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Biomedical subjects

Andre J Simpson

Publications and source records attributed to Andre J Simpson.

7 recordsLinked to original sources

Humic substances in soils: are they really chemically distinct?

Humic substances (HS) are an operationally defined fraction of soil organic matter, and they represent the largest pool of recalcitrant organic carbon in the terrestrial environment. It has traditionally been thought that extractable HS consist of novel categories of cross-linked macromolecular structures. In this study, advanced nuclear magnetic resonance approaches were used to study the major components (proteins, carbohydrates, aliphatic biopolymers, and lignin) that are known to be present in HS, and to identify their fingerprints in humic mixtures. Theoretically, once all known components have been identified, the remaining signals should be from materials with novel structures, themselves forming a distinct chemical category of humic materials. Surprisingly, nearly all of the NMR signals in traditional HS fractions could be assigned to intact and degrading biopolymers. We therefore suggest that the vast majority of operationally defined humic material in soils is a very complex mixture of microbial and plant biopolymers and their degradation products but not a distinct chemical category. It is important to note this work in no way rules out the existence of a distinct category of humic macromolecules, either at low abundance in the soluble fraction from young soils, in diagenetically evolved samples (for example lignites, etc.), or in the nonextractable humin fraction.

Albumins↗

Assessing the organic composition of urban surface films using nuclear magnetic resonance spectroscopy.

Recently it has been shown that urban surfaces are covered with a thin film which mediates the fate, distribution and accumulation of semi-volatile organic compounds in the environment. In this study we apply a combination of solution, semi-solids, and solid state nuclear magnetic resonance (NMR) methods to provide a general overview of the organic constituents. In surface film collected from 30 m2 of outside windows over an area of 12 km2 in downtown Toronto, we roughly estimate that the organic carbon is approximately 35% carbohydrate, approximately 35% aliphatics, approximately 20% aromatics, and approximately 10% carbonyl groups. Various aliphatic groups can be identified including a number of acids, alcohols, alkanes, and alkenes. Also, numerous intact aliphatic esters are apparent that have not been observed before, as well as carbohydrates. The aromatic species include a small portion that appears to be derived from a polymer of styrene, in addition a larger fraction is consistent with polyhydroxylated PAH derived material, although this assignment is tentative and based solely on 1-D NMR data only. In addition, signals from polybutadiene are present and while accurate quantification is not possible, it appears that this polymer may be up to a few percents by weight of the total organic material.

Air Pollutants↗

Purge NMR: effective and easy solvent suppression.

Presaturation utilizing relaxation gradients and echoes is an extremely easy and effective approach to solvent suppression in solution state nuclear magnetic resonance spectroscopy. The experiment produces flat baselines, excellent phase properties, and highly selective suppression that betters that of commonly used sequences. Furthermore, the only parameter that needs adjusting is the presaturation power, making it easy to implement even for non spectroscopists. Considering these factors, we envisage the approach will have wide spread applications.

Animals↗

The application of LC-NMR and LC-SPE-NMR to compositional studies of natural organic matter.

Non-living natural organic matter (NOM) is ubiquitous in the oceans, atmosphere, sediments, and soils, and represents the most abundant organic carbon reserves on earth. However, a large proportion is considered to be "molecularly uncharacterized" because the inherent complexity of NOM is problematic when applying conventional analytical techniques. This manuscript presents initial applications of LC-NMR (1H) and LC-SPE-NMR (1H) to the studies of NOM isolated from water and soil. LC-NMR is applied to dissolved natural organic matter (DNOM) collected from freshwater environments, and both LC-NMR and LC-SPE-NMR are applied to an alkaline soil extract. The polar and complex nature of the DNOM samples limits conventional reversed phase separation, which can be partially overcome with the use of an ion pair reagent, although such an approach further complicates the NMR detection. LC-SPE-NMR of the soil alkaline extract was encouraging, and specific components in the mixture could be assigned. This work demonstrates that it is both possible to separate and concentrate specific components in NOM such that NMR detection is possible. As NMR information will be critical in unraveling the novel and/or complex structures in NOM this represents a key analytical hurdle in this area.

Animals↗

Identifying residues in natural organic matter through spectral prediction and pattern matching of 2D NMR datasets.

This paper describes procedures for the generation of 2D NMR databases containing spectra predicted from chemical structures. These databases allow flexible searching via chemical structure, substructure or similarity of structure as well as spectral features. In this paper we use the biopolymer lignin as an example. Lignin is an important and relatively recalcitrant structural biopolymer present in the majority of plant biomass. We demonstrate how an accurate 2D NMR database of approximately 600 2D spectra of lignin fragments can be easily constructed, in approximately 2 days, and then subsequently show how some of these fragments can be identified in soil extracts through the use of various search tools and pattern recognition techniques. We demonstrate that once identified in one sample, similar residues are easily determined in other soil extracts. In theory, such an approach can be used for the analysis of any organic mixtures.

Benzopyrans↗

Solid-state and multidimensional solution-state NMR of solid phase extracted and ultrafiltered riverine dissolved organic matter.

In this study we used multidimensional solution-state NMR to elucidate the differences in the chemical composition of solid phase extracted and ultrafiltered DOM isolates. DOM was isolated from water sampled from an oligotrophic river, the River Tagliamento (Italy). The recovery of total DOM was up to 42% with both isolation techniques. In addition to 1- and 2-D solution-state NMR, we also applied 1-D solid-state 13C NMR spectroscopy for DOM characterization. 13C NMR spectroscopy only produced broad overlapping resonances, thus allowing a bulk characterization of DOM composition. However, it demonstrated that the bulk chemical composition of the two DOM fractions exhibited minor spatial-temporal changes. The 2-D experiments (TOCSY, HMQC) showed that the solid phase extracted hydrophobic DOM contained predominantly aliphatic esters, ethers, and hydroxyl groups, whereas the ultrafiltered DOM was comprised partially of peptides/protein, with further evidence for a small amount of aliphatic/fatty acid material. Sugars were present in both DOM fractions. The results show the two isolation techniques selected for different suites of compounds within the bulk DOM pool.

Environmental Monitoring↗

New insights on the structure of algaenan from Botryoccocus braunii race A and its hexane insoluble botryals based on multidimensional NMR spectroscopy and electrospray-mass spectrometry techniques.

Through solution state NMR spectroscopy and quadrupole-time-of-flight mass spectrometry (Q-TOF MS) studies of the hexane insoluble botryal extract of the algae Botryococcus braunii race A, coupled with high-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy of the algaenan from this alga, it has been possible to advance the structural understanding of this geochemically important biopolymer. It was found that the hexane insoluble botryals in this study constitute a mixture of low molecular weight unsaturated aliphatic aldehydes and unsaturated hydrocarbons with an average chain length of about 40 carbons. Exact assignments were provided for many of the structural units present and describe the average constitution of the mixture as a whole. Reticulation of the low molecular weight chains via acetal and ester links explains the primary make up of algaenan. In this study, it is concluded that the algaenan results from the reticulation of low molecular weight hexane insoluble botryal species rather than the polyaldehyde as previously observed in studies of algae at alternate stages of their growth cycle.

Aldehydes↗