Evaluation of a hepatic biomarker of nutritional imbalance in juvenile red drum (Sciaenops ocellatus) fed 60% soybean meal-based diets using NMR-based metabolomics

A 12-week feeding trial with juvenile red drum (Sciaenops ocellatus) fed high-soybean meal (SBM) diets was conducted to investigate a putative biomarker of nutritional imbalance, N-formimino-L-glutamate (FIGLU). Three fishmeal-free, 60% SBM pelleted diets (named B12, Fol, and Met, respectively) were tested to evaluate the effects on growth performance and tissue metabolite profiles of supplementation of vitamin B12 (0.012 mg/kg), folate (10 mg/kg), methionine (1 g/kg) respectively, above basal supplementation levels. A fourth SBM-based diet (named B12/Fol/Met) was formulated with a combination of B12, folate, and methionine to attain the above-mentioned target concentrations. A fifth 60% SBM diet (named FWS) with methionine supplementation (1 g/kg above basal supplementation levels), enriched with taurine, lysine and threonine as well as minerals, was also tested. This diet contained formulation targets and additives which have allowed for replacing fishmeal with plant proteins in rainbow trout feeds. Control diets included a fishmeal-based diet (named FM), an unsupplemented basal 60% SBM diet (named SBM60), and a "natural" diet (named N) made up of equal parts of fish (cigar minnows), squid and shrimp as a positive reference for growth performance. Formulated feeds contained approximately 37% total crude protein, approximately 14% total crude lipid and were energetically balanced. Standard growth performance metrics were measured, and tissues (liver, muscle) were collected at week 12 to evaluate diet-induced metabolic changes using nuclear magnetic resonance (NMR)-based metabolomics. Our results show that the FWS diet outperformed all other SBM diets and the FM diet under all performance metrics (P < 0.05). FIGLU was not detected in fish fed the N diet but was detected in those fed the SBM diets and the FM diet. Fish fed the FWS diet and the Met diet showed lower hepatic levels of FIGLU compared with the other SBM-based diets (P < 0.05), suggesting that among the different supplementation regimes, methionine supplementation was associated with lower FIGLU levels. The FWS diet produced tissue metabolite profiles that were more similar to those of fish fed the N diet. Based on our results, the FWS diet constitutes a promising SBM-based alternative diet to fishmeal for red drum.

Untargeted Metabolomics Analyses and Contaminant Chemistry of Dreissenid Mussels at the Maumee River Area of Concern in the Great Lakes

Bivalves serve as an ideal ecological indicator; hence, their use by the NOAA Mussel Watch Program to monitor environmental health. This study aimed to expand the baseline knowledge of using metabolic end points in environmental monitoring by investigating the dreissenid mussel metabolome in the field. Dreissenids were caged at four locations along the Maumee River for 30 days. The mussel metabolome was measured using nuclear magnetic resonance spectroscopy, and mussel tissue chemical contaminants were analyzed using gas or liquid chromatography coupled with mass spectrometry. All Maumee River sites had a distinct mussel metabolome compared to the reference site and revealed changes in the energy metabolism and amino acids. Data also highlighted the importance of considering seasonality or handling effects on the metabolome at the time of sampling. The furthest upstream site presented a specific mussel tissue chemical signature of pesticides (atrazine and metolachlor), while a downstream site, located at Toledo's wastewater treatment plant, was characterized by polycyclic aromatic hydrocarbons and other organic contaminants. Further research into the dreissenid mussel's natural metabolic cycle and metabolic response to specific anthropogenic stressors is necessary before successful implementation of metabolomics in a biomonitoring program.

Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite

There is a lack of experimental reference materials and standards for metabolomics measurements, such as urine, plasma, and other human fluid samples. Reasons include difficulties with supply, distribution, and dissemination of information about the materials. Additionally, there is a long lead time because reference materials need their compositions to be fully characterized with uncertainty, a labor-intensive process for material containing thousands of relevant compounds. Furthermore, data analysis can be hampered by different methods using different software by different vendors. In this work, we propose an alternative implementation of reference materials. Instead of characterizing biological materials based on their composition, we propose using untargeted metabolomic data such as nuclear magnetic resonance (NMR) or gas and liquid chromatography-mass spectrometry (GC-MS and LC-MS) profiles. The profiles are then distributed with the material accompanying the certificate, so that researchers can compare their own metabolomic measurements with the reference profiles. To demonstrate this approach, we conducted an interlaboratory study (ILS) in which seven National Institute of Standards and Technology (NIST) urine Standard Reference Material^®s (SRM^®s) were distributed to participants, who then returned the metabolomic data to us. We then implemented chemometric methods to analyze the data together to estimate the uncertainties in the current measurement techniques. The participants identified similar patterns in the profiles that distinguished the seven samples. Even when the number of spectral features is substantially different between platforms, a collective analysis still shows significant overlap that allows reliable comparison between participants. Our results show that a urine suite such as that used in this ILS could be employed for testing and harmonization among different platforms. A limited quantity of test materials will be made available for researchers who are willing to repeat the protocols presented here and contribute their data.

Investigation of graded levels of soybean meal diets for red drum, Sciaenops ocellatus, using quantitative PCR derived biomarkers

A twelve-week feeding trial was conducted to examine potential metabolic and gene expression changes that occur in juvenile red drum, Sciaenops ocellatus, fed diets with increasing soybean meal inclusion. Significant reduction in fish performance characteristics (feed consumption, weight gain, final weight) was observed within the soybean meal based diets as soybean meal level increased (R, linear regression); however, all soybean meal based diets performed statistically equivalent in regards to performance characteristics (weight gain, feed conversion ratio, condition factor, etc.) to a commercial (45% crude protein and 16% crude lipid) reference diet (R, ANOVA). To better understand the underlying physiological responses and metabolic changes driving performance differences, traditional aquaculture metrics were paired with high throughput -omics techniques. Nuclear magnetic resonance (NMR) spectroscopy-based metabolomics data and RNA transcript abundance differences observed in liver tissue were utilized to select multiple sets of genes to target with quantitative polymerase chain reaction (qPCR), both for pathway activity validation and as rapid and accessible biomarkers of performance as a result of soybean meal. Genes selected based on the metabolic pathways most affected by soybean meal level corroborate the metabolite profile and performance data indicating an increase in gluconeogenic precursor production as soybean meal increased. The metabolomic and gene expression tools utilized in our study present a novel framework for diet and fish health evaluation that may provide more rapid and improved techniques for evaluating dietary manipulations and improving production of juvenile fish on alternative feeds.

Investigation of graded-level soybean meal diets in red drum (Sciaenops ocellatus) using NMR-based metabolomics analysis

We investigated changes in the metabolome in juvenile red drum (Sciaenops ocellatus) induced by increasing amounts of soybean meal (0% to 60%) in extruded, fishmeal-free diets using a nuclear magnetic resonance spectroscopy (NMR)-based metabolomics approach in a 12-week feeding trial. All of the diets were composed of ≈40% total crude protein, ≈11% total crude lipid and were energetically balanced. A fishmeal-containing, commercial extruded diet was used as a control diet throughout the trial. Each week, liver, muscle, intestine and plasma samples were collected and analyzed by NMR to provide a "snapshot" of the metabolome at different time points. Results indicate significant time-dependence of the metabolic profiles in various tissues with stable metabolomic profiles forming after about 9-weeks on the experimental diets. We identify a previously unexploited biomarker of potential dietary stress (N‑formimino‑l‑glutamate (FIGLU)) in the fish that may prove to be useful for optimization of alternative diet formulations.

Towards quality assurance and quality control in untargeted metabolomics studies

We describe here the agreed upon first development steps and priority objectives of a community engagement effort to address current challenges in quality assurance (QA) and quality control (QC) in untargeted metabolomic studies. This has included (1) a QA and QC questionnaire responded to by the metabolomics community in 2015 which recommended education of the metabolomics community, development of appropriate standard reference materials and providing incentives for laboratories to apply QA and QC; (2) a 2-day 'Think Tank on Quality Assurance and Quality Control for Untargeted Metabolomic Studies' held at the National Cancer Institute's Shady Grove Campus and (3) establishment of the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) to drive forward developments in a coordinated manner.

Metabolomics Analysis of Effects of Commercial Soy-based Protein Products in Red Drum (Sciaenops ocellatus)

We investigated the metabolic effects of four different commercial soy-based protein products on red drum fish (Sciaenops ocellatus) using nuclear magnetic resonance (NMR) spectroscopy-based metabolomics along with unsupervised principal component analysis (PCA) to evaluate metabolic profiles in liver, muscle, and plasma tissues. Specifically, during a 12 week feeding trial, juvenile red drum maintained in an indoor recirculating aquaculture system were fed four different commercially available soy formulations, containing the same amount of crude protein, and two reference diets as performance controls: a 60% soybean meal diet that had been used in a previous trial in our lab and a natural diet. Red drum liver, muscle, and plasma tissues were sampled at multiple time points to provide a more accurate snapshot of specific metabolic states during the grow-out. PCA score plots derived from NMR spectroscopy data sets showed significant differences between fish fed the natural diet and the soy-based diets, in both liver and muscle tissues. While red drum tolerated the inclusion of soy with good feed conversion ratios, a comparison to fish fed the natural diet revealed that the soy-fed fish in this study displayed a distinct metabolic signature characterized by increased protein and lipid catabolism, suggesting an energetic imbalance. Furthermore, among the soy-based formulations, one diet showed a more pronounced catabolic signature.

Platelets subvert T cell immunity against cancer via GARP-TGFβ axis

Cancer-associated thrombocytosis has long been linked to poor clinical outcome, but the underlying mechanism is enigmatic. We hypothesized that platelets promote malignancy and resistance to therapy by dampening host immunity. We show that genetic targeting of platelets enhances adoptive T cell therapy of cancer. An unbiased biochemical and structural biology approach established transforming growth factor β (TGFβ) and lactate as major platelet-derived soluble factors to obliterate CD4⁺ and CD8⁺ T cell functions. Moreover, we found that platelets are the dominant source of functional TGFβ systemically as well as in the tumor microenvironment through constitutive expression of the TGFβ-docking receptor glycoprotein A repetitions predominant (GARP) rather than secretion of TGFβ per se. Platelet-specific deletion of the GARP-encoding gene Lrrc32 blunted TGFβ activity at the tumor site and potentiated protective immunity against both melanoma and colon cancer. Last, this study shows that T cell therapy of cancer can be substantially improved by concurrent treatment with readily available antiplatelet agents. We conclude that platelets constrain T cell immunity through a GARP-TGFβ axis and suggest a combination of immunotherapy and platelet inhibitors as a therapeutic strategy against cancer.

A scoring metric for multivariate data for reproducibility analysis using chemometric methods

Process quality control and reproducibility in emerging measurement fields such as metabolomics is normally assured by interlaboratory comparison testing. As a part of this testing process, spectral features from a spectroscopic method such as nuclear magnetic resonance (NMR) spectroscopy are attributed to particular analytes within a mixture, and it is the metabolite concentrations that are returned for comparison between laboratories. However, data quality may also be assessed directly by using binned spectral data before the time-consuming identification and quantification. Use of the binned spectra has some advantages, including preserving information about trace constituents and enabling identification of process difficulties. In this paper, we demonstrate the use of binned NMR spectra to conduct a detailed interlaboratory comparison and composition analysis. Spectra of synthetic and biologically-obtained metabolite mixtures, taken from a previous interlaboratory study, are compared with cluster analysis using a variety of distance and entropy metrics. The individual measurements are then evaluated based on where they fall within their clusters, and a laboratory-level scoring metric is developed, which provides an assessment of each laboratory's individual performance.

Effects of heat-treatment on the stability and composition of metabolomic extracts from the earthworm Eisenia fetida

Environmental metabolomics studies employing earthworms as sentinels for soil contamination are numerous, but the instability of the metabolite extracts from these organisms has been minimally addressed. This study evaluated the efficacy of adding a heat-treatment step in two commonly used extraction protocols (Bligh and Dyer and D₂O phosphate buffer) as a pre-analytical stabilization method. The resulting metabolic profiles of Eisenia fetida were assessed using principal component analysis and NMR spectral evaluations. The heated Bligh and Dyer extractions produced stabilized profiles with minimal variation of the extracted metabolomic profiles over time, providing a more suitable method for metabolomic analysis of earthworm extracts.

Application of NMR-based metabolomics for environmental assessment in the Great Lakes using zebra mussel (Dreissena polymorpha)

Zebra mussel, Dreissena polymorpha, in the Great Lakes is being monitored as a bio-indicator organism for environmental health effects by the National Oceanic and Atmospheric Administration's Mussel Watch program. In order to monitor the environmental effects of industrial pollution on the ecosystem, invasive zebra mussels were collected from four stations-three inner harbor sites (LMMB4, LMMB1, and LMMB) in Milwaukee Estuary, and one reference site (LMMB5) in Lake Michigan, Wisconsin. Nuclear magnetic resonance (NMR)-based metabolomics was used to evaluate the metabolic profiles of the mussels from these four sites. The objective was to observe whether there were differences in metabolite profiles between impacted sites and the reference site; and if there were metabolic profile differences among the impacted sites. Principal component analyses indicated there was no significant difference between two impacted sites: north Milwaukee harbor (LMMB and LMMB4) and the LMMB5 reference site. However, significant metabolic differences were observed between the impacted site on the south Milwaukee harbor (LMMB1) and the LMMB5 reference site, a finding that correlates with preliminary sediment toxicity results. A total of 26 altered metabolites (including two unidentified peaks) were successfully identified in a comparison of zebra mussels from the LMMB1 site and LMMB5 reference site. The application of both uni- and multivariate analysis not only confirmed the variability of altered metabolites but also ensured that these metabolites were identified via unbiased analysis. This study has demonstrated the feasibility of the NMR-based metabolomics approach to assess whole-body metabolomics of zebra mussels to study the physiological impact of toxicant exposure at field sites.

Novel structural features in Candida albicans hyphal glucan provide a basis for differential innate immune recognition of hyphae versus yeast

The innate immune system differentially recognizes Candida albicans yeast and hyphae. It is not clear how the innate immune system effectively discriminates between yeast and hyphal forms of C. albicans. Glucans are major components of the fungal cell wall and key fungal pathogen-associated molecular patterns. C. albicans yeast glucan has been characterized; however, little is known about glucan structure in C. albicans hyphae. Using an extraction procedure that minimizes degradation of the native structure, we extracted glucans from C. albicans hyphal cell walls. (1)H NMR data analysis revealed that, when compared with reference (1→3,1→6) β-linked glucans and C. albicans yeast glucan, hyphal glucan has a unique cyclical or "closed chain" structure that is not found in yeast glucan. GC/MS analyses showed a high abundance of 3- and 6-linked glucose units when compared with yeast β-glucan. In addition to the expected (1→3), (1→6), and 3,6 linkages, we also identified a 2,3 linkage that has not been reported previously in C. albicans. Hyphal glucan induced robust immune responses in human peripheral blood mononuclear cells and macrophages via a Dectin-1-dependent mechanism. In contrast, C. albicans yeast glucan was a much less potent stimulus. We also demonstrated the capacity of C. albicans hyphal glucan, but not yeast glucan, to induce IL-1β processing and secretion. This finding provides important evidence for understanding the immune discrimination between colonization and invasion at the mucosal level. When taken together, these data provide a structural basis for differential innate immune recognition of C. albicans yeast versus hyphae.

Evaluation of Pacific white shrimp (Litopenaeus vannamei) health during a superintensive aquaculture growout using NMR-based metabolomics

Success of the shrimp aquaculture industry requires technological advances that increase production and environmental sustainability. Indoor, superintensive, aquaculture systems are being developed that permit year-round production of farmed shrimp at high densities. These systems are intended to overcome problems of disease susceptibility and of water quality issues from waste products, by operating as essentially closed systems that promote beneficial microbial communities (biofloc). The resulting biofloc can assimilate and detoxify wastes, may provide nutrition for the farmed organisms resulting in improved growth, and may aid in reducing disease initiated from external sources. Nuclear magnetic resonance (NMR)-based metabolomic techniques were used to assess shrimp health during a full growout cycle from the nursery phase through harvest in a minimal-exchange, superintensive, biofloc system. Aberrant shrimp metabolomes were detected from a spike in total ammonia nitrogen in the nursery, from a reduced feeding period that was a consequence of surface scum build-up in the raceway, and from the stocking transition from the nursery to the growout raceway. The biochemical changes in the shrimp that were induced by the stressors were essential for survival and included nitrogen detoxification and energy conservation mechanisms. Inosine and trehalose may be general biomarkers of stress in Litopenaeus vannamei. This study demonstrates one aspect of the practicality of using NMR-based metabolomics to enhance the aquaculture industry by providing physiological insight into common environmental stresses that may limit growth or better explain reduced survival and production.

Biosynthesis of Athmu, a α,γ-hydroxy-β-amino acid of pahayokolides A-B

Pahayokolides A-B are cyanobacteria derived non-ribosomal peptides which exhibit cytotoxicity against a number of cancer cell lines. The biosynthetic origin of the 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid (Athmu) moiety has been investigated using stable isotope incorporation experiments. While α-ketoisocaproic acid (α-KIC), α-hydroxyisocaproic acid (α-HIC) and leucine all serve as precursors to Athmu, the feeding of [1-(13)C] α-KIC results in more than threefold greater (13)C enrichment than the other precursors. This result suggests that α-KIC is the immediate precursor which is selected and activated by the adenylation domain of the loading NRPS module and subsequently reduced in a fashion similar to that of the recently identified pathways for cryptophycins A-B, cereulide and valinomycin.

Identification of isethionic acid and other small molecule metabolites of Fragilariopsis cylindrus with nuclear magnetic resonance

Nuclear magnetic resonance (NMR) spectroscopy has been used to obtain metabolic profiles of the polar diatom Fragilariopsis cylindrus, leading to the identification of a novel metabolite in this organism. Initial results from an ongoing metabolomics study have led to the discovery of isethionic acid (2-hydroxyethanesulfonic acid, CAS: 107-36-8) as a major metabolite in F. cylindrus. This compound is being produced by the organism under normal culture conditions. This finding is the first report of a diatom producing isethionic acid. In addition to isethionic acid, four other metabolites, dimethylsulfoniopropionate (DMSP), betaine, homarine, and proline were present and may serve as osmoprotectants in F. cylindrus. NMR-based metabolite profiles of F. cylindrus were obtained along a growth curve of the organism. The relative concentration levels of the five metabolites were monitored over a growth period of F. cylindrus from 18 to 25 days. All showed an increase in relative concentration with time, except for proline, which began to decrease after day 21.

NMR analysis of metabolic responses to extreme conditions of the temperature-dependent coral pathogen Vibrio coralliilyticus

AIMS

To identify and understand the presence of metabolites responsible for the variation in the metabolic profile of Vibrio coralliilyticus under extreme conditions.

METHODS AND RESULTS

Multiple batches of V. coralliilyticus were grown under normal conditions. Four samples in one batch were subjected to extreme conditions via a freeze-thaw cycle during lyophilization. Polar metabolites were extracted using a combination of methanol, water and heat. Nuclear magnetic resonance (NMR)-based metabolic profiles indicated significant differences between the normal and stressed samples. Three compounds identified in the stressed metabolome were maltose, ethanolamine, and the bioplastic-type compound (BTC) 2-butenoic acid, 2-carboxy-1-methylethyl ester. This is the first report of the production of this BTC by V. coralliilyticus.

CONCLUSIONS

The presence of maltose and ethanolamine indicates a state of acute nutrient limitation; therefore, we hypothesize that the cell's metabolism turned to its own cell wall, or perhaps neighbouring cells, for sources of carbon and nitrogen. The presence of the BTC also supports the acute nutrient limitation idea because of the parallels with polyhydroxyalkanoate (PHA) production in other gram-negative bacteria, including other Vibrio species.

SIGNIFICANCE AND IMPACT OF THE STUDY

Recent metabolomics research on the temperature-dependent coral pathogen V. coralliilyticus has led to the discovery of several compounds produced by the organism as a response to high density, low nutrient conditions. The three metabolites, along with (1) H NMR metabolic fingerprints of the nutrient limited samples, are proposed to serve as metabolic markers for extremely stressful conditions of V. coralliilyticus.

Nanoscale fullerene compression of an yttrium carbide cluster

The nanoscale parameters of metal clusters and lattices have a crucial influence on the macroscopic properties of materials. Herein, we provide a detailed study on the size and shape of isolated yttrium carbide clusters in different fullerene cages. A family of diyttrium endohedral metallofullerenes with the general formula of Y(2)C(2n) (n = 40-59) are reported. The high field (13)C nuclear magnetic resonance (NMR) and density functional theory (DFT) methods are employed to examine this yttrium carbide cluster in certain family members, Y(2)C(2)@D(5)(450)-C(100), Y(2)C(2)@D(3)(85)-C(92), Y(2)C(2)@C(84), Y(2)C(2)@C(3v)(8)-C(82), and Y(2)C(2)@C(s)(6)-C(82). The results of this study suggest that decreasing the size of a fullerene cage with the same (Y(2)C(2))(4+) cluster results in nanoscale fullerene compression (NFC) from a nearly linear stretched geometry to a constrained "butterfly" structure. The (13)C NMR chemical shift and scalar (1)J(YC) coupling parameters provide a very sensitive measure of this NFC effect for the (Y(2)C(2))(4+) cluster. The crystal structural parameters of a previously reported metal carbide, Y(2)C(3) are directly compared to the (Y(2)C(2))(4+) cluster in the current metallofullerene study.

New insights into the structure of (1→3,1→6)-β-D-glucan side chains in the Candida glabrata cell wall

β-Glucan is a (1→3)-β-linked glucose polymer with (1→6)-β-linked side chains and a major component of fungal cell walls. β-Glucans provide structural integrity to the fungal cell wall. The nature of the (1-6)-β-linked side chain structure of fungal (1→3,1→6)-β-D-glucans has been very difficult to elucidate. Herein, we report the first detailed structural characterization of the (1→6)-β-linked side chains of Candida glabrata using high-field NMR. The (1→6)-β-linked side chains have an average length of 4 to 5 repeat units spaced every 21 repeat units along the (1→3)-linked polymer backbone. Computer modeling suggests that the side chains have a bent curve structure that allows for a flexible interconnection with parallel (1→3)-β-D-glucan polymers, and/or as a point of attachment for proteins. Based on these observations we propose new approaches to how (1→6)-β-linked side chains interconnect with neighboring glucan polymers in a manner that maximizes fungal cell wall strength, while also allowing for flexibility, or plasticity.

Biosynthetic origin of the 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid moiety and absolute configuration of pahayokolides A and B

Pahayokolides A and B are cyclic undecapeptides that were isolated from the cyanobacterium Lyngbya sp. They contain the unusual α-hydroxy-β-amino acid 3-amino-2,5,7,8-tetrahydroxy-10-methylundecanoic acid (Athmu). The absolute configurations of the amino acids of the pahayokolides, except for the four oxygen-bearing stereocenters of Athmu, have been determined by Marphy's method. Incorporation of labeled leucine and acetate precursors into the pahayokolides has established that Athmu is derived from a leucine or α-keto isocaproic acid starter unit, which is further extended with three acetate units.

Integrating omic technologies into aquatic ecological risk assessment and environmental monitoring: hurdles, achievements, and future outlook

BACKGROUND

In this commentary we present the findings from an international consortium on fish toxicogenomics sponsored by the U.K. Natural Environment Research Council (Fish Toxicogenomics-Moving into Regulation and Monitoring, held 21-23 April 2008 at the Pacific Environmental Science Centre, Vancouver, BC, Canada).

OBJECTIVES

The consortium from government agencies, academia, and industry addressed three topics: progress in ecotoxicogenomics, regulatory perspectives on roadblocks for practical implementation of toxicogenomics into risk assessment, and dealing with variability in data sets.

DISCUSSION

Participants noted that examples of successful application of omic technologies have been identified, but critical studies are needed to relate molecular changes to ecological adverse outcome. Participants made recommendations for the management of technical and biological variation. They also stressed the need for enhanced interdisciplinary training and communication as well as considerable investment into the generation and curation of appropriate reference omic data.

CONCLUSIONS

The participants concluded that, although there are hurdles to pass on the road to regulatory acceptance, omics technologies are already useful for elucidating modes of action of toxicants and can contribute to the risk assessment process as part of a weight-of-evidence approach.

NMR-based microbial metabolomics and the temperature-dependent coral pathogen Vibrio coralliilyticus

Coral bleaching occurs when the symbioses between coral animals and their zooxanthellae is disrupted, either as part of a natural cycle or as the result of unusual events. The bacterium Vibrio coralliilyticus (type strain ATCC BAA-450) has been linked to coral disease globally (for example in the Mediterranean, Red Sea, Indian Ocean, and Great Barrier Reef) and like many other Vibrio species exhibits a temperature-dependent pathogenicity. The temperature-dependence of V. corallillyticus in regard to its metabolome was investigated. Nuclear magnetic resonance (NMR) spectra were obtained of methanol-water extracts of intracellula rmetabolites (endometabolome) from multiple samples of the bacteria cultured into late stationary phase at 27 degrees C (virulent form) and 24 degrees C (avirulent form). The spectra were subjected to principal components analysis (PCA), and significant temperature-based separations in PC1, PC2, and PC3 dimensions were observed. Betaine, succinate, and glutamate were identified as metabolites that caused the greatest temperature-based separations in the PC scores plots. With increasing temperature, betaine was shown to be down regulated, while succinate and glutamate were up regulated.

International NMR-based environmental metabolomics intercomparison exercise

Several fundamental requirements must be met so that NMR-based metabolomics and the related technique of metabonomics can be formally adopted into environmental monitoring and chemical risk assessment. Here we report an intercomparison exercise which has evaluated the effectiveness of 1H NMR metabolomics to generate comparable data sets from environmentally derived samples. It focuses on laboratory practice that follows sample collection and metabolite extraction, specifically the final stages of sample preparation, NMR data collection (500, 600, and 800 MHz), data processing, and multivariate analysis. Seven laboratories have participated from the U.S.A., Canada, U.K., and Australia, generating a total of ten data sets. Phase 1 comprised the analysis of synthetic metabolite mixtures, while Phase 2 investigated European flounder (Platichthys flesus) liver extracts from clean and contaminated sites. Overall, the comparability of data sets from the participating laboratories was good. Principal components analyses (PCA) of the individual data sets yielded ten highly similar scores plots for the synthetic mixtures, with a comparable result for the liver extracts. Furthermore, the same metabolic biomarkers that discriminated fish from clean and contaminated sites were discovered by all the laboratories. PCA of the combined data sets showed excellent clustering of the multiple analyses. These results demonstrate that NMR-based metabolomics can generate data that are sufficiently comparable between laboratories to support its continued evaluation for regulatory environmental studies.

Isolation, purification, and full NMR assignments of cyclopamine from Veratrum californicum

BACKGROUND

The Hedgehog signaling pathway is essential for embryogenesis and for tissue homeostasis in the adult. However, it may induce malignancies in a number of tissues when constitutively activated, and it may also have a role in other forms of normal and maladaptive growth. Cyclopamine, a naturally occurring steroidal alkaloid, specifically inhibits the Hedgehog pathway by binding directly to Smoothened, an important Hedgehog response element. To use cyclopamine as a tool to explore and/or inhibit the Hedgehog pathway in vivo, a substantial quantity is required, and as a practical matter cyclopamine has been effectively unavailable for usage in animals larger than mice.

RESULTS

In this paper, we report a rapid and efficient isolation and purification of large quantities of cyclopamine from the roots and rhizomes of Veratrum californicum Dur. (the Corn Lily or Western false hellebore). We also provide unambiguous assignments of the carbon and proton resonances by using the multinuclear spectra and the spin coupling networks.

CONCLUSION

This method could meet a very real need within diverse scientific communities by allowing cyclopamine to become more readily available.

Ecosystem responses to extreme natural events: impacts of three sequential hurricanes in fall 1999 on sediment quality and condition of benthic fauna in the Neuse River Estuary, North Carolina

A study was conducted in November 1999 to assess sediment quality and condition of benthic fauna in the Neuse River Estuary (NRE), North Carolina, USA, following the passage of three Atlantic hurricanes during the two months prior. Samples for analysis of macroinfauna (>0.5 mm sieve size), chemical contamination of sediments, and other abiotic environmental variables (salinity, dissolved oxygen, pH, depth, sediment granulometry) were collected at 20 sites from the mouth of the Neuse River at Pamlico Sound to approximately 90 km upstream. Results were compared to those obtained from the same area in July 1998 using similar protocols. Depressed salinity, caused by extreme rainfall and associated high freshwater flow, persisted throughout much of the estuary, which had experienced periods of water-column stratification and hypoxia of underlying waters. Fifteen of the 20 sites, representing 299 km2 (76% of the survey area), also showed signs of benthic stress based on a multi-metric benthic index of biotic integrity (B-IBI). Benthic impacts included reductions in the abundance, diversity, and numbers of species and shifts in taxonomic composition, with a notable increase in dominance of the opportunistic polychaete Mediomastus ambiseta as other former dominant species declined. There was no significant increase in the extent of chemical contamination compared to pre-hurricane conditions. Storm-related reductions in dissolved oxygen and salinity were the more likely causes of the observed benthic impacts, though it was not possible, based on these results, to separate storm effects from seasonal changes in the benthos and annual episodes of summer anoxia and hypoxia.

Oviedomycin, an unusual angucyclinone encoded by genes of the oleandomycin-producer Streptomyces antibioticus ATCC11891

Our investigations on the discovery of novel natural metabolites using type II polyketide synthase gene probes (actI/III) yielded an unusual angucyclinone, oviedomycin (2), when applied to the oleandomycin (1) producer Streptomyces antibioticus ATCC11891. The novel natural product was produced using S. albus R(-)M(-) as a host strain, into which a cosmid containing the oviedomycin gene cluster was transformed. Its structure was elucidated by NMR spectroscopy and mass spectrometry.

Ketopremithramycins and ketomithramycins, four new aureolic acid-type compounds obtained upon inactivation of two genes involved in the biosynthesis of the deoxysugar moieties of the antitumor drug mithramycin by Streptomyces argillaceus, reveal novel insights into post-PKS tailoring steps of the mithramycin biosynthetic pathway

Mithramycin is an aureolic acid-type antimicrobial and antitumor agent produced by Streptomyces argillaceus. Modifying post-polyketide synthase (PKS) tailoring enzymes involved in the production of mithramycin is an effective way of gaining further information regarding the late steps of its biosynthetic pathway. In addition, new "unnatural" natural products of the aureolic acid-type class are likely to be produced. The role of two such post-PKS tailoring enzymes, encoded by mtmC and mtmTIII, was investigated, and four novel aureolic acid class drugs, two premithramycin-type molecules and two mithramycin derivatives, were isolated from mutant strains constructed by insertional gene inactivation of either of these two genes. From data bank comparisons, the corresponding proteins MtmC and MtmTIII were believed to act as a C-methyltransferase involved in the production of the D-mycarose (sugar E) of mithramycin and as a ketoreductase seemingly involved in the biosynthesis of the mithramycin aglycon, respectively. However, gene inactivation and analysis of the accumulated products revealed that both genes encode enzymes participating in the biosynthesis of the D-mycarose building block. Furthermore, the inactivation of MtmC seems to affect the ketoreductase responsible for 4-ketoreduction of sugar C, a D-olivose. Instead of obtaining premithramycin and mithramycin derivatives with a modified E-sugar upon inactivation of mtmC, compounds were obtained that completely lack the E-sugar moiety and that possess an unexpected 4-ketosugar moiety instead of the D-olivose at the beginning of the lower deoxysaccharide chain. The inactivation of mtmTIII led to the accumulation of 4E-ketomithramycin, showing that this ketoreductase is responsible for the 4-ketoreduction of the D-mycarose moiety. The new compounds of the mutant strains, 4A-ketopremithramycin A2, 4A-keto-9-demethylpremithramycin A2, 4C-keto-demycarosylmithramycin, and 4E-ketomithramycin, indicate surprising substrate flexibility of post-PKS enzymes of the mithramycin biosynthetic pathway. Although the glycosyltransferase responsible for the attachment of D-mycarose cannot transfer the unmethylated sugar to the existing lower disaccharide chain, it can transfer the 4-ketoform of sugar E. In addition, the glycosyltransferase MtmGIV, which is responsible for the linkage of sugar C, is also able to transfer an activated 4-ketosugar. The oxygenase MtmOIV, normally responsible for the oxidative cleavage of the tetracyclic premithramycin B into the tricyclic immediate precursor of mithramycin, can act on a substrate analogue with a modified or even incomplete trisaccharide chain. The same is true for glycosyltransferases MtmGI and MtmGII, both of which partake in the formation and attachment of the A-B disaccharide in mithramycin.

Detection of human asialo-alpha(1)-acid glycoprotein using a heterosandwich immunoassay in conjunction with the light addressable potentiometric sensor

Highly specific detection of human alpha 1-acid glycoprotein (AGP) and asialo-alpha 1-acid glycoprotein (asialo-AGP) was made possible by use of a sandwich immunoassay. The glycoproteins were sandwiched between biotinylated and fluoresceinated polyclonal rabbit anti-human AGP antibodies. Additionally, asialo-AGP could be distinctly detected, apart from AGP, via the formation of a heterosandwich immunoassay using biotinylated polyclonal rabbit anti-human AGP and the lectin, fluoresceinated ricin toxin. Streptavidin was added to the formed immunocomplexes and the immunocomplexes captured on a biotinylated nitrocellulose membrane. The signal generator, urease conjugate of an anti-fluorescein antibody, was then bound to the complex on the membrane. The rate of pH change under microvolume conditions (0.6 microliters) was monitored using a silicon chip-based, light addressable potentiometer sensor. Results indicated that AGP and asialo-AGP can be detected to the 2 pg level when two antibodies are used to form the immunocomplex. Asialo-AGP can be detected down to 250 pg when the heterosandwich immunoassay is used; this assay exhibited no response up to 10 ng for native AGP or asialofetuin. Both immunoassays can be used to quantify the level of AGP and asialo-AGP in solution. Although the assay presented is very specific for AGP, asialo-AGP and terminal galactose, it is readily adaptable for the detection of any glycoprotein and terminal carbohydrate (or branched structure) by use of a protein-specific antibody and various lectins.

Activation energies and formation rate constants for organic arsenical-antidote adducts as determined by dynamic NMR spectroscopy

Phenyldichloroarsine reacts with 1,3-dimercapto-2-propanol and 1,2-dimercaptopropane to form 1:1 adducts in the form of a six-membered and five-membered heteroatom rings. Two geometric isomers for each compound are present in dynamic equilibrium. Rate constants and the activation barriers for the interconversion of the geometric isomers were determined by dynamic NMR spectroscopy. The activation barriers indicate that the five-membered heteroatom ring is more stable than the six-membered heteroatom ring.