Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

BACKGROUND: The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales. RESULTS: Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further. CONCLUSIONS: Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level

Influence of Strong Acid Hydrolysis Processing on the Thermal Stability and Crystallinity of Cellulose Isolated from Wheat Straw

Cellulose extractions from wheat straw via hydrochloric, nitric, and sulfuric acid hydrolysis methods were carried out. X-ray diffraction spectral analyses reveal that depending on the acid conditions used the structure of the cellulose exhibited a mixture of polymorphs (i.e., CI and CIII cellulose phases). In addition, the percent crystallinity, diameter, and length of the cellulose fibers varied tremendously as determined by X-ray diffraction and scanning electron microscopy. Thermal gravimetric analysis measurements revealed that the thermal stability of the extracted cellulose varied as a function of the acid strength and conditions used. Scanning electron microscopy analysis revealed that the aggregation of cellulose fibers during the drying process is strongly dependent upon the drying process and strength of the acids used

High-energy emission from jet-clump interactions in microquasars

High-mass microquasars are binary systems consisting of a massive star and an accreting compact object from which relativistic jets are launched. There is considerable observational evidence that winds of massive stars are clumpy. Individual clumps may interact with the jets in high-mass microquasars to produce outbursts of high-energy emission. Gamma-ray flares have been detected in some high-mass X-ray binaries, such as Cygnus X-1, and probably in LS 5039 and LS I+61 303. We predict the high-energy emission produced by the interaction between a jet and a clump of the stellar wind in a high-mass microquasar. Assuming a hydrodynamic scenario for the jet-clump interaction, we calculate the spectral energy distributions produced by the dominant non-thermal processes: relativistic bremsstrahlung, synchrotron and inverse Compton radiation, for leptons, and for hadrons, proton-proton collisions. Significant levels of emission in X-rays (synchrotron), high-energy gamma rays (inverse Compton), and very high-energy gamma rays (from the decay of neutral pions) are predicted, with luminosities in the different domains in the range ~ 10^{32}-10^{35} erg/s. The spectral energy distributions vary strongly depending on the specific conditions. Jet-clump interactions may be detectable at high and very high energies, and provide an explanation for the fast TeV variability found in some high-mass X-ray binary systems. Our model can help to infer information about the properties of jets and clumpy winds by means of high-sensitivity gamma-ray astronomy.Comment: Accepted for publication in A&A (10 pages, 8 figures

Closed-Form Bayesian Inferences for the Logit Model via Polynomial Expansions

Articles in Marketing and choice literatures have demonstrated the need for incorporating person-level heterogeneity into behavioral models (e.g., logit models for multiple binary outcomes as studied here). However, the logit likelihood extended with a population distribution of heterogeneity doesn't yield closed-form inferences, and therefore numerical integration techniques are relied upon (e.g., MCMC methods). We present here an alternative, closed-form Bayesian inferences for the logit model, which we obtain by approximating the logit likelihood via a polynomial expansion, and then positing a distribution of heterogeneity from a flexible family that is now conjugate and integrable. For problems where the response coefficients are independent, choosing the Gamma distribution leads to rapidly convergent closed-form expansions; if there are correlations among the coefficients one can still obtain rapidly convergent closed-form expansions by positing a distribution of heterogeneity from a Multivariate Gamma distribution. The solution then comes from the moment generating function of the Multivariate Gamma distribution or in general from the multivariate heterogeneity distribution assumed. Closed-form Bayesian inferences, derivatives (useful for elasticity calculations), population distribution parameter estimates (useful for summarization) and starting values (useful for complicated algorithms) are hence directly available. Two simulation studies demonstrate the efficacy of our approach.Comment: 30 pages, 2 figures, corrected some typos. Appears in Quantitative Marketing and Economics vol 4 (2006), no. 2, 173--20

The Millennium Drought in southeast Australia (2001-2009): Natural and human causes and implications for water resources, ecosystems, economy, and society

The "Millennium Drought" (2001-2009) can be described as the worst drought on record for southeast Australia. Adaptation to future severe droughts requires insight into the drivers of the drought and its impacts. These were analyzed using climate, water

Oncogenic PI3K Mutations Lead to NF- B-Dependent Cytokine Expression following Growth Factor Deprivation

The PI3K pathway is one of the most commonly misregulated signaling pathways in human cancers, but its impact on the tumor microenvironment has not been considered as deeply as its autonomous impact on tumor cells. In this study we demonstrate that NF-κB is activated by the two most common PI3K mutations, PIK3CA E545K and H1047R. We found that markers of NF-κB are most strongly upregulated under conditions of growth factor deprivation. Gene expression analysis performed on cells deprived of growth factors identified the repertoire of genes altered by oncogenic PI3K mutations following growth factor deprivation. This gene set most closely correlated with gene signatures from claudin-low and basal-like breast tumors, subtypes frequently exhibiting constitutive PI3K/Akt activity. An NF-κB-dependent subset of genes driven by oncogenic PI3K mutations was also identified that encoded primarily secreted proteins, suggesting a paracrine role for this gene set. Interestingly, while NF-κB activated by oncogenes such as Ras and EGFR leads to cell-autonomous effects, abrogating NF-κB in PI3K-transformed cells did not decrease proliferation or induce apoptosis. However, conditioned media from PI3K mutant-expressing cells led to increased STAT3 activation in recipient THP-1 monocytes or normal epithelial cells in a NF-κB and IL-6-dependent manner. Together, our findings describe a PI3K-driven, NF-κB-dependent transcriptional profile which may play a critical role in promoting a microenvironment amenable to tumor progression. These data also indicate that NF-κB plays diverse roles downstream from different oncogenic signaling pathways

Radio emission and jets from microquasars

To some extent, all Galactic binary systems hosting a compact object are potential `microquasars', so much as all galactic nuclei may have been quasars, once upon a time. The necessary ingredients for a compact object of stellar mass to qualify as a microquasar seem to be: accretion, rotation and magnetic field. The presence of a black hole may help, but is not strictly required, since neutron star X-ray binaries and dwarf novae can be powerful jet sources as well. The above issues are broadly discussed throughout this Chapter, with a a rather trivial question in mind: why do we care? In other words: are jets a negligible phenomenon in terms of accretion power, or do they contribute significantly to dissipating gravitational potential energy? How do they influence their surroundings? The latter point is especially relevant in a broader context, as there is mounting evidence that outflows powered by super-massive black holes in external galaxies may play a crucial role in regulating the evolution of cosmic structures. Microquasars can also be thought of as a form of quasars for the impatient: what makes them appealing, despite their low number statistics with respect to quasars, are the fast variability time-scales. In the first approximation, the physics of the jet-accretion coupling in the innermost regions should be set by the mass/size of the accretor: stellar mass objects vary on 10^5-10^8 times shorter time-scales, making it possible to study variable accretion modes and related ejection phenomena over average Ph.D. time-scales. [Abridged]Comment: 28 pages, 13 figures, To appear in Belloni, T. (ed.): The Jet Paradigm - From Microquasars to Quasars, Lect. Notes Phys. 794 (2009

Global population divergence and admixture of the brown rat (Rattus norvegicus)

Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes

Weak Lensing with SDSS Commissioning Data: The Galaxy-Mass Correlation Function To 1/h Mpc

(abridged) We present measurements of galaxy-galaxy lensing from early commissioning imaging data from the Sloan Digital Sky Survey (SDSS). We measure a mean tangential shear around a stacked sample of foreground galaxies in three bandpasses out to angular radii of 600'', detecting the shear signal at very high statistical significance. The shear profile is well described by a power-law. A variety of rigorous tests demonstrate the reality of the gravitational lensing signal and confirm the uncertainty estimates. We interpret our results by modeling the mass distributions of the foreground galaxies as approximately isothermal spheres characterized by a velocity dispersion and a truncation radius. The velocity dispersion is constrained to be 150-190 km/s at 95% confidence (145-195 km/s including systematic uncertainties), consistent with previous determinations but with smaller error bars. Our detection of shear at large angular radii sets a 95% confidence lower limit $s>140^{\prime\prime}$, corresponding to a physical radius of $260h^{-1}$ kpc, implying that galaxy halos extend to very large radii. However, it is likely that this is being biased high by diffuse matter in the halos of groups and clusters. We also present a preliminary determination of the galaxy-mass correlation function finding a correlation length similar to the galaxy autocorrelation function and consistency with a low matter density universe with modest bias. The full SDSS will cover an area 44 times larger and provide spectroscopic redshifts for the foreground galaxies, making it possible to greatly improve the precision of these constraints, measure additional parameters such as halo shape, and measure the properties of dark matter halos separately for many different classes of galaxies.Comment: 28 pages, 11 figures, submitted to A