present in both mitochondria and peroxisomes, but the metabolic functions of these isoforms are not clear. The present study examined the possible function of these enzymes in metabolism of isobutyryl-CoA and propionyl-CoA, intermediates in the metabolism of valine and of odd-chain and branched-chain fatty acids. Using (13)C NMR, accumulation of beta-hydroxypropionate from [2-(13)C]propionate was observed in seedlings of Arabidopsis thaliana and a range of other plants, including both monocots and dicots. Examination of coding sequences and subcellular targeting elements indicated that the completed genome of A. thaliana likely codes for all the enzymes necessary to convert valine to propionyl-CoA in mitochondria. However, Arabidopsis mitochondria may lack some of the key enzymes for metabolism of propionyl-CoA. Known peroxisomal enzymes may convert propionyl-CoA to beta-hydroxypropionate by a modified beta-oxidation pathway. The chy1-3 mutation, creating a defect in a peroxisomal hydroxyacyl-CoA hydrolase, abolished the accumulation of beta-hydroxyisobutyrate from exogenous isobutyrate, but not the accumulation of beta-hydroxypropionate from exogenous propionate. The chy1-3 mutant also displayed a dramatically increased sensitivity to the toxic effects of excess propionate and isobutyrate but not of valine. (13)C NMR analysis of Arabidopsis seedlings exposed to [U-(13)C]valine did not show an accumulation of beta-hydroxypropionate. No evidence was observed for a modified beta-oxidation of valine. (13)C NMR analysis showed that valine was converted to leucine through the production of alpha-ketoisovalerate and isopropylmalate. These data suggest that peroxisomal enzymes for a modified beta-oxidation of isobutyryl-CoA and propionyl-CoA could function for metabolism of substrates other than valine.     

Calcium inhibition and calcium potentiation of Orai1, Orai2, and Orai3 calcium release-activated calcium channels

The recent discoveries of Stim1 and Orai proteins have shed light on the molecular makeup of both the endoplasmic reticulum Ca(2+) sensor and the calcium release-activated calcium (CRAC) channel, respectively. In this study, we investigated the regulation of CRAC channel function by extracellular Ca(2+) for channels composed primarily of Orai1, Orai2, and Orai3, by co-expressing these proteins together with Stim1, as well as the endogenous channels in HEK293 cells. As reported previously, Orai1 or Orai2 resulted in a substantial increase in CRAC current (I(crac)), but Orai3 failed to produce any detectable Ca(2+)-selective currents. However, sodium currents measured in the Orai3-expressing HEK293 cells were significantly larger in current density than Stim1-expressing cells. Moreover, upon switching to divalent free external solutions, Orai3 currents were considerably more stable than Orai1 or Orai2, indicating that Orai3 channels undergo a lesser degree of depotentiation. Additionally, the difference between depotentiation from Ca(2+) and Ba(2+) or Mg(2+) solutions was significantly less for Orai3 than for Orai1 or -2. Nonetheless, the Na(+) currents through Orai1, Orai2, and Orai3, as well as the endogenous store-operated Na(+) currents in HEK293 cells, were all inhibited by extracellular Ca(2+) with a half-maximal concentration of approximately 20 mum. We conclude that Orai1, -2, and -3 channels are similarly inhibited by extracellular Ca(2+), indicating similar affinities for Ca(2+) within the selectivity filter. Orai3 channels appeared to differ from Orai1 and -2 in being somewhat resistant to the process of Ca(2+) depotentiation.     

Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts

Metabolic profiling, metabolomic and metabonomic studies mainly involve the multicomponent analysis of biological fluids, tissue and cell extracts using NMR spectroscopy and/or mass spectrometry (MS). We summarize the main NMR spectroscopic applications in modern metabolic research, and provide detailed protocols for biofluid (urine, serum/plasma) and tissue sample collection and preparation, including the extraction of polar and lipophilic metabolites from tissues. 1H NMR spectroscopic techniques such as standard 1D spectroscopy, relaxation-edited, diffusion-edited and 2D J-resolved pulse sequences are widely used at the analysis stage to monitor different groups of metabolites and are described here. They are often followed by more detailed statistical analysis or additional 2D NMR analysis for biomarker discovery. The standard acquisition time per sample is 4-5 min for a simple 1D spectrum, and both preparation and analysis can be automated to allow application to high-throughput screening for clinical diagnostic and toxicological studies, as well as molecular phenotyping and functional genomics.     

Preparation of cultured myofibers from larval salamander limbs for cellular plasticity studies

Identification of the mechanisms underlying cellular plasticity in salamander cells is important because these may give pointers to the restricted regenerative ability of mammals. The myofibers from salamanders are remarkable for their ability to undergo cellularization and cell-cycle re-entry during regeneration. Here, we describe a detailed method for the isolation and culture of larval salamander myofibers in numbers suitable for cellular plasticity studies. The basic protocol for isolation and purification of cells can be completed in 4 h.