Regulation of amino-acid metabolism controls flux to lipid accumulation in <i>Yarrowia lipolytica</i>

Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation

Nonequilibrium corrections in the pressure tensor due to an energy flux

The physical interpretation of the nonequilibrium corrections in the pressure tensor for radiation submitted to an energy flux obtained in some previous works is revisited. Such pressure tensor is shown to describe a moving equilibrium system but not a real nonequilibrium situation.Comment: 4 pages, REVTeX, Brief Report to appear in PRE Dec 9

A molecular genetic toolbox for Yarrowia lipolytica

Background: Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. Results: We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. Conclusions: These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products

Information theory in the study of anisotropic radiation

Information theory is used to perform a thermodynamic study of non equilibrium anisotropic radiation. We limit our analysis to a second-order truncation of the moments, obtaining a distribution function which leads to a natural closure of the hierarchy of radiative transfer equations in the so-called variable Eddington factor scheme. Some Eddington factors appearing in the literature can be recovered as particular cases of our two-parameter Eddington factor. We focus our attention in the study of the thermodynamic properties of such systems and relate it to recent nonequilibrium thermodynamic theories. Finally we comment the possibility of introducing a nonequilibrium chemical potential for photons.Comment: 1 eps figure upon request by e-mail, to appear in Journal of Physics

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa

This is the publisher’s final pdf. The article is copyrighted by the New Phytologist Trust and published by John Wiley & Sons, Inc. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291469-8137. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work.•Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination.\ud •We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms.\ud •Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r² dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N[subscript e] ≈ 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features.\ud •Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed

Instabilities in the Envelopes and Winds of Very Massive Stars

The high luminosity of Very Massive Stars (VMS) means that radiative forces play an important, dynamical role both in the structure and stability of their stellar envelope, and in driving strong stellar-wind mass loss. Focusing on the interplay of radiative flux and opacity, with emphasis on key distinctions between continuum vs. line opacity, this chapter reviews instabilities in the envelopes and winds of VMS. Specifically, we discuss how: 1) the iron opacity bump can induce an extensive inflation of the stellar envelope; 2) the density dependence of mean opacity leads to strange mode instabilities in the outer envelope; 3) desaturation of line-opacity by acceleration of near-surface layers initiates and sustains a line-driven stellar wind outflow; 4) an associated line-deshadowing instability leads to extensive small-scale structure in the outer regions of such line-driven winds; 5) a star with super-Eddington luminosity can develop extensive atmospheric structure from photon bubble instabilities, or from stagnation of flow that exceeds the "photon tiring" limit; 6) the associated porosity leads to a reduction in opacity that can regulate the extreme mass loss of such continuum-driven winds. Two overall themes are the potential links of such instabilities to Luminous Blue Variable (LBV) stars, and the potential role of radiation forces in establishing the upper mass limit of VMS.Comment: 44 pages, 13 figures. Chapter to appear in the book "Very Massive Stars in the Local Universe", Springer, J.S. Vink, e

Neurospora from natural populations: Population genomics insights into the Life history of a model microbial Eukaryote

The ascomycete filamentous fungus Neurospora crassa played a historic role in experimental biology and became a model system for genetic research. Stimulated by a systematic effort to collect wild strains initiated by Stanford geneticist David Perkins, the genus Neurospora has also become a basic model for the study of evolutionary processes, speciation, and population biology. In this chapter, we will first trace the history that brought Neurospora into the era of population genomics. We will then cover the major contributions of population genomic investigations using Neurospora to our understanding of microbial biogeography and speciation, and review recent work using population genomics and genome-wide association mapping that illustrates the unique potential of Neurospora as a model for identifying the genetic basis of (potentially adaptive) phenotypes in filamentous fungi. The advent of population genomics has contributed to firmly establish Neurospora as a complete model system and we hope our review will entice biologists to include Neurospora in their research

Neutrino-Nucleon Interactions in Magnetized Neutron-Star Matter: The Effects of Parity Violation

We study neutrino-nucleon scattering and absorption in a dense, magnetized nuclear medium. These are the most important sources of neutrino opacity governing the cooling of a proto-neutron star in the first tens of seconds after its formation. Because the weak interaction is parity violating, the absorption and scattering cross-sections depend asymmetrically on the directions of the neutrino momenta with respect to the magnetic field. We develop the moment formalism of neutrino transport in the presence of such asymmetric opacities and derive explicit expressions for the neutrino flux and other angular moments of the Boltzmann transport equation. For a given neutrino species, there is a drift flux of neutrinos along the magnetic field in addition to the usual diffusive flux. This drift flux depends on the deviation of the neutrino distribution function from thermal equilibrium. Hence, despite the fact that the neutrino cross-sections are asymmetric throughout the star, asymmetric neutrino flux can be generated only in the outer region of the proto-neutron star where the neutrino distribution deviates significantly from thermal equilibrium. In addition to the asymmetric absorption opacity arising from nucleon polarization, we find the contribution of the electron (or positron) ground state Landau level. For neutrinos of energy less than a few times the temperature, this is the dominant source of asymmetric opacity. Lastly, we discuss the implication of our result to the origin of pulsar kicks: in order to generate kick velocity of a few hundred km/s from asymmetric neutrino emission using the parity violation effect, the proto-neutron star must have a dipole magnetic field of at least $10^{15}-10^{16}$ G.Comment: 35 pages, no figures, submitted to Phys.Rev.

Radiation transport in diffractive media

We consider radiation transport theory applied to non-dispersive but refractive media. This setting is used to discuss Minkowski's and Abraham's electromagnetic momentum, and to derive conservation equations independent of the choice of momentum definition. Using general relativistic kinetic theory, we derive and discuss a radiation gas energy-momentum conservation equation valid in arbitrary curved spacetime with diffractive media.Comment: 10 pages, typos and equation numbers corrected, version to appear in J. Phys. A: Math. Ge

Regulation of Yeast-to-Hyphae Transition in <i>Yarrowia lipolytica</i>

The yeast Yarrowia lipolytica undergoes a morphological transition from yeast-to-hyphal growth in response to environmental conditions. A forward genetic screen was used to identify mutants that reliably remain in the yeast phase, which were then assessed by whole-genome sequencing. All the smooth mutants identified, so named because of their colony morphology, exhibit independent loss of DNA at a repetitive locus made up of interspersed ribosomal DNA and short 10- to 40-mer telomere-like repeats. The loss of repetitive DNA is associated with downregulation of genes with stress response elements (5'-CCCCT-3') and upregulation of genes with cell cycle box (5'-ACGCG-3') motifs in their promoter region. The stress response element is bound by the transcription factor Msn2p in Saccharomyces cerevisiae We confirmed that the Y. lipolyticamsn2 (Ylmsn2) ortholog is required for hyphal growth and found that overexpression of Ylmsn2 enables hyphal growth in smooth strains. The cell cycle box is bound by the Mbp1p/Swi6p complex in S. cerevisiae to regulate G1-to-S phase progression. We found that overexpression of either the Ylmbp1 or Ylswi6 homologs decreased hyphal growth and that deletion of either Ylmbp1 or Ylswi6 promotes hyphal growth in smooth strains. A second forward genetic screen for reversion to hyphal growth was performed with the smooth-33 mutant to identify additional genetic factors regulating hyphal growth in Y. lipolytica Thirteen of the mutants sequenced from this screen had coding mutations in five kinases, including the histidine kinases Ylchk1 and Ylnik1 and kinases of the high-osmolarity glycerol response (HOG) mitogen-activated protein (MAP) kinase cascade Ylssk2, Ylpbs2, and Ylhog1 Together, these results demonstrate that Y. lipolytica transitions to hyphal growth in response to stress through multiple signaling pathways.IMPORTANCE Many yeasts undergo a morphological transition from yeast-to-hyphal growth in response to environmental conditions. We used forward and reverse genetic techniques to identify genes regulating this transition in Yarrowia lipolytica We confirmed that the transcription factor Ylmsn2 is required for the transition to hyphal growth and found that signaling by the histidine kinases Ylchk1 and Ylnik1 as well as the MAP kinases of the HOG pathway (Ylssk2, Ylpbs2, and Ylhog1) regulates the transition to hyphal growth. These results suggest that Y. lipolytica transitions to hyphal growth in response to stress through multiple kinase pathways. Intriguingly, we found that a repetitive portion of the genome containing telomere-like and rDNA repeats may be involved in the transition to hyphal growth, suggesting a link between this region and the general stress response