Characterising chlorogenic acid biosynthesis in coffee

Coffee is an important commodity and a major export for developing countries. There are two commercially grown species: Robusta and Arabica. The latter is more desirable, but more difficult to cultivate. It is susceptible to pests and diseases and less tolerant to environmental changes. This vulnerability is partly due to Arabica accumulating less chlorogenic acid (CGA) than Robusta. There are high levels of CGAs in the coffee beverage which contribute to the flavour and confer health benefits. In this study, I characterised enzymes involved in the biosynthesis of CGAs in coffee and investigated the function of transcription factors in controlling the phenylpropanoid pathway that lead to CGA production. The enzyme hydroxycinnamoyl-CoA quinate hydroxycinnamoyltransferase (HQT) is entirely responsible for the synthesis of the major CGA, 5-caffeoylquinic acid (5-CQA). I also discovered two routes for the synthesis of dicaffeoylquinic acids (diCQAs) from 5-CQA utilising two different enzymes in different subcellular compartments. HQT could synthesise diCQAs in the presence of high concentrations of 5-CQA when localised to the vacuole. Hydroxycinnamoyl-CoA quinate/shikimate hydroxycinnamoyltransferase (HCT) could synthesise diCQAs through the same route but can also synthesise diCQAs at neutral pH using 5-CQA and caffeoyl CoA. Tissue distribution patterns of metabolites in developing coffee fruit confirmed the presence of these biosynthetic routes. I cloned and characterised several R2R3MYB genes encoding potential regulators of CGA biosynthesis. Their analysis also led to a possible explanation for the usually high levels of CGA in coffee. Distinct MYB12-like transcription factors activated the transcription of a non-functional chalcone synthase (CHS) gene which is important for the synthesis of flavonols. This results in high levels of CGAs at the expenses of flavonol accumulation. Understanding CGA biosynthesis in coffee will be useful for sustainable cultivation of this important crop

Binary evolution with LOFT

This is a White Paper in support of the mission concept of the Large Observatory for X-ray Timing (LOFT), proposed as a medium-sized ESA mission. We discuss the potential of LOFT for the study of very faint X-ray binaries, orbital period distribution of black hole X-ray binaries and neutron star spin up. For a summary, we refer to the paper.Comment: White Paper in Support of the Mission Concept of the Large Observatory for X-ray Timing. (v2 few typos corrected

Heating and ionization of the primordial intergalactic medium by high mass x-ray binaries

We investigate the influence of high-mass X-ray binaries (HMXBs) on their high-redshift environments. Using a one-dimensional radiative transfer code, we predict the ionization and temperature profiles surrounding a coeval stellar population, composed of main-sequence stars and HMXBs, at various times after its formation. We consider both uniform density surroundings, and a cluster embedded in a 108 M⊙ Navarro–Frenk–White (NFW) halo. HMXBs in a constant density environment produce negligible enhanced ionization because of their high-energy spectral energy distributions and short lifetimes. In this case, HMXBs only marginally contribute to the local heating rate. For NFW profiles, radiation from main-sequence stars cannot prevent the initially ionized volume from recombining since it is unable to penetrate the high-density galactic core. However, HMXB photons stall recombinations behind the front, keeping it partially ionized for longer. The increased electron density in these partially ionized regions promotes further cooling, resulting in lower intergalactic medium (IGM) temperatures. In the context of this starburst model, we have shown that HMXBs do not make a major contribution to reionization or IGM heating. However, X-ray escape fractions are high in both density profile cases. Continuous star formation may result in the build up of X-rays over time, reducing the ionization time-scale and potentially leading to low level ionization of the distant IGM

Magnetically gated accretion in an accreting ‘non-magnetic’ white dwarf

White dwarfs are often found in binary systems with orbital periods ranging from tens of minutes to hours in which they can accrete gas from their companion stars. In about 15 per cent of these binaries, the magnetic field of the white dwarf is strong enough (at 106 gauss or more) to channel the accreted matter along field lines onto the magnetic poles1,2. The remaining systems are referred to as ‘non-magnetic’, because until now there has been no evidence that they have a magnetic field that is strong enough to affect the accretion dynamics. Here we report an analysis of archival optical observations of the ‘non-magnetic’ accreting white dwarf in the binary system MV Lyrae, whose light curve displays quasi-periodic bursts of about 30 minutes duration roughly every 2 hours. The timescale and amplitude of these bursts indicate the presence of an unstable, magnetically regulated accretion mode, which in turn implies the existence of magnetically gated accretion3,4,5, in which disk material builds up around the magnetospheric boundary (at the co-rotation radius) and then accretes onto the white dwarf, producing bursts powered by the release of gravitational potential energy. We infer a surface magnetic field strength for the white dwarf in MV Lyrae of between 2 × 104 gauss and 1 × 105 gauss, too low to be detectable by other current methods. Our discovery provides a new way of studying the strength and evolution of magnetic fields in accreting white dwarfs and extends the connections between accretion onto white dwarfs, young stellar objects and neutron stars, for which similar magnetically gated accretion cycles have been identified6,7,8,9

Early galaxy formation and its large-scale effects

Galaxy formation is at the heart of our understanding of cosmic evolution. Although there is a consensus that galaxies emerged from the expanding matter background by gravitational instability of primordial fluctuations, a number of additional physical processes must be understood and implemented in theoretical models before these can be reliably used to interpret observations. In parallel, the astonishing recent progresses made in detecting galaxies that formed only a few hundreds of million years after the Big Bang is pushing the quest for more sophisticated and detailed studies of early structures. In this review, we combine the information gleaned from different theoretical models/studies to build a coherent picture of the Universe in its early stages which includes the physics of galaxy formation along with the impact that early structures had on large-scale processes as cosmic reionization and metal enrichment of the intergalactic medium

Improved synthesis of commercially valuable opiates : development of reactions for industrial applications

Describes the synthesis of thebaine and noroxymorphone - key intermediates in the synthesis of opiate drugs. The design and optimisation of these synthetic pathways were developed keeping in mind the concerns of industry

Black hole X-ray binaries : radiation and high-redshift feedback

The accretion of matter onto black holes results in their characteristic spectrum through which we can identify them and study their properties. Furthermore, this radiation can couple to their surroundings, resulting in complex interactions between black holes and their environments. In this thesis, I study the accreting properties of stellar mass black holes, and examine the effect that such interactions may have had on the early universe. I also consider the observational characteristics of the lowest luminosity stellar mass black hole binary systems in our own galaxy. Approximately one billion years after the Big Bang, the universe underwent a huge baryonic phase change, in which neutral hydrogen became ionized by the first sources of radiation. Massive stars are thought to drive this process, but their ionizing lifetimes could have been extended by a later phase in their evolution: black hole X-ray binary formation. However, the extent of this enhancement is not known, and has been highly debated in recent literature. In this thesis, I show that X-ray binaries were unlikely to be present in sufficient numbers to exert a significant effect on the intergalactic medium. Using a stellar population synthesis model of a single starburst event, I show that radiation from X-ray binaries dominates the ionizing power of a cluster after the most massive stars have ended their lives. However, their high energy spectra and short lifetimes mean their ionizing timescales are too long for them to affect the progress of reionization. Even so, the high escape fraction of X-rays from galaxies still provides scope for low level heating and ionization of the distant intergalactic medium under different circumstances, such as in the context of continuous star formation. I also assess the detectability of the dimmest black hole binary systems in the Milky Way. Using a catalogue of black hole binaries in our galaxy, I find that there is a statistically significant lack of short orbital period systems, when compared to the neutron star binary population. I show that these sources may be hidden from view, rather than being truly absent, due to radiatively inefficient accretion, in which energy is lost to the black hole. However, this conclusion requires that the switch to inefficient accretion occurs sharply at a threshold mass accretion rate. In the case of a smoother switch, alternative observational or evolutionary arguments must be put forward to explain this dearth

Black holes in short period X-ray binaries and the transition to radiatively inefficient accretion

By comparing the orbital period distributions of black hole and neutron star low-mass X-ray binaries (LMXBs) in the Ritter–Kolb catalogue we show that there is statistical evidence for a dearth of black hole systems at short orbital periods (Porb < 4 h). This could either be due to a true divergence in orbital period distributions of these two types of system, or to black hole LMXBs being preferentially hidden from view at short orbital periods. We explore the latter possibility, by investigating whether black hole LMXBs could be concealed by a switch to radiatively inefficient accretion at low luminosities. The peak luminosity and the duration of X-ray binary outbursts are related to the disc radius and, hence, the orbital period. At short periods, where the peak outburst luminosity drops close to the threshold for radiatively inefficient accretion, black hole LMXBs have lower outburst luminosities, shorter outburst durations and lower X-ray duty cycles than comparable neutron star systems. These factors can combine to severely reduce the detection probability of short period black hole LMXBs relative to those containing neutron stars. We estimate the outburst properties and orbital period distribution of black hole LMXBs using two models of the transition to radiatively inefficient accretion: an instantaneous drop in accretion efficiency (η) to zero, at a fraction (f) of the Eddington luminosity (LEdd) and a power-law efficiency decrease, η∝M˙n, for L < f LEdd. We show that a population of black hole LMXBs at short orbital periods can only be hidden by a sharp drop in efficiency, either instantaneous or for n ≳ 3. This could be achieved by a genuine drop in luminosity or through abrupt spectral changes that shift the accretion power out of a given X-ray band