BACTERIAL BIOTRANSFORMATION OF LIGNIN IN ANOXIC ENVIRONMENTS

There is a growing need to reduce reliance on non-renewable fuels, especially fossil fuels that contribute to the climate crisis. Plant lignocellulose is an abundant and undervalued source of energy, but its use is hindered due to the recalcitrance of the lignin-component. Current methods to remove lignin have sustainability concerns and are costly for industrial applications such as paper mill pulping. An alternative and greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. The work presented in this dissertation investigates anaerobic bacteria as a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable byproducts. We first ask if anaerobic aromatic metabolism is vertically inherited or horizontally transferred across bacteria. We analyzed seven out of the nine known central intermediate pathways. Of the seven, benzoyl-CoA metabolism had the strongest phylogenetic signal, suggesting vertical inheritance is the driver of its phylogenetic distribution. This information can be used in future studies to test if predictions can be made for uncharacterized taxa and anaerobic benzoyl-CoA related metabolism. We also investigated the mechanisms of two uncharacterized isolates, Sodalis sp. strain 159R and Tolumonas lignolytica BRL6-1. Strain 159R contains many genes related to both aerobic and anaerobic aromatic metabolism but lacks extracellular enzymes for anaerobic lignin depolymerization. Conversely, strain BRL6-1 did not demonstrate lignin metabolism but instead relies on iron redox and organic radicals to potentially modify lignin structure under anoxic conditions. The electron exchange between iron, lignin, and BRL6-1 suggests a protein that acts as a chelator and redox molecule is the intermediate between the bacteria and substrate. The two isolates demonstrate the importance that lignin depolymerization and metabolism may be found separately in organisms and should be considered in future designs for anaerobic biopulping and lignin valorization to be a competitive process on the market

Pain in the Neck: the Enigmatic Presentation of an Embedded Acupuncture Needle

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A new experimental procedure for characterizing quantum effects in small magnetic particle systems

A new experimental procedure is discussed, which aims at separating thermal from quantum behavior independently of the energy barrier distribution in small particle systems. Magnetization relaxation data measured between 60 mK and 5 K on a sample of nanoparticles is presented. The comparison between experimental data and numerical calculations shows a clear departure from thermal dynamics for our sample, which was not obvious without using the new procedure presented here.Comment: LaTeX source, 6 pages, 5 PostScript figure

Effect of chromophore-chromophore electrostatic interactions in the NLO response of functionalized organic-inorganic sol-gel materials

In the last years, important non-linear optical results on sol-gel and polymeric materials have been reported, with values comparable to those found in crystals. These new materials contain push-pull chromophores either incorporated as guest in a high Tg polymeric matrix (doped polymers) or grafted onto the polymeric matrix. These systems present several advantages; however they require significant improvement at the molecular level - by designing optimized chromophores with very large molecular figure of merit, specific to each application targeted. Besides, it was recently stated in polymers that the chromophore-chromophore electrostatic interactions, which are dependent of chromophore concentration, have a strong effect into their non-linear optical properties. This has not been explored at all in sol-gel systems. In this work, the sol-gel route was used to prepare hybrid organic-inorganic thin films with different NLO chromophores grafted into the skeleton matrix. Combining a molecular engineering strategy for getting a larger molecular figure of merit and by controlling the intermolecular dipole-dipole interactions through both: the tuning of the push-pull chromophore concentration and the control of TEOS (Tetraethoxysilane) concentration, we have obtained a r33 coefficient around 15 pm/V at 633 nm for the classical DR1 azo-chromophore and a r33 around 50 pm/V at 831 nm for a new optimized chromophore structure.Comment: 10 pages, 11 figures, 1 tabl

Inadequate Decontamination Procedures: Sepsis Following Uneventful Endoscopy

Exogenous infection following endoscopy remains rare, however, recent attention in the media and the rise of antibacterial resistant strains of bacteria have emphasized the importance of proper sterilization techniques involved in the reprocessing of endoscopes and accessory devices. This chapter serves as comprehensive review into the epidemiology of exogenous infections as well as basic reprocessing techniques and guidelines for all medical professionals that treat patients that would benefit from endoscopy

Profiling microbial communities in manganese remediation systems treating coal mine drainage

Author Posting. © American Society for Microbiology, 2015. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 81 (2015): 2189-2198, doi:10.1128/AEM.03643-14.Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal and archaeal communities in four variably-performing MRBs in Pennsylvania to determine whether they differed among MRBs and from surrounding soil, and to establish the relative abundance of known Mn(II)-oxidizers. Archaea were not detected; PCRs with archaeal primers returned only non-target bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but OTU-based analyses showed significant clustering by MRB with all four groups (p<0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known.This project was funded by Smithsonian Scholarly Studies and Next-Generation Sequencing grants to C.M.S., by a Smithsonian Postdoctoral Fellowship to D.L.C., and by the National Science Foundation, grant numbers EAR-1249489 (awarded to C.M.H.) and CBET-1336496 (awarded to C.M.H. and C.M.S.)

A Photochemical Organocatalytic Strategy for the α-Alkylation of Ketones by using Radicals

Reported herein is a visible-light-mediated radical approach to the α-alkylation of ketones. This method exploits the ability of a nucleophilic organocatalyst to generate radicals upon SN2-based activation of alkyl halides and blue light irradiation. The resulting open-shell intermediates are then intercepted by weakly nucleophilic silyl enol ethers, which would be unable to directly attack the alkyl halides through a traditional two-electron path. The mild reaction conditions allowed functionalization of the α position of ketones with functional groups that are not compatible with classical anionic strategies. In addition, the redox-neutral nature of this process makes it compatible with a cinchona-based primary amine catalyst, which was used to develop a rare example of enantioselective organocatalytic radical α-alkylation of ketones

Non-monotonic field-dependence of the ZFC magnetization peak in some systems of magnetic nanoparticles

We have performed magnetic measurements on a diluted system of gamma-Fe2O3 nanoparticles (~7nm), and on a ferritin sample. In both cases, the ZFC-peak presents a non-monotonic field dependence, as has already been reported in some experiments,and discussed as a possible evidence of resonant tunneling. Within simple assumptions, we derive expressions for the magnetization obtained in the usual ZFC, FC, TRM procedures. We point out that the ZFC-peak position is extremely sensitive to the width of the particle size distribution, and give some numerical estimates of this effect. We propose to combine the FC magnetization with a modified TRM measurement, a procedure which allows a more direct access to the barrier distribution in a field. The typical barrier values which are obtained with this method show a monotonic decrease for increasing fields, as expected from the simple effect of anisotropy barrier lowering, in contrast with the ZFC results. From our measurements on gamma-Fe2O3 particles, we show that the width of the effective barrier distribution is slightly increasing with the field, an effect which is sufficient for causing the observed initial increase of the ZFC-peak temperatures.Comment: LaTeX file 19 pages, 9 postscript figures. To appear in Phys. Rev. B (tentative schedule: Dec.97

On the temporal stability of the coda of ambient noise correlations

We analyze the sensitivity of cross correlations to the anisotropy of the incident field in the context of seismic ambient noise monitoring of small velocity changes. Numerical simulations of elastic waves are performed in a 2D scattering plate with a focus on the comparative character of the direct and coda waves in the cross-correlation. We show that coda waves reconstructed from cross-correlations are far more robust than direct waves in the presence of azimuthal anisotropy of the incident field. We observe similar behavior with real data recorded on Erebus volcano, where a database of impulsive icequakes is used to simulate an anisotropic source field. We propose a simplified approach to evaluate the sensitivity of scattered waves to the anisotropy of the incoming noise field. We rely on previous results obtained for direct waves and on intrinsic properties of scattered waves to predict the errors produced by strong source anisotropy with numerical experiments. These results also yield realistic values for monitoring the accuracy to be expected with real data at crustal scales. Our analysis shows that high-precision noise-based monitoring could be performed with coda waves in the correlation functions, even in the presence of variations in the azimuthal distribution of the ambient noise field