Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

The effect of caffeine,different fixation regimes and low temperature on microtubules in the cells of higher plants

Caffeine, (1:3:7-tri-methyl-xanthine), either as a prefixation treatment or included with glutaralde-hyde as the primary fixative, destroys or disorganises the microtubules associated with the formation of secondary walls in fibres from the flowering stem of the grass Lolium temulentum L. There is no observable effect of caffeine treatment on the microtubules associated with primary wall formation in collenchyma and young fibres from L. temulentum or in root cap cells of Zea mays L. and Phaseolus vulgaris L. The microtubules associated with primary wall formation are destroyed by cold treatment but not those associated with secondary wall formation. Tannic acid included in the fixative shows the microtubules associated with secondary wall formation in fibres of L. temulentum to be composed of 13 subunits. Treatment with lanthanum hydroxide does not stain the core or the halo of the microtubules.Abbreviation PIPES Piperazine N-N- bis 2 ethanol sulphonic acid The Grassland Research Institute is financed through the Agricultural Research Council     

Clinical Problems: Progressive Neurological Deficits in Primary Polycythaemia

Patients with primary polycythaemia may present clinical features which lead to an erroneous diagnosis of intracerebral neoplasm. Three such cases are described in detail in this report.     

Invertebrate predator-prey body size relationships: an explanation for upper triangular food webs and patterns in food web structure?

Summary It has been suggested by Cohen and Newman (1985) that many of the patterns in published food webs can be derived from a stochastic model in which the species are arranged in a trophic hierarchy (the cascade model). We suggest that, if predators are larger than their prey, a trophic hierarchy can be generated on the basis of body size Empirical evidence from the literature shows that there is a positive relationship between predator and prey size for a range of invertebrates and that predators are usually larger than their prey. Using experimental data on an aquatic food web we show that body size can lead to the type of trophic hierarchy used in the cascade model, suggesting that many food web patterns may be a product of body size. This conclusion is discussed with respect to the limitations of the food web data and the relationship between static and dynamic models of web structure.     

Use of a rapid bioluminescence assay for detecting cyanobacterial microcystin toxicity

The recent rise in the awareness of the occurrence of toxic cyanobacterial blooms in aquatic environments, with associated human health problems and animal deaths, has increased the need for rapid, reliable and sensitive methods of determining cyanobacterial toxicity. A luminescent bacterial toxicity test was assessed as a complement to the established mouse bioassay. Seventeen samples including pure cyanobacterial microcystin-LR hepatotoxin, laboratory isolates and natural blooms of cyanobacteria were tested and toxicity data compared with mouse LD50 values. Microcystin-LR and all five microcystin-containing cyanobacterial samples, hepatotoxic by mouse test gave EC50 values of less than 0.46 mg/ml in bioluminescence-based Microtox assays. Of 11 samples non-toxic by mouse bioassay, only two gave an EC50 of less than 0.98 mg/ml by bioluminescence assay. It is suggested that the Microtox bioluminescence assay may prove useful in the preliminary screening of cyanobacterial blooms for microcystin-based toxicity.     

Food-web models that generate constant predator-prey ratios

Summary An approximately constant ratio of number of predator species/number of prey species is observed in several natural communities, although the exact value of the ratio may vary with habitat and the types of organisms in the food web. We test the hypothesis that a constant predator/prey ratio can be generated by what Holt (1977) terms apparent competition and what Jeffries and Lawton (1984) call competition for enemy-free space. We create simple, two trophic-level communities by drawing species of predators and prey at random from a species pool, simulating their interactions using Lotka-Volterra models. The simulated food webs converge over successive periods of invasion and extinction to locally stable systems with approximately constant ratios of number of predator species/number of prey species, despite varying initial conditions. As expected, predator/prey ratios take different values depending upon the biology of the simulated species. We conclude that apparent competition between prey species via shared enemies may be one mechanism whereby approximately constant predator/prey ratios are generated in natural communities.     

Effects of storage on microbial loads of two commercially important shellfish species, Crassostrea virginica and Mercenaria campechiensis.

The effects of storage on the microbial load in two commercially important species of shellfish were examined. Oysters (Crassostrea virginica) were stored as shellstock, shucked meats, and fully processed meats at four temperatures for up to 21 days, and clams (Mercenaria campechiensis) were stored only as shellstock. The concentrations of most microbiological groups of organisms increased with the duration and temperature of storage in both shellfish species, although the increases were significantly lower in claims. Concentrations of Vibrio cholerae rose by approximately 1 log in oysters stored as shellstock after 7 days at 2 degrees C, and Lac+ vibrios increased 2 logs at 8 degrees C. Total counts of bacteria, fungi, coliforms, fecal streptococci, Aeromonas hydrophila, and clostridia were significantly higher in shucked oysters than in those stored as shellstock. Fecal coliforms were statistically the same, but V. cholerae, Vibrio parahaemolyticus, and the Lac+ vibrios were higher in oysters stored as shellstock. The concentrations of all microbial groups were higher in fully processed oysters than in shucked meats, with the exception of the vibrios, which showed no significant difference among the treatments. The results showed that although traditional methods of storing shellfish resulted in an overall increase in the microbial load, vibrio levels increased only in oysters stored as shellstock. Although fecal coliform and total bacterial counts did not correlate with those for vibrios in fresh oysters, strong correlations were observed in oysters stored for 7 days, suggesting that these indicators may be useful in monitoring oyster quality when meats are stored for a limited time as shellstock.