BioLogicTool : A Simple Visual Tool for Assisting in the Logical Selection of Pathways from Biomass to Products

The current chemical industry has been heavily optimized for the use of petroleum-derived base chemicals as its primary source of building blocks. However, incorporation of heteroatoms, absent in the base chemicals, is necessary to meet the different property requirements in the plethora of products the industry makes such as plastics, cosmetics, and pharmaceuticals. As global oil reserves deplete, a shift toward renewable bioderived building blocks, so-called platform molecules, will become a necessity. Bioderived platform molecules are typically rich in heteroatoms as a result of their biomass feedstock also being heteroatom rich, and it would therefore seem logical to carry these heteroatoms through to the aforementioned products. A tool was herein developed to assess the rationality of a synthetic route from feedstock to product, designed specifically to give a visual representation of the pathways and options available. BioLogicTool plots (%heteroatom by mass vs M) are an alternative to the conventional van Krevelen diagram, and are designed to better consider the diversity in heteroatom content encountered in biobased chemicals. The tool can rapidly help its user to design more logical multistep synthetic routes and enhance the mass efficiency of pathways. Several examples were selected to demonstrate the power and limitations of the BioLogicTool, but it was clear from these examples that removing heteroatoms from platform molecules to reincorporate them later in the final product is, in most cases, not logical in a mass efficiency sense

Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis

<p>Abstract</p> <p>Background</p> <p>Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H₂and other substrates to produce methane. <it>Methanococcus maripaludis </it>is a model for studies of the global response to nutrient limitations.</p> <p>Results</p> <p>We used high-coverage quantitative proteomics to determine the response of <it>M. maripaludis </it>to growth-limiting levels of H₂, nitrogen, and phosphate. Six to ten percent of the proteome changed significantly with each nutrient limitation. H₂limitation increased the abundance of a wide variety of proteins involved in methanogenesis. However, one protein involved in methanogenesis decreased: a low-affinity [Fe] hydrogenase, which may dominate over a higher-affinity mechanism when H₂is abundant. Nitrogen limitation increased known nitrogen assimilation proteins. In addition, the increased abundance of molybdate transport proteins suggested they function for nitrogen fixation. An apparent regulon governed by the euryarchaeal nitrogen regulator NrpR is discussed. Phosphate limitation increased the abundance of three different sets of proteins, suggesting that all three function in phosphate transport.</p> <p>Conclusion</p> <p>The global proteomic response of <it>M. maripaludis </it>to each nutrient limitation suggests a wider response than previously appreciated. The results give new insight into the function of several proteins, as well as providing information that should contribute to the formulation of a regulatory network model.</p

Work-hardening Photopolymer from Renewable Photoactive 3,3’-(2,5-Furandiyl)bisacrylic Acid

The design of a photopolymer around a renewable furan-derived chromophore is presented herein. An optimised semi-continuous oxidation method using MnO2 affords 2,5-diformylfuran from 5-(hydroxymethyl)furfural in gram quantities, allowing the subsequent synthesis of 3,3’-(2,5-furandiyl)bisacrylic acid in good yield and excellent stereoselectivity. The photoactivity of the diester of this monomer is confirmed by reaction under UV irradiation, and the proposed [2+2] cycloaddition mechanism supported further by TD-DFT calculations. Oligoesters of the photoreactive furan diacid with various aliphatic diols are prepared via chemo- and enzyme-catalysed polycondensation. The latter enzyme-catalysed (Candida antarctica lipase B) method results in the highest Mn (3.6 kDa), suggesting milder conditions employed with this protocol minimised unwanted side reactions, including untimely [2+2] cycloadditions, whilst preserving the monomer's photoactivity and stereoisomerism. The photoreactive polyester is solvent cast into a film where subsequent initiator-free UV curing leads to an impressive increase in the material stiffness, with work-hardening characteristics observed during tensile strength testing

Accounting for aerosol scattering in the CLARS retrieval of column averaged CO_2 mixing ratios

The California Laboratory for Atmospheric Remote Sensing Fourier transform spectrometer (CLARS‐FTS) deployed at Mount Wilson, California, has been measuring column abundances of greenhouse gases in the Los Angeles (LA) basin in the near‐infrared spectral region since August 2011. CLARS‐FTS measures reflected sunlight and has high sensitivity to absorption and scattering in the boundary layer. In this study, we estimate the retrieval biases caused by aerosol scattering and present a fast and accurate approach to correct for the bias in the CLARS column averaged CO2 mixing ratio product, X_(CO2). The high spectral resolution of 0.06 cm^(−1) is exploited to reveal the physical mechanism for the bias. We employ a numerical radiative transfer model to simulate the impact of neglecting aerosol scattering on the CO_2 and O_2 slant column densities operationally retrieved from CLARS‐FTS measurements. These simulations show that the CLARS‐FTS operational retrieval algorithm likely underestimates CO_2 and O_2 abundances over the LA basin in scenes with moderate aerosol loading. The bias in the CO_2 and O_2 abundances due to neglecting aerosol scattering cannot be canceled by ratioing each other in the derivation of the operational product of X_(CO2). We propose a new method for approximately correcting the aerosol‐induced bias. Results for CLARS X_(CO2) are compared to direct‐Sun X_(CO2) retrievals from a nearby Total Carbon Column Observing Network (TCCON) station. The bias‐correction approach significantly improves the correlation between the X_(CO2) retrieved from CLARS and TCCON, demonstrating that this approach can increase the yield of useful data from CLARS‐FTS in the presence of moderate aerosol loading

Constraining Aerosol Vertical Profile in the Boundary Layer Using Hyperspectral Measurements of Oxygen Absorption

This study attempts to infer aerosol vertical structure in the urban boundary layer using passive hyperspectral measurements. A spectral sorting technique is developed to retrieve total aerosol optical depth (AOD) and effective aerosol layer height (ALH) from hyperspectral measurements in the 1.27‐μm oxygen absorption band by the mountaintop Fourier Transform Spectrometer at the California Laboratory for Atmospheric Remote Sensing instrument (1,673 m above sea level) overlooking the LA basin. Comparison to AOD measurements from Aerosol Robotic Network and aerosol backscatter profile measurements from a Mini MicroPulse Lidar shows agreement, with coefficients of determination (r^2) of 0.74 for AOD and 0.57 for effective ALH. On average, the AOD retrieval has an error of 24.9% and root‐mean‐square error of 0.013, while the effective ALH retrieval has an error of 7.8% and root‐mean‐square error of 67.01 m. The proposed method can potentially be applied to existing and future satellite missions with hyperspectral oxygen measurements to constrain aerosol vertical distribution on a global scale

Fifteen years of clinical liver transplantation

Liver transplantation in humans was first attempted more than 15 yr ago. The 1-yr survival has slowly improved until it has now reached about 50%. In our experience, 46 patients have lived for at least 1 yr, with the longest survival being 9 yr. The high acute mortality in early trials was due in many cases to technical and management errors and to the use of damaged organs. With elimination of such factors, survival increased. Further improvements will depend upon better immunosuppression. Orthotopic liver transplantation (liver replacement) is the preferred operation in most cases, but placement of an extra liver (auxiliary transplantation) may have a role under special circumstances. © 1979

Aerosol scattering effects on water vapor retrievals over the Los Angeles Basin

In this study, we propose a novel approach to describe the scattering effects of atmospheric aerosols in a complex urban environment using water vapor (H_2O) slant column measurements in the near infrared. This approach is demonstrated using measurements from the California Laboratory for Atmospheric Remote Sensing Fourier Transform Spectrometer on the top of Mt. Wilson, California, and a two-stream-exact single scattering (2S-ESS) radiative transfer (RT) model. From the spectral measurements, we retrieve H_2O slant column density (SCD) using 15 different absorption bands between 4000 and 8000 cm^(−1). Due to the wavelength dependence of aerosol scattering, large variations in H_2O SCD retrievals are observed as a function of wavelength. Moreover, the variations are found to be correlated with aerosol optical depths (AODs) measured at the AERONET-Caltech station. Simulation results from the RT model reproduce this correlation and show that the aerosol scattering effect is the primary contributor to the variations in the wavelength dependence of the H_2O SCD retrievals. A significant linear correlation is also found between variations in H_2O SCD retrievals from different bands and corresponding AOD data; this correlation is associated with the asymmetry parameter, which is a first-order measure of the aerosol scattering phase function. The evidence from both measurements and simulations suggests that wavelength-dependent aerosol scattering effects can be derived using H_2O retrievals from multiple bands. This understanding of aerosol scattering effects on H_2O retrievals suggests a promising way to quantify the effect of aerosol scattering on greenhouse gas retrievals and could potentially contribute towards reducing biases in greenhouse gas retrievals from space

The influence of HLA genotype on the development of metal hypersensitivity following joint replacement

We thank Innovate UK Edge for providing funding to allow this research to be carried out.Background  Over five million joint replacements are performed across the world each year. Cobalt chrome (CoCr) components are used in most of these procedures. Some patients develop delayed type hypersensitivity (DTH) responses to CoCr implants, resulting in tissue damage and revision surgery. DTH is unpredictable and genetic links have yet to be definitively established. Methods At a single site, we carried out an initial investigation to identify HLA alleles associated with development of DTH following metal-on-metal hip arthroplasty. We then recruited patients from other centres to train and validate an algorithm incorporating patient age, gender, HLA genotype44 and blood metal concentrations to predict the development of DTH. Accuracy of the modelling was assessed using performance metrics including time dependent receiver operator curves. Results Using next generation sequencing, here we determine the HLA genotypes of 606 patients. 176 of these patients had experienced failure of their prostheses; the remaining 430 remain asymptomatic at a mean follow up of twelve years. We demonstrate that the development of DTH is associated with patient age, gender, the magnitude of metal exposure and the presence of certain HLA class II alleles. We show that the predictive algorithm developed from this investigation performs to an accuracy suitable for clinical use, with weighted mean survival probability errors of 1.8% and 3.1%53 for pre-operative and post-operative models respectively. Conclusions The development of DTH following joint replacement appears to be determined by the interaction between implant wear and a patient’s genotype. The algorithm described in this paper may improve implant selection and help direct patient surveillance following surgery. Further consideration should be given towards understanding patient specific responses to different biomaterials.Publisher PDFPeer reviewe

Continuous Symmetries of Difference Equations

Lie group theory was originally created more than 100 years ago as a tool for solving ordinary and partial differential equations. In this article we review the results of a much more recent program: the use of Lie groups to study difference equations. We show that the mismatch between continuous symmetries and discrete equations can be resolved in at least two manners. One is to use generalized symmetries acting on solutions of difference equations, but leaving the lattice invariant. The other is to restrict to point symmetries, but to allow them to also transform the lattice.Comment: Review articl

Metabolic modeling of a mutualistic microbial community

The rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. To enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of Desulfovibrio vulgaris and Methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. Model results were compared to data on growth of the co-culture on lactate in the absence of sulfate. The model accurately predicted several ecologically relevant characteristics, including the flux of metabolites and the ratio of D. vulgaris to M. maripaludis cells during growth. In addition, the model and our data suggested that it was possible to eliminate formate as an interspecies electron shuttle, but hydrogen transfer was essential for syntrophic growth. Our work demonstrated that reconstructed metabolic networks and stoichiometric models can serve not only to predict metabolic fluxes and growth phenotypes of single organisms, but also to capture growth parameters and community composition of simple bacterial communities