The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

<p>Abstract</p> <p>Background</p> <p><it>Dunaliella salina </it>Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because <it>D. salina </it>can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of <it>D. salina </it>have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of <it>D. salina </it>and compares them with those of the model green algae <it>Chlamydomonas reinhardtii </it>and <it>Volvox carteri</it>.</p> <p>Results</p> <p>The <it>D. salina </it>organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the <it>D. salina </it>plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the <it>D. salina </it>ptDNA.</p> <p>Conclusions</p> <p>These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of <it>D. salina </it>and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the <it>D. salina </it>organelle DNA sequences will aid in the development of a viable plastid transformation system for this model alga, and they will complement the forthcoming <it>D. salina </it>nuclear genome sequence, placing <it>D. salina </it>in a group of a select few photosynthetic eukaryotes for which complete genome sequences from all three genetic compartments are available.</p

Plant Functional Groups and Species Contribute to Ecological Resilience a Decade After Woodland Expansion Treatments

Woody plant expansions are altering ecosystem structure and function, as well as fire regimes, around the globe. Tree-reduction treatments are widely implemented in expanding woodlands to reduce fuel loads, increase ecological resilience, and improve habitat, but few studies have measured treatment outcomes over long timescales or large geographic areas. The Sagebrush Treatment Evaluation Project (SageSTEP) evaluated the ecological effects of prescribed fire and cut-and-leave treatments in sagebrush communities experiencing tree expansion in North American cold desert shrublands. We used 10 yr of data from the SageSTEP network to test how treatments interacted with pre-treatment tree dominance, soil climate, and time since treatment to affect plant functional groups and dominant species. Non-sprouting shrub (Artemisia spp.), sprouting shrub, perennial graminoid, and annual grass responses depended on tree dominance and soil climate, and responses were related to the dominant species\u27 life-history traits. Sites with warm and dry soils showed increased perennial graminoid but reduced Artemisia shrub cover across the tree dominance gradient after prescribed burning, while sites with cool and moist soils showed favorable post-burn responses for both functional types, particularly at low to moderate tree dominance. Cut-and-leave treatments sustained or increased native perennial plant functional groups and experienced smaller increases in exotic annual plants in both soil climates across the tree dominance gradient. Both treatments reduced biocrust cover. Selecting appropriate tree-reduction treatments to achieve desired long-term outcomes requires consideration of dominant species, site environmental conditions, and the degree of woodland expansion. Careful selection of management treatments will reduce the likelihood of undesirable consequences to the ecosystem

Planning the Future of U.S. Particle Physics (Snowmass 2013): Chapter 4: Cosmic Frontier

These reports present the results of the 2013 Community Summer Study of the APS Division of Particles and Fields ("Snowmass 2013") on the future program of particle physics in the U.S. Chapter 4, on the Cosmic Frontier, discusses the program of research relevant to cosmology and the early universe. This area includes the study of dark matter and the search for its particle nature, the study of dark energy and inflation, and cosmic probes of fundamental symmetries.Comment: 61 page

From the Birkhoff-Gustavson normalization to the Bertrand-Darboux integrability condition

The Bertrand-Darboux integrability condition for a certain class of perturbed harmonic oscillators is studied from the viewpoint of the Birkhoff-Gustavson(BG)-normalization: By solving an inverse problem of the BG-normalization on computer algebra, it is shown that if the perturbed harmonic oscillators with a homogeneous-{\it cubic} polynomial potential and with a homogeneous-{\it quartic} polynomial potentials admit the same BG-normalization up to degree-4 then both oscillators satisfy the Bertrand-Darboux integrability condition.Comment: 23 pages, LaTeX (iop.sty), typos and Appendix adde

Relationship of molecular breeding value for beef tenderness with heifer traits through weaning of their first calf

Polymorphisms in μ-calpain (CAPN1) that beneficially associate with beef tenderness are reported to antagonistically associate with calving day in beef heifers and post-partum interval to estrus in beef cows. We, therefore, hypothesized that a molecular breeding value for slice shear force, calculated based on CAPN1 and calpastatin (CAST) genotypes, would demonstrate an antagonistic relationship between genomically predicted slice shear force and ordinal calving date in replacement beef heifers. A secondary objective of this study was to evaluate the association of a polymorphism in diacylglycerol O-acyltransferase (DGAT1) with reproductive traits in beef heifers. One hundred eighty-seven MARC III heifers (¼ Angus, ¼ Hereford, ¼ Red Poll, and ¼ Pinzgauer) that had been selectively bred to increase the frequency of these polymorphisms were submitted for monthly ultrasound exams beginning at 333 d of age and continuing until the start of breeding to determine pubertal status. At the last exam before breeding, all antral follicles were counted, and the length and height of each ovary was measured to determine if genomic selection for slice shear force associated with ovarian follicle number. Calving date, calf gender, and calf birth weight were recorded at parturition. Regression analysis of the molecular breeding value for slice shear force of the heifers on ordinal calving date indicated no association between genomic prediction of tenderness and calving date (P = 0.16); however, there was a tendency for age at puberty to be delayed in heifers as genetic merit for tenderness improved (P = 0.09). The results of the present study indicate that within experimental precision, selecting for tenderness using genomic predictions had minimal or no antagonistic association with reproductive performance in heifers. Further analysis of reproductive performance as cows is needed within this population but applying these genetic markers to select for tenderness in steers does not antagonize reproductive traits influencing conception or first calf birth date and birth weight in replacement beef heifers

Can Biomarkers Identify Women at Increased Stroke Risk? The Women's Health Initiative Hormone Trials

Objective: The Women's Health Initiative hormone trials identified a 44% increase in ischemic stroke risk with combination estrogen plus progestin and a 39% increase with estrogen alone. We undertook a case-control biomarker study to elucidate underlying mechanisms, and to potentially identify women who would be at lower or higher risk for stroke with postmenopausal hormone therapy (HT). Design: The hormone trials were randomized, double-blind, and placebo controlled. Setting: The Women's Health Initiative trials were conducted at 40 clinical centers in the United States. Participants: The trials enrolled 27,347 postmenopausal women, aged 50-79 y. Interventions: We randomized 16,608 women with intact uterus to conjugated estrogens 0.625 mg with medroxyprogesterone acetate 2.5 mg daily or placebo, and 10,739 women with prior hysterectomy to conjugated estrogens 0.625 mg daily or placebo. Outcome Measures: Stroke was ascertained during 5.6 y of follow-up in the estrogen plus progestin trial and 6.8 y of follow-up in the estrogen alone trial. Results: No baseline clinical characteristics, including gene polymorphisms, identified women for whom the stroke risk from HT was higher. Paradoxically, women with higher baseline levels of some stroke-associated biomarkers had a lower risk of stroke when assigned to estrogen plus progestin compared to placebo. For example, those with higher IL-6 were not at increased stroke risk when assigned to estrogen plus progestin (odds ratio 1.28) but were when assigned to placebo (odds ratio 3.47; p for difference = 0.02). Similar findings occurred for high baseline PAP, leukocyte count, and D-dimer. However, only an interaction of D-dimer during follow-up interaction with HT and stroke was marginally significant (p = 0.03). Conclusions: Biomarkers did not identify women at higher stroke risk with postmenopausal HT. Some biomarkers appeared to identify women at lower stroke risk with estrogen plus progestin, but these findings may be due to chance

Vanishing Twist near Focus-Focus Points

We show that near a focus-focus point in a Liouville integrable Hamiltonian system with two degrees of freedom lines of locally constant rotation number in the image of the energy-momentum map are spirals determined by the eigenvalue of the equilibrium. From this representation of the rotation number we derive that the twist condition for the isoenergetic KAM condition vanishes on a curve in the image of the energy-momentum map that is transversal to the line of constant energy. In contrast to this we also show that the frequency map is non-degenerate for every point in a neighborhood of a focus-focus point.Comment: 13 page

Sensitive Search for a Permanent Muon Electric Dipole Moment

We are proposing a new method to carry out a dedicated search for a permanent electric dipole moment (EDM) of the muon with a sensitivity at a level of 10^{-24} e cm. The experimental design exploits the strong motional electric field sensed by relativistic particles in a magnetic storage ring. As a key feature, a novel technique has been invented in which the g-2 precession is compensated with radial electric field. This technique will benefit greatly when the intense muon sources advocated by the developers of the muon storage rings and the muon colliders become available.Comment: 16 pages, 3 figures. Submitted for publication in Proceedings of the International Workshop on High Intensity Muon Sources (HIMUS99), KEK, Japan, December 1-4 199

Role of the placenta in developmental programming: Observations from models using large animals

Developmental programming, which proposes that “insults” or “stressors” during intrauterine or postnatal development can have not only immediate but also long-term consequences for healthy and productivity, has emerged as a major biological principle, and based on studies in many animal species also seems to be a universal phenomenon. In eutherians, the placenta appears to be programmed during its development, which has consequences for fetal growth and development throughout pregnancy, and likewise has long-term consequences for postnatal development, leading to programming of organ function of the offspring even into adulthood. This review summarizes our current understanding of the placenta’s role in developmental programming, the mechanisms involved, and the challenges remaining

Identification of Genes Encoding Enzymes Catalyzing the Early Steps of Carrot Polyacetylene Biosynthesis

Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is largely unknown. To begin filling this gap and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp. sativus). Using gas chromatography and mass spectrometry, we identified three known polyacetylenes and assigned provisional structures to two novel polyacetylenes. We also quantified these compounds in carrot leaf, petiole, root xylem, root phloem, and root periderm extracts. Falcarindiol and falcarinol predominated and accumulated primarily in the root periderm. Since the multiple double and triple carbon-carbon bonds that distinguish polyacetylenes from ubiquitous fatty acids are often introduced by Δ12 oleic acid desaturase (FAD2)-type enzymes, we mined the carrot genome for FAD2 genes. We identified a FAD2 family with an unprecedented 24 members and analyzed public, tissue-specific carrot RNA-Seq data to identify coexpressed members with root periderm-enhanced expression. Six candidate genes were heterologously expressed individually and in combination in yeast and Arabidopsis (Arabidopsis thaliana), resulting in the identification of one canonical FAD2 that converts oleic to linoleic acid, three divergent FAD2-like acetylenases that convert linoleic into crepenynic acid, and two bifunctional FAD2s with Δ12 and Δ14 desaturase activity that convert crepenynic into the further desaturated dehydrocrepenynic acid, a polyacetylene pathway intermediate. These genes can now be used as a basis for discovering other steps of falcarin-type polyacetylene biosynthesis, to modulate polyacetylene levels in plants, and to test the in planta function of these molecules