The sedimentary flux of nutrients at a Delaware salt marsh site: A geochemical perspective

A basic geochemical approach has been used to study the diagenetic cycling and sediment-water exchange rates of essential nutrients at a site in a Delaware salt marsh. The pore water nutrients Si (OH)₄, NH₄ ⁺, PO₄ ^–3, and NO₃ ^– were analyzed and compared seasonally, and potential diffusive fluxes were calculated from the corresponding pore water concentration gradients. Concurrent direct flux measurements were also made using closed chambers deployed on the salt marsh surface under ambient and controlled conditions. The differences in these two approaches allows for estimation of nutrient production and consumption in the root zone and at the salt marsh surface. Silicate and phosphate appear to be primarily geochemically controlled, while the nitrogen species undergo dynamic seasonal redox fluctuations resulting from microbial mediation (e.g., nitrification and denitrification). Specifically:     

A comparison of the free radical chemistry of tobacco-burning cigarettes and cigarettes that only heat tobacco

Cigarette smoke contains free radicals both in the particulate matter (tar) and in vapor-phase smoke. Vapor-phase smoke decreases the activity of alpha-1-proteinase inhibitor (alpha 1PI) in vitro. The free radical content of the tar and vapor-phase smoke from a cigarette that heats rather than burns tobacco has been compared with data on a standard 1R4F cigarette. No radicals were detected in the tar from the new cigarette and radicals in its vapor-phase smoke are lower by more than 99% relative to the 1R4F standard cigarettes. The vapor-phase smoke from the new cigarette causes essentially no reduction of alpha 1PI activity in vitro. These findings support our previously published mechanisms for the production of radicals in tar and in vapor-phase smoke.     

X-ray structure study of thermotropic phases in isoacylphosphatidylcholine multibilayers.

Structures of lamellar phases in aqueous dispersions of diisoacylphosphatidylcholines (17iPC and 20iPC) were determined by x-ray diffraction methods. In agreement with previous DSC studies, subgel, gel, and liquid crystal phases were observed in each homolog. The subgel Lc(c') phases of both homologs show significant two-dimensional long range order and can be described by rectangular lattices. The dimensions of the two rectangular unit cells differ in that the side chains are canted (approximately 33 degrees) in the 20iPC homolog, while in 17iPC the side chains are normal to the bilayer plane. The gel L beta phases of 17iPC (Tgg = 17-19.5 degrees C) and 20iPC (Tgg = 44 degrees C) are similar but not identical and are consistent with a distorted, pseudohexagonal lattice for the rotationally disordered side chains. The liquid crystal phases of 17iPC (Tgl = 28 degrees C) and 20iPC (Tgl = 52 degrees C) are structurally similar and are typical of lipids with fluid side chains. Significant but different changes occur in the long spacings at Tgg and Tgl for the two homologs. This implies that interfacial states (particularly in the subgel phases) differ in the two homologs below the liquid crystal phase transition temperature.     

Arrhenius thermodynamics and birth defects: Chemical teratogen synergy. Untested,testable, and projected relevance

This article addresses the issue of hyperthermia‐induced birth defects with an accompanying additional teratogen, be it a chemical or a physical agent (i.e., a simultaneous “combinational” exposure to two teratogens, one of which is hyperthermia). Hyperthermia per se is a recognized human and animal teratogen. An excellent example of such combinational exposures is an epileptic woman who becomes pregnant while taking valproic acid (VPA) to control seizures. VPA is a recognized chemical teratogen, and fever (hyperthermia) is not an uncommon event during pregnancy. While VPA also may occasionally induce fever as a side effect, we are concerned here with fevers arising from other, unrelated causes. There is a small but internally consistent literature on these combinational‐teratogen exposures involving hyperthermia plus a chemical teratogen; in each instance, the effect level has been observed to be synergistically elevated above levels induced by the separate teratogenic components. The data were empirical. The observed synergy is, however, consistent with Arrhenius thermodynamics, a well‐known chemical rate equation. The need for information about combinational teratogen exposures is acute; fever is a common occurrence during pregnancy; and there are many instances whereby there is also the simultaneous presence of some other teratogen(s). Given that the rate of autism spectrum disorders in the United States was recently presented as 1 in 88 births, it seems reasonable to suspect that such combinational regimens are much more prevalent than previously thought. Our hypothesis is that synergistic birth defect levels from combinational regimens are consistent with Arrhenius thermodynamics. Birth Defects Research (Part C) 99:50–60, 2013. © 2013 Wiley Periodicals, Inc.     

The closely related estrogen-regulated trefoil proteins TFF1 and TFF3 have markedly different hydrodynamic properties,overall charge,and distribution of surface charge

The human trefoil proteins TFF1 and TFF3 are expressed predominantly in the gastrointestinal tract. They are also expressed and regulated by estrogens in malignant breast epithelial cells. TFF1 and TFF3 are small cysteine-rich acidic secreted proteins of 60 and 59 amino acids with similar isoelectric points of 4.75 and 3.94, respectively. Each contains one trefoil domain that is characterized by several conserved features including six cysteine residues with conserved spacing. TFF1 and TFF3 form intermolecular disulfide bonds via an extra-trefoil domain cysteine residue and are present in vivo as monomers and homodimers and as complexes with other proteins. The TFF1 dimer is more active than the TFF1 monomer. In the present study the hydrodynamic and charge properties of TFF1 and TFF3 monomers and homodimers have been compared and shown to differ markedly. Notably, TFF1 is significantly more asymmetric than TFF3 (frictional coefficients 1.25 and 1.12, respectively, p < 0.001), and homodimerization of TFF1 results in a greater increase in asymmetry than for TFF3. The overall charges of TFF1 and TFF3 are very different at neutral pH. Titration curves predicted significant differences in charge across a wide pH range that agreed well with experimental data. The locations of charged amino acids in the primary sequences and in the tertiary structures of TFF1 and TFF3 were examined. This revealed interesting divergence in both the distribution and local topology of charged amino acid side chains. The significant differences between the shape, size, and surface charge of these two closely related molecules may account for their divergent biological activities.     

Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL

MOTIVATION: For large-scale structural assignment to sequences, as in computational structural genomics, a fast yet sensitive sequence search procedure is essential. A new approach using intermediate sequences was tested as a shortcut to iterative multiple sequence search methods such as PSI-BLAST. RESULTS: A library containing potential intermediate sequences for proteins of known structure (PDB-ISL) was constructed. The sequences in the library were collected from a large sequence database using the sequences of the domains of proteins of known structure as the query sequences and the program PSI-BLAST. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using pairwise sequence comparison methods to find homologues in PDB-ISL. Searches of PDB-ISL were calibrated, and the number of correct matches found at a given error rate was the same as that found by PSI-BLAST. The advantage of this library is that it uses pairwise sequence comparison methods, such as FASTA or BLAST2, and can, therefore, be searched easily and, in many cases, much more quickly than an iterative multiple sequence comparison method. The procedure is roughly 20 times faster than PSI-BLAST for small genomes and several hundred times for large genomes. AVAILABILITY: Sequences can be submitted to the PDB-ISL servers at http://stash.mrc-lmb.cam.ac.uk/PDB_ISL/ or http://cyrah.ebi.ac.uk:1111/Serv/PDB_ISL/ and can be downloaded from ftp://ftp.ebi.ac.uk/pub/contrib/jong/PDB_+ ++ISL/ CONTACT: sat@mrc-lmb.cam.ac.uk and jong@ebi.ac.uk     

Leukocyte chemoattractant peptides from the serpin heparin cofactor II

Heparin cofactor II (HC) is a plasma serine proteinase inhibitor (serpin) that inhibits the coagulant proteinase alpha-thrombin. We have recently demonstrated that proteolysis of HC by catalytic amounts of polymorphonuclear leukocyte proteinases (elastase or cathepsin G) generates leukocyte chemotaxins (Hoffman, M., Pratt, C. W., Brown, R. L., and Church, F. C. (1989) Blood 73, 1682-1685). One of four peptides produced when HC is degraded by neutrophil elastase has chemotactic activity for both monocytes and neutrophils with maximal migration comparable to formyl-Met-Leu-Phe, the "gold standard" bacterially derived chemotaxin. The amino-terminal sequence of this HC peptide is Asp-Phe-His-Lys-Glu-Asn-Thr-Val-... and the peptide corresponds to Asp-39 to Ile-66 of HC. A variety of synthetic peptides derived from this sequence were evaluated for leukocyte migration activity, and a dodecapeptide from Asp-49 to Tyr-60 (Asp-Trp-Ile-Pro-Glu-Gly-Glu-Glu-Asp-Asp-Asp-Tyr) was identified as the active site for leukocyte chemotactic action. The 12-mer synthetic peptide possesses significant neutrophil chemotactic action at 1 nM (60% of the maximal activity of formyl-Met-Leu-Phe), while a peptide with the reverse sequence has essentially no chemotactic activity. Cross-desensitization experiments also show that pretreatment of neutrophils with a 19-mer peptide (Asn-48 to Ile-66) greatly reduces subsequent chemotaxis to HC-neutrophil elastase proteolysis reaction products. When injected intraperitoneally in mice, the HC-neutrophil elastase digest elicits neutrophil migration. Our results demonstrate that not only does HC function as a thrombin inhibitor, but that limited proteolysis of HC near the amino terminus yields biologically active peptide(s) which might participate in inflammation and in wound healing and tissue repair processes.     

Cigarette tar causes single-strand breaks in DNA

The results of this study demonstrate, for the first time, that cigarette tar causes DNA damage. Incubation in vitro of phage PM2 DNA with aqueous extracts of cigarette tar results in the introduction of DNA single-strand breaks. The effects of protective enzymes and radical scavengers indicate the involvement of active oxygen species. Although the semiquinone components of tar reduce dioxygen forming superoxide radicals and hydrogen peroxide, our results suggest that hydroxyl radicals formed via metal catalyzed decomposition of hydrogen peroxide are ultimately responsible for the DNA lesions. Our results also suggest that the metals in tar are reduced by the semiquinone components of tar and by superoxide at comparable rates.