Andrew J. Davis

Unravelling obese black holes in the first galaxies

We predict the existence and observational signatures of a new class of objects that assembled early, during the first billion years of cosmic time: Obese Black-hole Galaxies (OBGs). OBGs are objects in which the mass of the central black hole initially exceeds that of the stellar component of the host galaxy, and the luminosity from black-hole accretion dominates the starlight. From a cosmological simulation, we demonstrate that there are sites where star formation is initially inhibited and direct-collapse black holes (DCBHs) form due to the photo-dissociating effect of Lyman-Werner radiation on molecular hydrogen. We show that the formation of OBGs is inevitable, because the probability of finding the required extra-galactic environment and the right physical conditions in a halo conducive to DCBH formation is quite high in the early universe. We estimate an OBG number density of 0.009/Mpc^3 at z~8 and 0.03/Mpc^3 at z~6. Extrapolating from our simulation volume, we infer that the most luminous quasars detected at z~6 likely transited through an earlier OBG phase. We find that these primordial galaxies start off with an over-massive BH and acquire their stellar component from subsequent merging as well as in-situ star formation. In doing so, they inevitably go through an OBG phase dominated by the accretion luminosity at the Eddington rate or below, released from the growing BH. The OBG phase is characterised by an ultra-violet (UV) spectrum with slope of beta ~ -2.3 and the absence of a Balmer Break. OBGs should also be spatially unresolved, and are expected to be brighter than the majority of known high-redshift galaxies. OBGs could potentially be revealed via HST follow-up imaging of samples of brighter Lyman-break galaxies provided by wide-area ground-based surveys such as UltraVISTA, and should be easily uncovered and studied with instruments aboard JWST...(abridged)

A network perspective on the topological importance of enzymes and their phylogenetic conservation

BackgroundA metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while others occur only in a few. We ask if there are relationships between the phylogenetic profile of an enzyme, or the number of different bacterial species that contain it, and its topological importance in the metabolic network. Our null hypothesis is that phylogenetic profile is independent of topological importance. To test our null hypothesis we constructed an enzyme network from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. We calculated three network indices of topological importance: the degree or the number of connections of a network node; closeness centrality, which measures how close a node is to others; and betweenness centrality measuring how frequently a node appears on all shortest paths between two other nodes.ResultsEnzyme phylogenetic profile correlates best with betweenness centrality and also quite closely with degree, but poorly with closeness centrality. Both betweenness and closeness centralities are non-local measures of topological importance and it is intriguing that they have contrasting power of predicting phylogenetic profile in bacterial species. We speculate that redundancy in an enzyme network may be reflected by betweenness centrality but not by closeness centrality. We also discuss factors influencing the correlation between phylogenetic profile and topological importance.ConclusionOur analysis falsifies the hypothesis that phylogenetic profile of enzymes is independent of enzyme network importance. Our results show that phylogenetic profile correlates better with degree and betweenness centrality, but less so with closeness centrality. Enzymes that occur in many bacterial species tend to be those that have high network importance. We speculate that this phenomenon originates in mechanisms driving network evolution. Closeness centrality reflects phylogenetic profile poorly. This is because metabolic networks often consist of distinct functional modules and some are not in the centre of the network. Enzymes in these peripheral parts of a network might be important for cell survival and should therefore occur in many bacterial species. They are, however, distant from other enzymes in the same network.

Flavan-3-ols in Norway spruce: Biosynthesis, accumulation and function in response to attack by the bark beetle-associated fungus Ceratocystis polonica

Monomeric and polymeric flavan-3-ols are antifungal defense compounds in Norway spruce (Picea abies). Proanthocyanidins (PAs) are common polyphenolic polymers of plants found in foliage, fruit, bark, roots, rhizomes, and seed coats that consist of flavan-3-ol units such as 2,3-trans-(+)-catechin and 2,3-cis-(–)-epicatechin. Although the biosynthesis of flavan-3-ols has been studied in angiosperms, little is known about their biosynthesis and ecological roles in gymnosperms. In this study, the genes encoding leucoanthocyanidin reductase, a branch point enzyme involved in the biosynthesis of 2,3-trans-(+)-flavan-3-ols, were identified and functionally characterized in Norway spruce (Picea abies), the most widespread and economically important conifer in Europe. In addition, the accumulation of flavan-3-ols and PAs was investigated in Norway spruce saplings after wounding or inoculation with the fungal pathogen Ceratocystis polonica, which is vectored by bark beetles (Ips typographus) and is usually present during fatal beetle attacks. Monomeric and dimeric flavan-3-ols were analyzed by reverse-phase high-pressure liquid chromatography, while the size and subunit composition of larger PAs were characterized using a novel acid hydrolysis method and normal phase chromatography. Only flavan-3-ol monomers with 2,3-trans stereochemistry were detected in spruce bark; dimeric and larger PAs contained flavan-3-ols with both 2,3-trans and 2,3-cis stereochemistry. Levels of monomers as well as PAs with a higher degree of polymerization increased dramatically in spruce bark after infection by C. polonica. In accordance with their role in the biosynthesis of 2,3-trans-(+)-flavan-3-ols, transcript abundance of Norway spruce LEUCOANTHOCYANIDIN REDUCTASE genes also increased significantly during fungal infection. Bioassays with C. polonica revealed that the levels of 2,3-trans-(+)-catechin and PAs that are produced in the tree in response to fungal infection inhibit C. polonica growth and can therefore be considered chemical defense compounds.

Eating chemically defended prey: alkaloid metabolism in an invasive ladybird predator of other ladybirds (Coleoptera: Coccinellidae).

SUMMARY By comparison with studies of herbivore physiological adaptation to plant allelochemicals, work on predator physiological adaptation to potentially toxic prey has been very limited. Such studies are important in understanding how evolution could shape predator diets. An interesting question is the specificity of predator adaptation to prey allelochemicals, given that many predators consume diverse prey with different chemical defences. The ladybird Harmonia axyridis, an invasive species in America, Europe and Africa, is considered a significant predatory threat to native invertebrates, particularly other aphid-eating ladybirds of which it is a strong intraguild predator. Although ladybirds possess species-specific alkaloid defences, H. axyridis exhibits high tolerance for allospecific ladybird prey alkaloids. Nonetheless, it performs poorly on species with novel alkaloids not commonly occurring within its natural range. We examined alkaloid fate in H. axyridis larvae after consumption of two other ladybird species, one containing an alkaloid historically occurring within the predators native range (isopropyleine) and one containing a novel alkaloid that does not (adaline). Our results indicate that H. axyridis rapidly chemically modifies the alkaloid to which it has been historically exposed to render it less harmful: this probably occurs outside of the gut. The novel, more toxic alkaloid persists in the body unchanged for longer. Our results suggest metabolic alkaloid specialisation, in spite of the diversity of chemically defended prey that the predator consumes. Physiological adaptations appear to have made H. axyridis a successful predator of other ladybirds; however, limitations are imposed by its physiology when it eats prey with novel alkaloids.

Spin and structural halo properties at high redshift in a LCDM Universe

In this paper, we examine in detail the key structural properties of high redshift dark matter haloes as a function of their spin parameter. We perform and analyze high resolution cosmological simulations of the formation of structure in a LCDM Universe. We study the mass function, ellipticities, shapes, density profiles, rotation curves and virialization for a large sample of dark matter haloes from z = 15 - 6. We also present detailed convergence tests for individual haloes. We find that high spin haloes have stronger clustering strengths (up to 25%) at all mass and redshift ranges at these early epochs. High redshift spherical haloes are also up to 50% more clustered than aspherical haloes. High spin haloes at these redshifts are also preferentially found in high density environments, and have more neighbors than their low spin counterparts. We report a systematic offset in the peak of the circular velocity curves for high and low spin haloes of the same mass. Therefore, estimating halo masses without knowledge of the spin, using only the circular velocity can yield errors of up to 40%. The strong dependence of key structural properties on spin that we report here likely have important implications for studies of star formation and feedback from these galaxies.

The First Billion Years project: dark matter haloes going from contraction to expansion and back again

We study the effect of baryons on the inner dark matter profile of the first galaxies using the First Billion Years simulation between z=16-6 before secular evolution sets in. Using a large statistical sample from two simulations of the same volume and cosmological initial conditions, one with and one without baryons, we are able to directly compare haloes with their baryon-free counterparts, allowing a detailed study of the modifications to the dark matter density profile due to the presence of baryons during the first billion years of galaxy formation. For each of the ~ 5000 haloes in our sample we quantify the impact of the baryons using eta, defined as the ratio of dark matter mass enclosed in 100 pc in the baryonic run to its counterpart without baryons. During this epoch of rapid growth of galaxies, we find that many haloes of these first galaxies show an enhancement of dark matter in the halo centre compared to the baryon-free simulation, while many others show a deficit. We find that the mean value of eta is close to unity, but there is a large dispersion, with a standard deviation of 0.677. The enhancement is cyclical in time and tracks the star formation cycle of the galaxy; as gas falls to the centre and forms stars, the dark matter moves in as well. Supernova feedback then removes the gas, and the dark matter again responds to the changing potential. We study three physical models relating the motion of baryons to that of the dark matter: adiabatic contraction, dynamical friction, and rapid outflows. Abridged, see text for full abstract

Population structure of Cylindrocladium parasiticum infecting peanuts (Arachis hypogaea) in Georgia, USA

Cylindrocladium parasiticum is an important pathogen of peanut (Arachis hypogaea) causing the disease Cylindrocladium black rot. The genetic structure of this haploid pathogen was determined for populations associated with peanut in Georgia, USA. Ten polymorphic microsatellite markers were used to determine genetic and genotypic diversity among three sub-populations representing the geographic distribution of peanut production in Georgia. Among 200 isolates collected, only 10 unique multilocus haplotypes were identified, with one multilocus haplotype occurring 176 times. Although no evidence for random mating was observed, the existence of loops in a constructed haplotype network hint at the possibility of recombination events. The absence of random mating might therefore be attributed to the homothallic nature of C. parasiticum as well as the clonality of the population, without excluding the possible occurrence of recombination. Cylindrocladium parasiticum thus appears to consist of a genetically homogeneous population throughout Georgia with mainly clonal reproduction or inbreeding contributing to the observed population genetic structure.