Alkaloids from the Sponge Stylissa carteri Present Prospective Scaffolds for the Inhibition of Human Immunodeficiency Virus 1 (HIV-1).

The sponge Stylissa carteri is known to produce a number of secondary metabolites displaying anti-fouling, anti-inflammatory, and anti-cancer activity. However, the anti-viral potential of metabolites produced by S. carteri has not been extensively explored. In this study, an S. carteri extract was HPLC fractionated and a cell based assay was used to evaluate the effects of HPLC fractions on parameters of Human Immunodeficiency Virus (HIV-1) infection and cell viability. Candidate HIV-1 inhibitory fractions were then analyzed for the presence of potential HIV-1 inhibitory compounds by mass spectrometry, leading to the identification of three previously characterized compounds, i.e., debromohymenialdisine (DBH), hymenialdisine (HD), and oroidin. Commercially available purified versions of these molecules were re-tested to assess their antiviral potential in greater detail. Specifically, DBH and HD exhibit a 30%-40% inhibition of HIV-1 at 3.1 μM and 13 μM, respectively; however, both exhibited cytotoxicity. Conversely, oroidin displayed a 50% inhibition of viral replication at 50 μM with no associated toxicity. Additional experimentation using a biochemical assay revealed that oroidin inhibited the activity of the HIV-1 Reverse Transcriptase up to 90% at 25 μM. Taken together, the chemical search space was narrowed and previously isolated compounds with an unexplored anti-viral potential were found. Our results support exploration of marine natural products for anti-viral drug discovery

An overview of the latest metabolomics studies on atopic eczema with new directions for study

Atopic eczema (AE) is an inflammatory skin disorder affecting approximately 20% of children worldwide and early onset can lead to asthma and allergies. Currently, the mechanisms of the disease are not fully understood. Metabolomics, the analysis of small molecules in the skin produced by the host and microbes, opens a window to observe the mechanisms of the disease which then may lead to new drug targets for AE treatment. Here, we review the latest advances in AE metabolomics, highlighting both the lipid and non-lipid molecules, along with reviewing the metabolites currently known to reside in the skin

Chemodiversity of dissolved organic matter in the Amazon Basin

Regions in the Amazon Basin have been associated with specific biogeochemical processes, but a detailed chemical classification of the abundant and ubiquitous dissolved organic matter (DOM), beyond specific indicator compounds and bulk measurements, has not yet been established. We sampled water from different locations in the Negro, Madeira/Jamari and Tapajós River areas to characterize the molecular DOM composition and distribution. Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) combined with excitation emission matrix (EEM) fluorescence spectroscopy and parallel factor analysis (PARAFAC) revealed a large proportion of ubiquitous DOM but also unique area-specific molecular signatures. Unique to the DOM of the Rio Negro area was the large abundance of high molecular weight, diverse hydrogen-deficient and highly oxidized molecular ions deviating from known lignin or tannin compositions, indicating substantial oxidative processing of these ultimately plant-derived polyphenols indicative of these black waters. In contrast, unique signatures in the Madeira/Jamari area were defined by presumably labile sulfur- and nitrogen-containing molecules in this white water river system. Waters from the Tapajós main stem did not show any substantial unique molecular signatures relative to those present in the Rio Madeira and Rio Negro, which implied a lower organic molecular complexity in this clear water tributary, even after mixing with the main stem of the Amazon River. Beside ubiquitous DOM at average H ∕ C and O ∕ C elemental ratios, a distinct and significant unique DOM pool prevailed in the black, white and clear water areas that were also highly correlated with EEM-PARAFAC components and define the frameworks for primary production and other aspects of aquatic life

Temporal dynamics of halogenated organic compounds in Marcellus Shale flowback

The chemistry of hydraulic fracturing fluids and wastewaters is complex and is known to vary by operator, geologic formation, and fluid age. A time series of hydraulic fracturing fluids, flowback fluids, and produced waters was collected from two adjacent Marcellus Shale gas wells for organic chemical composition analyses using ultrahigh resolution mass spectrometry. Hierarchical clustering was used to compare and extract ions related to different fluid ages and many halogenated organic molecular ions were identified in flowback fluids and early produced waters based on exact mass. Iodinated organic compounds were the dominant halogen class in these clusters and were nearly undetectable in hydraulic fracturing fluid prior to injection. The iodinated ions increased in flowback and remained elevated after ten months of well production. We suggest that these trends are mainly driven by dissolved organic matter reacting with reactive halogen species formed abiotically through oxidizing chemical additives applied to the well and biotically via iodide-oxidizing bacteria. Understanding the implications of these identified halogenated organic compounds will require future investigation in to their structures and environmental fate

FT-ICR-MS reveals the molecular imprints of the brewing process

The study of fermentation and brewing has a long history of pioneering discoveries that continue to influence modern industrial food production. Since then, numerous research endeavors have yielded conventional criteria that guide contemporary brewing practices. However, the intricate open challenges faced today necessitate a more exhaustive understanding of the process at the molecular scale. We have developed an ultra-high-resolution mass spectrometric analysis (FT-ICR-MS) of the brewing process that can rapidly and comprehensively resolve thousands of molecules. This approach allows us to track molecular fluctuation during brewing at the level of chemical compositions. Employing biological triplicates, our investigation of two brewing lines that are otherwise identical except for the malt used revealed over 8,000 molecular descriptors of the brewing process. Metabolite imprints of both the similarities and differences arising from deviating malting temperatures were visualized. Additionally, we translated traditional brewing attributes such as the EBC-value, free amino nitrogen, pH-value, and concentration curves of specific molecules, into highly correlative molecular patterns consisting of hundreds of metabolites. These in-depth molecular imprints provide a better understanding of the molecular circumstances leading to various changes throughout the brewing process. Such chemical maps go beyond the observation of traditional brewing attributes and are of great significance in the investigation strategies of current open challenges in brewing research. The molecular base of knowledge, along with advancements in technological and data integration schemes, can facilitate the efficient monitoring of brewing and other productions processes

Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

Marine chromophoric dissolved organic matter (CDOM) and its related fluorescent components (FDOM), which are widely distributed but highly photobleached in the surface ocean, are critical in regulating light attenuation in the ocean. However, the origins of marine FDOM are still under investigation. Here we show that cultured picocyanobacteria, Synechococcus and Prochlorococcus, release FDOM that closely match the typical fluorescent signals found in oceanic environments. Picocyanobacterial FDOM also shows comparable apparent fluorescent quantum yields and undergoes similar photo-degradation behaviour when compared with deep-ocean FDOM, further strengthening the similarity between them. Ultrahigh-resolution mass spectrometry (MS) and nuclear magnetic resonance spectroscopy reveal abundant nitrogen-containing compounds in Synechococcus DOM, which may originate from degradation products of the fluorescent phycobilin pigments. Given the importance of picocyanobacteria in the global carbon cycle, our results indicate that picocyanobacteria are likely to be important sources of marine autochthonous FDOM, which may accumulate in the deep ocean

Investigation of fennel protein extracts by shot-gun Fourier transform ion cyclotron resonance mass spectrometry

A rapid shot-gun method by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is proposed for the characterization of fennel proteins. After enzymatic digestion with trypsin, few microliters of extract were analyzed by direct infusion in positive ion mode. A custom-made non-redundant fennel-specific proteome database was derived from the well-known NCBI database; additional proteins belonging to recognized allergenic sources (celery, carrot, parsley, birch, and mugwort) were also included in our database, since patients hypersensitive to these plants could also suffer from fennel allergy. The peptide sequence of each protein from that derived list was theoretically sequenced to produce calculated m/z lists of possible m/z ions after tryptic digestions. Then, by using a home-made Matlab algorithm, those lists were matched with the experimental FT-ICR mass spectrum of the fennel peptide mixture. Finally, Peptide Mass Fingerprint searches confirmed the presence of the matched proteins inside the fennel extract with a total of 70 proteins (61 fennel specific and 9 allergenic proteins)

Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber

Since its discovery in 1998, representatives of the extremely halophilic bacterium Salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. Here, we review the available information about the distribution, abundance and diversity of this member of the Bacteroidetes

Triviality of the ground-state metastate in long-range Ising spin glasses in one dimension

We consider the one-dimensional model of a spin glass with independent Gaussian-distributed random interactions, that have mean zero and variance $1/|i-j|^{2\sigma}$, between the spins at sites $i$ and $j$ for all $i\neq j$. It is known that, for $\sigma>1$, there is no phase transition at any non-zero temperature in this model. We prove rigorously that, for $\sigma>3/2$, any Newman-Stein metastate for the ground states (i.e.\ the frequencies with which distinct ground states are observed in finite size samples in the limit of infinite size, for given disorder) is trivial and unique. In other words, for given disorder and asymptotically at large sizes, the same ground state, or its global spin flip, is obtained (almost) always. The proof consists of two parts: one is a theorem (based on one by Newman and Stein for short-range two-dimensional models), valid for all $\sigma>1$, that establishes triviality under a convergence hypothesis on something similar to the energies of domain walls, and the other (based on older results for the one-dimensional model) establishes that the hypothesis is true for $\sigma>3/2$. In addition, we derive heuristic scaling arguments and rigorous exponent inequalities which tend to support the validity of the hypothesis under broader conditions. The constructions of various metastates are extended to all values $\sigma>1/2$. Triviality of the metastate in bond-diluted power-law models for $\sigma>1$ is proved directly.Comment: 18 pages. v2: subsection on bond-diluted models added, few extra references. 19 pages. v3: published version; a few changes; 20 page