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.     

Cancer chemotherapy and somatic cell mutation

The occurrence of a second neoplasm is one of the major obstacles in cancer chemotherapy. The elucidation of the genotoxic effects induced by anti-cancer drugs is considered to be helpful in identifying the degree of cancer risk. Numerous investigations on cancer patients after chemotherapy have demonstrated: (i) an increase in the in vivo somatic cell mutant frequency (Mf) at three genetic loci, including hypoxanthine–guanine phosphoribosyl-transferase (hprt), glycophorin A (GPA), and the T-cell receptor (TCR), and (ii) alterations in the mutational spectra of hprt mutants. However, the time required for and the degree of such changes are quite variable among patients even if they have received the same chemotherapy, suggesting the existence of underlying genetic factor(s). Accordingly, some cancer patients prior to chemotherapy as well as patients with cancer-prone syndrome have been found to show an elevated Mf. Based on the information obtained from somatic cell mutation assays, an individualized chemotherapy should be considered in order to minimize the risk of a second neoplasm.     

Climate change and cereal aphids: the relative effects of increasing CO2 and temperature on aphid population dynamics

Experimental evidence regarding the responses of cereal aphids to rising atmospheric CO₂ has been ambiguous. Some studies suggest increased population sizes under future CO₂ levels, others suggest decreased population sizes, and still others suggest little or no difference. Recently, Newman et al. (2003) constructed a general mathematical model of the aphid–grass interaction to investigate whether or not we should, in fact, expect a general aphid response to rising CO₂. They concluded that aphid populations are likely to be larger under future CO₂ concentrations if soil N levels are high, the aphid species' nitrogen requirement is low and the aphid species' density‐dependent response in winged morph production is weak. In that model, and in field experiments, CO₂ concentration influences aphid population dynamics through the effect it has on plant quality. However, future CO₂ concentrations are also likely to be accompanied by higher ambient temperatures, a combination that has received little focus to date. In the present paper, the Newman et al. model is used to consider the combined effects of increased CO₂ concentrations and temperature on aphid population sizes. It is concluded that, when both factors are elevated, aphid population dynamics will be more similar to current ambient conditions than expected from the results of experiments studying either factor alone. This result has important implications for future experimentation.     

Interaction between CO2 enrichment and salinity stress in the C4 non-halophyte Andropogon glomeratus (Walter) BSP

Abstract Increasing atmospheric CO₂ may result in alleviation of salinity stress in salt-sensitive plants. In order to assess the effect of enriched CO₂ on salinity stress in Andropogon glomeratus, a C₄ non-halophyte found in the higher regions of salt marshes, plants were grown at 350, 500, and 650 cm³ m^?3 CO₂ with 0 or 100 mol m^?3 NaCl watering treatments. Increases in leaf area and biomass with increasing CO₂ were measured in salt-stressed plants, while decreases in these same parameters were measured in non-salt-stressed plants. Tillering increased substantially with increasing CO₂ in salt-stressed plants, resulting in the increased biomass. Six weeks following initiation of treatments, there was no difference in photosynthesis on a leaf area basis with increasing CO₂ in salt-stressed plants, although short-term increases probably occurred. Stomatal conductance decreased with increasing CO₂ in salt-stressed plants, resulting in higher water-use efficiency, and may have improved the diurnal water status of the plants. Concentrations of Na⁺ and Cl^? were higher in salt stressed-plants while the converse was found for K ⁺. There were no differences in leaf ion content between CO₂ treatments in the salt-stressed plants. Decreases in photosynthesis in salt-stressed plants occurred primarily as a result of decreased internal (non-stomatal) conductance.     

Microbial communities colonising nutrient-enriched marine sediment

Sediment cores were set up to study microbial colonisation and interactions on marine sand grains under enrichment conditions. Cores were enriched with photosynthetic media in the light and dark (PL, PD) and heterotrophic media in the light and dark (HL, HD), and were incubated for 25 days. Sediment chlorophylls were then measured by acetone extraction, viable heterotrophic bacteria by plate counts, and numbers of cells mm^–2 sand grain surface by s.e.m. Chlorophyll a occurred in all sediments but was highest in the PL sediment. Bacteriochlorophyll a was only observed in the HL sediment. Heterotrophic viable counts were high in the HL and HD sediments. Dense growth of diatoms and blue-green algae, and a marine fungal Thraustochytrid sp. occurred on PL grains. The blue-green alga Schizothrix was often associated with the diatom Amphora on PL grains. Many different bacteria grew on HL and HD grains and some unusual colony and cell morphologies were recorded (Caulobacter, Flexibacter, polymer strands). Characteristic flakey material sometimes occurred in hollows on grains. The results are discussed in relation to microbial communities in low energy sedimentary environments.     

Evidence for a periodic excretion of nitrogen by roots of grass-legume associations

Diurnal variation in ion content of the solution bathing roots of two plants growing together in sand culture was analysed for three pairs of grass-legume species (Lolium multiflorum andTrifolium pratense; Zea mays andGlycine hispida; Avena sativa andVicia sativa) and their monospecific controls. Biomass and nitrogen content of plants were determined. Ion concentration (NO ₃ ⁻ , NO ₂ ⁻ , NH ₄ ⁺ , and K⁺) and pH of root solutions were measured for Lolium-Trifolium plant pairs and controls at 6 hours intervals over 36 h, starting at 8 am within a circadian cycle. Root solutions were regularly depleted in NO ₃ ⁻ by the grasses (Lolium-Lolium control) throughout the cycle. For associations involving the legume (Lolium-Trifolium and Trifolium-Trifolium), NO ₃ ⁻ depletion was followed by NO ₃ ⁻ enrichment at night, from late afternoon to early morning; the enrichment was more marked for the Lolium-Trifolium association. Solutions which did not contain NO ₂ ⁻ ions, were enriched by trace amounts of NH ₄ ⁺ ions, largely depleted in K⁺ and alkalanized for all associations throughout the cycle. Repeating the experiment with the three pairs of species at the vegetative phase of development confirmed the previous results: NO ₃ ⁻ enrichment during the night for associations with legumes. When the experiment was repeated with older plants which had almost completed their flowering stage, depletion only was observed and no NO ₃ ⁻ enrichment. These data suggest that NO ₃ ⁻ enrichment results from N excretion from active nodulated roots of the legume, accounting for the increase in both biomass and nitrogen content of the companion grass in grass-legume association. The quantitative importance and periodicity of nitrogen excretion as well as the origin of nitrate enrichment are discussed.     

Mechanisms of transmembrane signalling in human T cell activation

Several monoclonal antibodies directed against a number of T cell surface molecules are used to elucidate the role of these molecules (cell surface molecules) in T cell activation. The activation of T cells via these molecules are both antigen-dependent (CD3/TcR complex) and antigen-independent. Irrespective of their antigen-dependency, these monoclonal antibodies activate T cells by a classical signal transduction pathway, in which the binding of monoclonal antibodies to their cell surface receptors leads to activation of phospholipase C resulting in the the depolarization of plasma membrane, hydrolysis of IP2 and IP3 and DAG, the second messengers. IP3 leads to mobilization of intracellular calcium to contribute to an increase in [Ca⁺⁺]_i, whereas DAG causes activation and translocation of PKC and an increasing apparent affinity for Ca⁺⁺. The role of IN in the mobilization of intracellular calcium is emerging. In addition, influx of extracellular calcium also contributes to increase in [Ca^–+];. The increase in [Ca⁺⁺]; following activation via some T cell surface antigen is predominantly due to intracellular mobilization of Ca^–+ (e.g. CD3/TcR complex), whereas activation via other T cell surface antigen, the increase in [Ca^+–]_i is almost entirely due to an influx of extracellular calcium (e.g. CD5 antigen). All these molecules activate autocrine system of T cell growth, namely IL-2 production, IL-2 receptor expression and T cell proliferation.