Reducing Biomass Recalcitrance by Heterologous Expression of a Bacterial Peroxidase in Tobacco (\u3cem\u3eNicotiana benthamiana\u3c/em\u3e)

Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and extracts from transgenic leaves showed higher activity on classic peroxidase substrates than the control. Intriguingly, in situ DypB activation and subsequent saccharification released nearly 200% more fermentable sugars from transgenic lines than controls, which were not explained by variation in initial structural and non-structural carbohydrates and lignin content. Pyrolysis-GC-MS analysis showed more reduction in the level of lignin associated pyrolysates in the transgenic lines than the control primarily when the enzyme is activated prior to pyrolysis, consistent with increased lignin degradation and improved saccharification. The findings reveal for the first time that accumulation and in situ activation of a peroxidase improves biomass digestibility

The ATLAS3D project - XXVII : Cold gas and the colours and ages of early-type galaxies

Date of Acceptance: 16/12/2013We present a study of the cold gas contents of the ATLAS3D early-type galaxies, in the context of their optical colours, near-ultraviolet colours and Hβ absorption line strengths. Early-type (elliptical and lenticular) galaxies are not as gas poor as previously thought, and at least 40 per cent of local early-type galaxies are now known to contain molecular and/or atomic gas. This cold gas offers the opportunity to study recent galaxy evolution through the processes of cold gas acquisition, consumption (star formation) and removal. Molecular and atomic gas detection rates range from 10 to 34 per cent in red sequence early-type galaxies, depending on how the red sequence is defined, and from 50 to 70 per cent in blue early-type galaxies. Notably, massive red sequence early-type galaxies (stellar masses >5 × 1010 M⊙, derived from dynamical models) are found to have H I masses up to M(H I)/M* ∼ 0.06 and H2 masses up to M(H2)/M* ∼ 0.01. Some 20 per cent of all massive early-type galaxies may have retained atomic and/or molecular gas through their transition to the red sequence. However, kinematic and metallicity signatures of external gas accretion (either from satellite galaxies or the intergalactic medium) are also common, particularly at stellar masses ≤5 × 1010 M⊙, where such signatures are found in ∼50 per cent of H2-rich early-type galaxies. Our data are thus consistent with a scenario in which fast rotator early-type galaxies are quenched former spiral galaxies which have undergone some bulge growth processes, and in addition, some of them also experience cold gas accretion which can initiate a period of modest star formation activity. We discuss implications for the interpretation of colour–magnitude diagramsPeer reviewedFinal Accepted Versio

Connection between dynamically derived initial mass function normalization and stellar population parameters

Date of Acceptance: 10/08/2014We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS3D project. We study trends between our dynamically derived IMF normalization αdyn ≡ (M/L)stars/(M/L)Salp and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of αdyn at a given population parameter. As a result, we find weak αdyn-[α/Fe] and αdyn -Age correlations and no significant αdyn -[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis.Peer reviewe

Accurate and sensitive quantification of protein-DNA binding affinity

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes

Phase behaviour of a model of colloidal particles with a fluctuating internal state

Colloidal particles are not simple rigid particles, in general an isolated particle is a system with many degrees of freedom in its own right, e.g., the counterions around a charged colloidal particle.The behaviour of model colloidal particles, with a simple phenomenological model to account for these degrees of freedom, is studied. It is found that the interaction between the particles is not pairwise additive. It is even possible that the interaction between a triplet of particles is attractive while the pair interaction is repulsive. When this is so the liquid phase is either stable only in a small region of the phase diagram or absent altogether.Comment: 12 pages including 4 figure

Patient and public involvement (PPI) in UK surgical trials: a survey and focus groups with stakeholders to identify practices, views, and experiences

Background and aims Historically, patient and public involvement (PPI) in the design and conduct of surgical trials has been absent or minimal, but it is now routinely recommended and even required by some research funders. We aimed to identify and describe current PPI practice in surgical trials in the United Kingdom, and to explore the views and experiences of surgical trial staff and patient or public contributors in relation to these practices. This was part of a larger study to inform development of a robust PPI intervention aimed at improving recruitment and retention in surgical trials. Methods Our study had two stages: 1) an online survey to identify current PPI practice in active UK-led, adult surgical trials; and 2) focus groups and interviews with key stakeholders (surgical trial investigators, administrators, and patient or public contributors) to explore their views and experiences of PPI. Results Of 129 eligible surgical trial teams identified, 71 (55%) took part in the survey. In addition, 54 stakeholders subsequently took part in focus groups or interviews. Sixty-five (92%) survey respondents reported some kind of PPI, most commonly at the design and dissemination stages and in oversight or advisory roles. The single most common PPI activity was developing participant information sheets (72%). Participants reported mixed practice and views on a variety of issues including the involvement of patients versus lay members of the public, recruitment methods, use of role descriptions and payment for the time of PPI contributors. They suggested some solutions, including the use of written role descriptions and databases of potential PPI contributors to aid recruitment. Conclusions UK surgical trials involve patients and members of the public in a variety of different ways, most commonly at the beginning and end of the trial lifecycle and in oversight or advisory roles. These are not without challenges and there remain uncertainties about who best to involve, why, and how. Future research should aim to address these issues

A systematic variation of the stellar initial mass function in early-type galaxies

Much of our knowledge of galaxies comes from analysing the radiation emitted by their stars. It depends on the stellar initial mass function (IMF) describing the distribution of stellar masses when the population formed. Consequently knowledge of the IMF is critical to virtually every aspect of galaxy evolution. More than half a century after the first IMF determination, no consensus has emerged on whether it is universal in different galaxies. Previous studies indicated that the IMF and the dark matter fraction in galaxy centres cannot be both universal, but they could not break the degeneracy between the two effects. Only recently indications were found that massive elliptical galaxies may not have the same IMF as our Milky Way. Here we report unambiguous evidence for a strong systematic variation of the IMF in early-type galaxies as a function of their stellar mass-to-light ratio, producing differences up to a factor of three in mass. This was inferred from detailed dynamical models of the two-dimensional stellar kinematics for the large Atlas3D representative sample of nearby early-type galaxies spanning two orders of magnitude in stellar mass. Our finding indicates that the IMF depends intimately on a galaxy's formation history.Comment: 4 pages, 2 figures, LaTeX. Accepted for publication as a Nature Letter. More information about our Atlas3D project is available at http://purl.org/atlas3

The ATLAS3D project - XXX : Star formation histories and stellar population scaling relations of early-type galaxies

Peer reviewedFinal Accepted Versio

Cenários de futuros possíveis para a Enfermagem em Portugal: algumas reflexões

info:eu-repo/semantics/publishedVersio

The ATLAS3D project - XXIX : The new look of early-type galaxies and surrounding fields disclosed by extremely deep optical images

Date of Acceptance: 25/09/2014Galactic archaeology based on star counts is instrumental to reconstruct the past mass assembly of Local Group galaxies. The development of new observing techniques and data reduction, coupled with the use of sensitive large field of view cameras, now allows us to pursue this technique in more distant galaxies exploiting their diffuse low surface brightness (LSB) light. As part of the ATLAS3D project, we have obtained with the MegaCam camera at the Canada-France-Hawaii Telescope extremely deep, multiband images of nearby early-type galaxies (ETGs). We present here a catalogue of 92 galaxies from the ATLAS3D sample, which are located in low- to medium-density environments. The observing strategy and data reduction pipeline, which achieve a gain of several magnitudes in the limiting surface brightness with respect to classical imaging surveys, are presented. The size and depth of the survey are compared to other recent deep imaging projects. The paper highlights the capability of LSB-optimized surveys at detecting new prominent structures that change the apparent morphology of galaxies. The intrinsic limitations of deep imaging observations are also discussed, among those, the contamination of the stellar haloes of galaxies by extended ghost reflections, and the cirrus emission from Galactic dust. The detection and systematic census of fine structures that trace the present and past mass assembly of ETGs are one of the prime goals of the project. We provide specific examples of each type of observed structures - tidal tails, stellar streams and shells - and explain how they were identified and classified. We give an overview of the initial results. The detailed statistical analysis will be presented in future papers.Peer reviewedFinal Accepted Versio