Extraction efficiency and quantification of dissolved metabolites in targeted marine metabolomics

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography: Methods 15 (2017): 417–428, doi:10.1002/lom3.10181.The field of metabolomics seeks to characterize the suite of small molecules that comprise the end-products of cellular regulation. Metabolomics has been used in biomedical applications as well as environmental studies that explore ecological and biogeochemical questions. We have developed a targeted metabolomics method using electrospray ionization–liquid chromatography tandem mass spectrometry to analyze metabolites dissolved in seawater. Preparation of samples from the marine environment presents challenges because dilute metabolites must be concentrated and desalted. We present the extraction efficiencies of 89 metabolites in our targeted method using solid phase extraction (SPE). In addition, we calculate the limits of detection and quantification for the metabolites in the method and compare the instrument response factors in five different matrices ranging from deionized water to spent medium from cultured marine microbes. High background organic matter content reduces the instrument response factor for only a small group of metabolites, yet enhances the extraction efficiency for other metabolites on the SPE cartridge used here, a modified styrene-divinylbenzene polymer called PPL. Aromatic or larger uncharged compounds, in particular, are reproducibly well retained on the PPL polymer. This method is suitable for the detection of dissolved metabolites in marine samples, with limits of detection ranging from < 1 pM to ∼ 2 nM dependent on the dual impacts of seawater matrix on extraction efficiency and on instrument response factors.Gordon and Betty Moore Foundation Grant Number: 3304; National Science Foundation Grant Number: OCE-1154320; Simons Foundation Internationa

Evidence for quorum sensing and differential metabolite production by a marine bacterium in response to DMSP

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 10 (2016): 2304–2316, doi:10.1038/ismej.2016.6.Microbes, the foundation of the marine foodweb, do not function in isolation, but rather rely on molecular level interactions among species to thrive. Although certain types of interactions between autotrophic and heterotrophic microorganisms have been well documented, the role of specific organic molecules in regulating inter-species relationships and supporting growth are only beginning to be understood. Here, we examine one such interaction by characterizing the metabolic response of a heterotrophic marine bacterium, Ruegeria pomeroyi DSS-3, to growth on dimethylsulfoniopropionate (DMSP), an abundant organosulfur metabolite produced by phytoplankton. When cultivated on DMSP, R. pomeroyi synthesized a quorum-sensing molecule, N-(3-oxotetradecanoyl)-l-homoserine lactone, at significantly higher levels than during growth on propionate. Concomitant with the production of a quorum-sensing molecule, we observed differential production of intra- and extracellular metabolites including glutamine, vitamin B2 and biosynthetic intermediates of cyclic amino acids. Our metabolomics data indicate that R. pomeroyi changes regulation of its biochemical pathways in a manner that is adaptive for a cooperative lifestyle in the presence of DMSP, in anticipation of phytoplankton-derived nutrients and higher microbial density. This behavior is likely to occur on sinking marine particles, indicating that this response may impact the fate of organic matter.This research is funded in part by the Gordon and Betty Moore Foundation through Grant GBMF3304 as well as by the National Science Foundation (Grants OCE-0928424 and OCE-1154320)

Confirmation of a one-dimensional spin-1/2 Heisenberg system with ferromagnetic first-nearest-neighbor and antiferromagnetic second-nearest-neighbor interactions in Rb2{}_{2}Cu2{}_{2}Mo3{}_{3}O12{}_{12}

We have investigated magnetic properties of Rb$_2$Cu$_2$Mo$_3$O$_{12}$ powder. Temperature dependence of magnetic susceptibility and magnetic-field dependence of magnetization have shown that this cuprate is a model compound of a one-dimensional spin-1/2 Heisenberg system with ferromagnetic first-nearest-neighbor (1NN) and antiferromagnetic second-nearest-neighbor (2NN) competing interactions (competing system). Values of the 1NN and 2NN interactions are estimated as $J_1 = -138$ K and $J_2 = 51$ K ($\alpha \equiv J_2 / J_1 = -0.37$). This value of $\alpha$ suggests that the ground state is a spin-singlet incommensurate state. In spite of relatively large $J_1$ and $J_2$, no magnetic phase transition appears down to 2 K, while an antiferromagnetic transition occurs in other model compounds of the competing system with ferromagnetic 1NN interaction. For that reason, Rb$_2$Cu$_2$Mo$_3$O$_{12}$ is an ideal model compound to study properties of the incommensurate ground state that are unconfirmed experimentally.Comment: 6 pages, 4 figure

Designing molecules to bypass the singlet-triplet bottleneck in the electroluminescence of organic light-emitting-diode materials

Electroluminescence in organic light emitting diode (OLED) materials occurs via the recombination of excitonic electrons-hole pairs Only the singlet excitons of commonly used OLED materials, e.g., Aluminum trihydroxyquinoline (AlQ$_3$), decay radiatively, limiting the external quantum efficiency to a maximum 25%. Thus 75% of the energy is lost due to the triplet bottleneck for radiative recombination. We consider molecules derived from AlQ$_3$ which bypass the triplet bottleneck by designing structures which contain strong spin-orbit coupling. As a first stage of this work, groundstate energies and vertical excitation energies of Al-arsenoquinolines and Al-boroarsenoquinolines are calculated. It is found that the substitution of N by As leads to very favourable results, while the boron substitution leads to no advantage.Comment: 4 pages, 4 figue

Risk factors of fracture following curettage for bone giant cell tumors of the extremities

Background: Following curettage of giant cell tumor of bone (GCTB), it is common to fill the cavity with polymethylmethacrylate (PMMA) bone cement, bone allograft, or artificial bone to maintain bone strength; however, there is a 2–14% risk of postoperative fractures. We conducted this retrospective study to clarify the risk factors for fractures after curettage for GCTB of the extremities. Methods: This study included 284 patients with GCTBs of the extremities who underwent curettage at our institutions between 1980 and 2018 after excluding patients whose cavities were not filled with anything or who had additional plate fixation. The tumor cavity was filled with PMMA bone cement alone (n =&nbsp;124), PMMA bone cement and bone allograft (n =&nbsp;81), bone allograft alone (n =&nbsp;63), or hydroxyapatite graft alone (n =&nbsp;16). Results: Fractures after curettage occurred in 10 (3.5%) patients, and the median time from the curettage to fracture was 3.5 months (interquartile range [IQR], 1.8–8.3 months). The median postoperative follow-up period was 86.5 months (IQR, 50.3–118.8 months). On univariate analysis, patients who had GCTB of the proximal or distal femur (1-year fracture-free survival, 92.5%; 95% confidence interval [CI]: 85.8–96.2) presented a higher risk for postoperative fracture than those who had GCTB at another site (100%; p = 0.0005). Patients with a pathological fracture at presentation (1-year fracture-free survival, 88.2%; 95% CI: 63.2–97.0) presented a higher risk for postoperative fracture than those without a pathological fracture at presentation (97.8%; 95% CI: 95.1–99.0; p = 0.048). Patients who received bone grafting (1-year fracture-free survival, 99.4%; 95% CI: 95.7–99.9) had a lower risk of postoperative fracture than those who did not receive bone grafting (94.4%; 95% CI: 88.7–97.3; p = 0.003). Conclusions: For GCTBs of the femur, especially those with pathological fracture at presentation, bone grafting after curettage is recommended to reduce the risk of postoperative fracture. Additional plate fixation should be considered when curettage and cement filling without bone grafting are performed in patients with GCTB of the femur. This should be specially performed for those patients with a pathological fracture at presentation