Optimization of ethanol production by yeasts from lignocellulosic feedstocks

Ethanol from lignocellulosic feedstocks is not currently competitive with corn-based ethanol in terms of yields and commercial feasibility. Through optimization of the pretreatment and fermentation steps this could change. The overall goal of this study was to evaluate, characterize, and optimize ethanol production from lignocellulosic feedstocks by the yeasts Saccharomyces cerevisiae (strain Ethanol Red, ER) and Pichia stipitis CBS 6054. Through a series of fermentations and growth studies, P. stipitis CBS 6054 and S. cerevisiae (ER) were evaluated on their ability to produce ethanol from both single substrate (xylose and glucose) and mixed substrate (five sugars present in hemicellulose) fermentations. The yeasts were also evaluated on their ability to produce ethanol from dilute acid pretreated hydrolysate and enzymatic hydrolysate. Hardwood (aspen), softwood (balsam), and herbaceous (switchgrass) hydrolysates were also tested to determine the effect of the source of the feedstock. P. stipitis produced ethanol from 66-98% of the theoretical yield throughout the fermentation studies completed over the course of this work. S. cerevisiae (ER) was determined to not be ideal for dilute acid pretreated lignocellulose because it was not able to utilize all the sugars found in hemicellulose. S. cerevisiae (ER) was instead used to optimize enzymatic pretreated lignocellulose that contained only glucose monomers. It was able to produce ethanol from enzymatically pretreated hydrolysate but the sugar level was so low (\u3e3 g/L) that it would not be commercially feasible. Two lignocellulosic degradation products, furfural and acetic acid, were evaluated for whether or not they had an inhibitory effect on biomass production, substrate utilization, and ethanol production by P. stipitis and S. cerevisiae (ER). It was determined that inhibition is directly related to the concentration of the inhibitor and the organism. The final phase for this thesis focused on adapting P. stipitis CBS 6054 to toxic compounds present in dilute acid pretreated hydrolysate through directed evolution. Cultures were transferred to increasing concentrations of dilute acid pretreated hydrolysate in the fermentation media. The adapted strains’ fermentation capabilities were tested against the unadapted parent strain at each hydrolysate concentration. The fermentation capabilities of the adapted strain were significantly improved over the unadapted parentstrain. On media containing 60% hydrolysate the adapted strain yielded 0.30 g_ethanol/g_sugar ± 0.033 (g/g) and the unadapted parent strain yielded 0.11 g/g ±0.028. The culture has been successfully adapted to growth on media containing 65%, 70%, 75%, and 80% hydrolysate but with below optimal ethanol yields (0.14-0.19 g/g). Cell recycle could be a viable option for improving ethanol yields in these cases. A study was conducted to determine the optimal media for production of ethanol from xylose and mixed substrate fermentations by P. stipitis. Growth, substrate utilization, and ethanol production were the three factors used to evaluate the media. The three media tested were Yeast Peptone (YP), Yeast Nitrogen Base (YNB), and Corn Steep Liquor (CSL). The ethanol yields (g/g) for each medium are as follows: YP - 0.40-0.42, YNB -0.28-.030, and CSL - 0.44-.051. The results show that media containing CSL result in slightly higher ethanol yields then other fermentation media. P. stipitis was successfully adapted to dilute acid pretreated aspen hydrolysate in increasing concentrations in order to produce higher ethanol yields compared to the unadapted parent strain. S. cerevisiae (ER) produced ethanol from enzymatic pretreated cellulose containing low concentrations of glucose (1-3g/L). These results show that fermentations of lignocellulosic feedstocks can be optimized based on the substrate and organism for increased ethanol yields

A complete census of AGN and their hosts from optical surveys?

Large optical surveys provide an unprecedented census of galaxies in the local Universe, forming an invaluable framework into which more detailed studies of objects can be placed. But how useful are optical surveys for understanding the co-evolution of black holes and galaxies, given their limited wavelength coverage, selection criteria, and depth? In this conference paper I present work-in-progress comparing optical and mid-IR diagnostics of three "unusual" low redshift populations (luminous Seyferts, dusty Balmer-strong AGN, ULIRGs) with a set of ordinary star-forming galaxies from the SDSS. I address the questions: How well do the mid-infrared and optical diagnostics of star formation and AGN strength agree? To what extent do optical surveys allow us to include extreme, dusty, morphologically disturbed galaxies in our "complete" census of black hole-galaxy co-evolution?Comment: Proceedings of contributed talk at "Co-Evolution of Central Black Holes and Galaxies" (eds. B.M. Peterson, R.S. Somerville, and T. Storchi-Bergmann), IAU symposium 267, August 2009. 6 pages, 5 figure

Optical vs. infrared studies of dusty galaxies and AGN: (I) Nebular emission lines

Optical nebular emission lines are commonly used to estimate the star formation rate of galaxies and the black hole accretion rate of their central active nucleus. The accuracy of the conversion from line strengths to physical properties depends upon the accuracy to which the lines can be corrected for dust attenuation. For studies of single galaxies with normal amounts of dust, most dust corrections result in the same derived properties within the errors. However, for statistical studies of populations of galaxies, or for studies of galaxies with higher dust contents such as might be found in some classes of "transition" galaxies, significant uncertainty arises from the dust attenuation correction. We compare the strength of the predominantly unobscured mid-IR [NeII]15.5um + [NeIII]12.8um emission lines to the optical H alpha emission lines in four samples of galaxies: (i) ordinary star forming galaxies, (ii) optically selected dusty galaxies, (iii) ULIRGs, (iv) Seyfert 2 galaxies. We show that a single dust attenuation curve applied to all samples can correct H alpha emission for dust attenuation to a factor better than 2. Similarly, we compare mid-IR [OIV] and optical [OIII] luminosities to find that [OIII] can be corrected to a factor better than 3. This shows that the total dust attenuation suffered by the AGN narrow line region is not significantly different to that suffered by the starforming HII regions in the galaxy. We provide explicit dust attenuation corrections, together with errors, for [OII], [OIII] and H alpha. The best-fit average attenuation curve is slightly greyer than the Milky-Way extinction law, indicating either that external galaxies have slightly different typical dust properties to the Milky Way, or that there is a significant contribution from scattering. Finally, we uncover an intriguing correlation between Silicate absorption and Balmer decrement.Comment: 19 pages, 9 figures, accepted for publication in MNRA

Spiral-Induced Star Formation in the Outer Disks of Galaxies

The outer regions of galactic disks have received increased attention since ultraviolet observations with GALEX demonstrated that nearly 30% of galaxies have UV emission beyond their optical extents, indicating star formation activity. These galaxies have been termed extended UV (XUV) disks. Here, we address whether these observations contradict the gas surface density threshold for star formation inferred from Halpha radial profiles of galaxies. We run smoothed particle hydrodynamics simulations of isolated disk galaxies with fiducial star formation prescriptions and show that over-densities owing to the presence of spiral structure can induce star formation in extended gas disks. For direct comparison with observations, we use the 3-D radiative transfer code Sunrise to create simulated FUV and K_s band images. We find that galaxies classified as Type I XUV disks are a natural consequence of spiral patterns, but we are unable to reproduce Type II XUV disks. We also compare our results to studies of the Kennicutt-Schmidt relation in outer disks.Comment: Published in Ap

Dissecting galaxies: spatial and spectral separation of emission excited by star formation and AGN activity

The optical spectra of Seyfert galaxies are often dominated by emission lines excited by both star formation and active galactic nucleus (AGN) activity. Standard calibrations (such as for the star formation rate) are not applicable to such composite (mixed) spectra. In this paper, we describe how integral field data can be used to spectrally and spatially separate emission associated with star formation from emission associated with accretion on to an AGN. We demonstrate our method using integral field data for two AGN host galaxies (NGC 5728 and NGC 7679) from the Siding Spring Southern Seyfert Spectroscopic Snapshot Survey (S7). The spectra of NGC 5728 and NGC 7679 form clear sequences of AGN fraction on standard emission line ratio diagnostic diagrams. We show that the emission line luminosities of the majority (>85 per cent) of spectra along each AGN fraction sequence can be reproduced by linear superpositions of the emission line luminosities of one AGN dominated spectrum and one star formation dominated spectrum. We separate the Hα, Hβ, [N II]λ6583, [S II]λλ6716, 6731, [O III]λ5007 and [O II]λλ3726, 3729 luminosities of every spaxel into contributions from star formation and AGN activity. The decomposed emission line images are used to derive the star formation rates and AGN bolometric luminosities for NGC 5728 and NGC 7679. Our calculated values are mostly consistent with independent estimates from data at other wavelengths. The recovered star-forming and AGN components also have distinct spatial distributions which trace structures seen in high-resolution imaging of the galaxies, providing independent confirmation that our decomposition has been successful

The Impact of Membrane Lipid Composition on Macrophage Activation in the Immune Defense against Rhodococcus equi and Pseudomonas aeruginosa

Nutritional fatty acids are known to have an impact on membrane lipid composition of body cells, including cells of the immune system, thus providing a link between dietary fatty acid uptake, inflammation and immunity. In this study we reveal the significance of macrophage membrane lipid composition on gene expression and cytokine synthesis thereby highlighting signal transduction processes, macrophage activation as well as macrophage defense mechanisms. Using RAW264.7 macrophages as a model system, we identified polyunsaturated fatty acids (PUFA) of both the n-3 and the n-6 family to down-regulate the synthesis of: (i) the pro-inflammatory cytokines IL-1β, IL-6 and TNF-α; (ii) the co-stimulatory molecule CD86; as well as (iii) the antimicrobial polypeptide lysozyme. The action of the fatty acids partially depended on the activation status of the macrophages. It is particularly important to note that the anti-inflammatory action of the PUFA could also be seen in case of infection of RAW264.7 with viable microorganisms of the genera R. equi and P. aeruginosa. In summary, our data provide strong evidence that PUFA from both the n-3 and the n-6 family down-regulate inflammation processes in context of chronic infections caused by persistent pathogens

Rapid Detection of Biological and Chemical Threat Agents Using Physical Chemistry, Active Detection, and Computational Analysis

Basic technologies have been successfully developed within this project: rapid collection of aerosols and a rapid ultra-sensitive immunoassay technique. Water-soluble, humidity-resistant polyacrylamide nano-filters were shown to (1) capture aerosol particles as small as 20 nm, (2) work in humid air and (3) completely liberate their captured particles in an aqueous solution compatible with the immunoassay technique. The immunoassay technology developed within this project combines electrophoretic capture with magnetic bead detection. It allows detection of as few as 150-600 analyte molecules or viruses in only three minutes, something no other known method can duplicate. The technology can be used in a variety of applications where speed of analysis and/or extremely low detection limits are of great importance: in rapid analysis of donor blood for hepatitis, HIV and other blood-borne infections in emergency blood transfusions, in trace analysis of pollutants, or in search of biomarkers in biological fluids. Combined in a single device, the water-soluble filter and ultra-sensitive immunoassay technique may solve the problem of early âwarning typeâ detection of aerosolized pathogens. These two technologies are protected with five patent applications and are ready for commercialization

Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement

Systematic reviews should build on a protocol that describes the rationale, hypothesis, and planned methods of the review; few reviews report whether a protocol exists. Detailed, well-described protocols can facilitate the understanding and appraisal of the review methods, as well as the detection of modifications to methods and selective reporting in completed reviews. We describe the development of a reporting guideline, the Preferred Reporting Items for Systematic reviews and Meta-Analyses for Protocols 2015 (PRISMA-P 2015). PRISMA-P consists of a 17-item checklist intended to facilitate the preparation and reporting of a robust protocol for the systematic review. Funders and those commissioning reviews might consider mandating the use of the checklist to facilitate the submission of relevant protocol information in funding applications. Similarly, peer reviewers and editors can use the guidance to gauge the completeness and transparency of a systematic review protocol submitted for publication in a journal or other medium

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant