Carotenoids are the likely precursor of a significant fraction of marine dissolved organic matter.

The ocean's biota sequester atmospheric carbon dioxide (CO2) in part by producing dissolved organic matter (DOM) that persists in the ocean for millennia. This long-term accumulation of carbon may be facilitated by abiotic and biotic production of chemical structures that resist degradation, consequently contributing disproportionately to refractory DOM. Compounds that are selectively preserved in seawater were identified in solid-phase extracted DOM (PPL-DOM) using comprehensive gas chromatography (GC) coupled to mass spectrometry (MS). These molecules contained cyclic head groups that were linked to isoprenoid tails, and their overall structures closely resembled carotenoid degradation products (CDP). The origin of these compounds in PPL-DOM was further confirmed with an in vitro β-carotene photooxidation experiment that generated water-soluble CDP with similar structural characteristics. The molecular-level identification linked at least 10% of PPL-DOM carbon, and thus 4% of total DOM carbon, to CDP. Nuclear magnetic resonance spectra of experimental CDP and environmental PPL-DOM overlapped considerably, which indicated that even a greater proportion of PPL-DOM was likely composed of CDP. The CDP-rich DOM fraction was depleted in radiocarbon (14C age > 1500 years), a finding that supports the possible long-term accumulation of CDP in seawater. By linking a specific class of widespread biochemicals to refractory DOM, this work provides a foundation for future studies that aim to examine how persistent DOM forms in the ocean

Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions

The osmotic virial coefficient $B_2$ of globular protein solutions is calculated as a function of added salt concentration at fixed pH by computer simulations of the ``primitive model''. The salt and counter-ions as well as a discrete charge pattern on the protein surface are explicitly incorporated. For parameters roughly corresponding to lysozyme, we find that $B_2$ first decreases with added salt concentration up to a threshold concentration, then increases to a maximum, and then decreases again upon further raising the ionic strength. Our studies demonstrate that the existence of a discrete charge pattern on the protein surface profoundly influences the effective interactions and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek (DLVO) theory fail for large ionic strength. The observed non-monotonicity of $B_2$ is compared to experiments. Implications for protein crystallization are discussed.Comment: 43 pages, including 17 figure

Olefin cross metathesis and ring-closing metathesis in polymer chemistry

The use of olefin cross metathesis in preparing functional polymers, through either pre-functionalisation of monomers or post-polymerisation functionalisation is growing in both scope and breadth. The broad functional group tolerance of olefin metathesis offers a wealth of opportunities for introducing a broad range of functional groups into the polymer backbone, tuning polymer properties and expanding potential applications. Similarly, ring-closing metathesis offers the ability to tune the polymer macrostructure and microstructure to similar effect. In this review, we explore the importance of understanding selectivity in olefin cross metathesis in designing functional polymers, the manipulation of this reactivity to prepare (multi)functional polymers, and show how polymer systems can be constructed to favour ring closing and change backbone structure and properties

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants.

This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.3448Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.We thank all participants of all the studies included for enabling this research by their participation in these studies. Computer resources for this project have been provided by the high-performance computing centers of the University of Michigan and the University of Regensburg. Group-specific acknowledgments can be found in the Supplementary Note. The Center for Inherited Diseases Research (CIDR) Program contract number is HHSN268201200008I. This and the main consortium work were predominantly funded by 1X01HG006934-01 to G.R.A. and R01 EY022310 to J.L.H

Carbon disulfide. Just toxic or also bioregulatory and/or therapeutic?

The overview presented here has the goal of examining whether carbon disulfide (CS2) may play a role as an endogenously generated bioregulator and/or has therapeutic value. The neuro- and reproductive system toxicity of CS2 has been documented from its long-term use in the viscose rayon industry. CS2 is also used in the production of dithiocarbamates (DTCs), which are potent fungicides and pesticides, thus raising concern that CS2 may be an environmental toxin. However, DTCs also have recognized medicinal use in the treatment of heavy metal poisonings as well as having potency for reducing inflammation. Three known small molecule bioregulators (SMBs) nitric oxide, carbon monoxide, and hydrogen sulfide were initially viewed as environmental toxins. Yet each is now recognized as having intricate, though not fully elucidated, biological functions at concentration regimes far lower than the toxic doses. The literature also implies that the mammalian chemical biology of CS2 has broader implications from inflammatory states to the gut microbiome. On these bases, we suggest that the very nature of CS2 poisoning may be related to interrupting or overwhelming relevant regulatory or signaling process(es), much like other SMBs

Chemical characterization of refractory dissolved organic matter

The primary objective of this thesis was to combine a chemical degradation technique together with an analytical framework centered primarily around gas chromatography (GC) to more fully interrogate the composition of aquatic dissolved organic matter (DOM). Previous studies had suggested that aliphatic compounds could represent a significant fraction of refractory organic matter isolated by solid phase extraction (SPE). These studies had also uncovered the vast complexity of DOM. Gas chromatography coupled to mass spectrometry provides superior separation capability and is ideal for examining complex mixtures of lipid-derived molecules. As such I sought to develop a comprehensive GC analysis methods to provide molecular level information for DOM isolated by solid phase extraction (SPE) onto a hydrophobic resin- PPL (Agilent Bond Elut). In Chapter II, a comprehensive chemical reduction procedure was developed and first applied to the environmental DOM standard Suwannee River Fulvic Acid (SRFA) as a proxy for marine DOM. The resulting hydrocarbons were amenable to comprehensive gas chromatography time-of-flight mass spectrometry (GCxGC-TOF-MS), and effectively resolved into multiple series of alicyclic, unsaturated compounds. This was the first direct demonstration of the isomeric complexity of aquatic DOM. Similar alicyclic compounds were recovered from the reduction of terrestrial source material, implicating resin acids and sterols as potential precursors of SRFA. In Chapter III the reduction process was applied to marine surface DOM from the Scripps Institution of Oceanography Pier, and similar alicylic compounds were found. The GCxGC-TOF-MS identified carbon backbones closely resembling carotenoids, implicating these ubiquitous and highly reactive biomolecules as the source of a significant fraction of DOM accumulating in the marine water column. The structural assignment was supported by the identification of carotenoid derived resonances in two dimensional nuclear magnetic resonance (NMR) spectra, which indicated that these molecules were highly oxidized compared to the parent molecules consistent with their present in DOM. Following up on this work in Chapter IV the carotenoid β-carotene was irradiated with natural sunlight to test the hypothesis that photodegradation was one pathway that converted carotenoids into water-soluble degradation products. The first finding was that the reaction produced a series of compounds identical to compounds isolated from marine DOM. The second important result was that the reaction produced a complex mixture of isomers from a single compound that helps to at least partly explain the compositional diversity in marine DOM. Together, the data in Chapters III and IV allowed us to link a large fraction of DOM to a ubiquitous biomolecule that can now serve as a model for studies examining the formation and fate of DOM that accumulates in the ocean on long timescales. Finally, in Chapter V we sought to examine how the composition of DOM – both the complex alicyclic fraction and small, polar biomolecules, which are considered a “fresher” signal of biological input – evolved across a salinity gradient. Although core biochemical classes were present in all regions the data supported in situ production of compositionally similar material rather than mixing across the gradients as proposed in some studies. Together, the chapters in my thesis provide new insight in the composition of dissolved organic matter in marine and terrestrial environments. The thesis also represents the most comprehensive molecular level characterization of DOM isolated by this solid phase extraction method, which is the most commonly used isolation method in the field. My findings also provide an important foundation for future lab-based mechanistic studies of DOM cycling in the marine environment

Chemical characterization of refractory dissolved organic matter

The primary objective of this thesis was to combine a chemical degradation technique together with an analytical framework centered primarily around gas chromatography (GC) to more fully interrogate the composition of aquatic dissolved organic matter (DOM). Previous studies had suggested that aliphatic compounds could represent a significant fraction of refractory organic matter isolated by solid phase extraction (SPE). These studies had also uncovered the vast complexity of DOM. Gas chromatography coupled to mass spectrometry provides superior separation capability and is ideal for examining complex mixtures of lipid-derived molecules. As such I sought to develop a comprehensive GC analysis methods to provide molecular level information for DOM isolated by solid phase extraction (SPE) onto a hydrophobic resin- PPL (Agilent Bond Elut). In Chapter II, a comprehensive chemical reduction procedure was developed and first applied to the environmental DOM standard Suwannee River Fulvic Acid (SRFA) as a proxy for marine DOM. The resulting hydrocarbons were amenable to comprehensive gas chromatography time-of-flight mass spectrometry (GCxGC-TOF-MS), and effectively resolved into multiple series of alicyclic, unsaturated compounds. This was the first direct demonstration of the isomeric complexity of aquatic DOM. Similar alicyclic compounds were recovered from the reduction of terrestrial source material, implicating resin acids and sterols as potential precursors of SRFA. In Chapter III the reduction process was applied to marine surface DOM from the Scripps Institution of Oceanography Pier, and similar alicylic compounds were found. The GCxGC-TOF-MS identified carbon backbones closely resembling carotenoids, implicating these ubiquitous and highly reactive biomolecules as the source of a significant fraction of DOM accumulating in the marine water column. The structural assignment was supported by the identification of carotenoid derived resonances in two dimensional nuclear magnetic resonance (NMR) spectra, which indicated that these molecules were highly oxidized compared to the parent molecules consistent with their present in DOM. Following up on this work in Chapter IV the carotenoid β-carotene was irradiated with natural sunlight to test the hypothesis that photodegradation was one pathway that converted carotenoids into water-soluble degradation products. The first finding was that the reaction produced a series of compounds identical to compounds isolated from marine DOM. The second important result was that the reaction produced a complex mixture of isomers from a single compound that helps to at least partly explain the compositional diversity in marine DOM. Together, the data in Chapters III and IV allowed us to link a large fraction of DOM to a ubiquitous biomolecule that can now serve as a model for studies examining the formation and fate of DOM that accumulates in the ocean on long timescales. Finally, in Chapter V we sought to examine how the composition of DOM – both the complex alicyclic fraction and small, polar biomolecules, which are considered a “fresher” signal of biological input – evolved across a salinity gradient. Although core biochemical classes were present in all regions the data supported in situ production of compositionally similar material rather than mixing across the gradients as proposed in some studies. Together, the chapters in my thesis provide new insight in the composition of dissolved organic matter in marine and terrestrial environments. The thesis also represents the most comprehensive molecular level characterization of DOM isolated by this solid phase extraction method, which is the most commonly used isolation method in the field. My findings also provide an important foundation for future lab-based mechanistic studies of DOM cycling in the marine environment

Direct Identification of Diverse Alicyclic Terpenoids in Suwannee River Fulvic Acid

The chemical complexity of dissolved organic matter (DOM) obstructs our ability to definitively recover source compounds from within DOM, an objective which has the capacity to alter our understanding of carbon sequestration on a global scale. To advance compositional studies of DOM we have applied a previously published reduction method to an environmental standard, Suwannee River Fulvic Acid (SRFA). The reduction products, comprising 12% of the prereduced carbon, were then separated by comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOF-MS). Results indicate that the majority of observed reduced compounds corresponded to alicyclic hydrocarbons in the size range C₁₀ to C₁₇. Cyclic terpenoids are the only biomolecule class with contiguous, alicyclic carbon backbones of this size. These terpenoid reduction products contain series offset by CH₂ and exhibit great isomeric diversity, features previously inferred from ultrahigh resolution mass spectrometry and NMR studies of unreduced SRFA. Reduction of <i>Taxodium</i> leaf litter as a source material to SRFA confirmed the prevalence of terpenoids in SRFA and provided insight into the parent compounds that must be diagenetically modified on relatively short time scales. These data corroborate several recent studies that suggest alicyclic hydrocarbons to be important components of longer-lived DOM