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.     

Inhibitory factors affecting the process of enhanced biological phosphorus removal (EBPR) – A mini-review

Enhanced biological phosphorus removal (EBPR) technology has been widely considered as a key strategy in preventing eutrophication and recognized as the advancing front of research in wastewater treatment. The key to keep its high efficiency in biological phosphorus removal is to optimize the operation and management of the system. Previous research in this field has undoubtedly improved understanding of the factors hindered overall efficiency of EBPR. However, it is obvious that much remains to be learnt. This paper attempts to review the fundamental understanding in factors inhibiting the stability and reliability of the EBPR systems in the state-of-the-art research. In view of modeling the EBPR systems, an appropriate extension of the current mechanistic models with these inhibitory factors is recommended in order to better simulate and predict the behavior of full-scale and lab-scale EBPR plants. From the perspectives of the further mechanistic and multi-factors study, the direction of denitrifying dephosphatation and granules/biofilms are also discussed. This comprehensive overview will not only help us to understand the overall mechanism of the EBPR process, but also benefit the researchers and engineers to consider all the possible factors affecting the process in the urban sewage treatment plants.     

The effect of dielectric polarization of the electrode on anomalous temperature effects in the electrical double layer

Monte Carlo simulations and a modified Poisson–Boltzmann (MPB) theory are used to investigate the temperature dependence of the capacitance (around the potential of zero charge) of an electric double layer in the presence of surface polarization due to a dielectric boundary. Within the context of the restricted primitive model planar double layer, whose solvent dielectric constant is ε₂, the cases when the electrode is an insulator (ε₁ = 1), when the electrode and the electrolyte have the same permittivity (ε₁ = ε₂, no polarization), and when the electrode is a conductor (ε₁ → ∞) are studied for the case where the electrolyte concentration is 0.1 M. The simulations reveal a capacitance anomaly, that is, a positive temperature dependence of the capacitance at low temperatures for the former two situations. The MPB theory also shows this effect for these two situations and is in qualitative or better agreement with the simulation data. In these two cases, both the simulations and theory show a dramatic increase of the diffuse layer potential in the temperature regime where capacitance anomaly occurs. However, in the latter situation, where the electrode is metallic, the capacitance always has a negative temperature derivative for the MPB theory and probably also for the simulation data.     

Location of crosslinks in chemically stabilized horseradish peroxidase: implications for design of crosslinks.

The bifunctional compound, ethylene-glycol bis(N-hydroxysuccinimidylsuccinate) (EGNHS), stabilizes horseradish peroxidase C (HRP) by reaction with the enzyme's lysine residues. In this study we compare native and modified HRP by proteolytic fragmentation, peptide sequencing, and mass spectroscopy, and identify the sites of modification. Most significantly, EGNHS is shown to form a crosslink between Lys232 and Lys241 of HRP and modifies Lys174 without formation of a crosslink. These findings are in agreement with the lysine side-chain reactivities predicted from the surface accessibility of the amino groups, and the maximal span of 16 A of the EGNHS crosslinker.     

Evolution of erect helical colony form in the Bryozoa: phylogenetic, functional, and ecological factors

Erect helical colony forms have evolved at least six separate times within the Bryozoa, but only among those in which branches are composed of a single layer of feeding zooids. The four best known genera with helical colony forms evolved independently, and each occupied different benthic marine environments, achieved different growth habits, and utilized different aspects of an array of functional potentials resulting from the radially symmetrical colonies. Examination of the distribution of these four genera ( Archimedes , Bugula , Crisidmonea , and Retiflustra ) within a theoretical morphospace of hypothetical helical colony form reveals that each occupies its own characteristic region of morphospace, broadly overlapping in some dimensions but separated in others. The genera differ markedly in the branching densities within their filtration-sheet whorls, reflecting their phylogenetic legacies rather than constructional or functional constraints associated with helical growth. In contrast, all tend toward helices in which the radiating whorls of the unilaminate branches are held at an average of 50–60° to the central axis of the colony, and this may reflect a common functional optimum associated with the cilia-driven, auto-generated currents within the helix. The region of morphospace characterized by high values of surface area – i.e. helical geometries with branches orientated at very low angles to the central axis, and with very closely spaced whorls along the axis – is entirely empty of bryozoans, and these geometries apparently represent functionally unrealistic colony forms.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 235–260.     

An upper limit to the abundance of aquatic organisms

Summary The maximum density achievable by aquatic organisms is an inverse linear function of their body size. As a consequence, the maximum achievable biomass is independent of body size, and is 2 orders of magnitude higher than the biomass in natural populations. The minimum interorganismic terorganismic distance, calculated from the maximum density to allow comparison between aquatic and terrestrial organisms, scales as the 1/3 power of body size in both habitats. The similarities in the interorganismic distance of terrestrial and aquatic plant and animal communities suggest a fundamental regularity in the way organisms use the space.     

Periodic electric field as a biopolymer conformation switch: a possible mechanism

A theoretical model is proposed to describe the influence of a periodic electric field (PEF) upon a biopolymer. The biopolymer is treated as a classical mechanical system consisting of subsystems (molecular groups) which interact with each other through potential forces. The PEF is treated as a periodic driving force applied to a molecular group. The energy dissipation is considered using the model of fluid (viscous) friction. Arguments for the non-linear character of the friction-velocity dependence caused by the non-Newtonian rheology of a viscous medium are formulated.A forced molecular-group motion is investigated for the situation of a small driving-force period, with oscillations overdamped and a driving force consisting of more than one harmonic. As a result, it is established that the motion always gets to a terminal stage when only a small-scale vibration about some point, X ^*, takes place. The terminal motion is preceded by a transient characterized by the presence of a directional velocity component and so by a drift along a potential profile. the drift goes on until a barrier is met which has a sufficiently large steepness (the barrier height is not important). As a result, the point X ^* may happen to be remote from the conformation potential local minimum (conformational state). The physical reasons for the drift are described.If we consider the small-scale vibration about X ^* in the framework of the hierarchy of scales for intramolecular mobility, it can be regarded as an equilibrium mobility, whereas the drift can be regarded as a functionally important motion, and X ^* as a new conformational state which is realizable only in the presence of the PEF. It may be concluded, as the result of a consistent treatment and neglecting the small-scale vibration, that the conformational potential is modified by adding a linear term (in the one-dimensional case). In this connection, the set of conformational states can both deform (deviation of the positions of minima and their relative depth) and rearrange qualitatively (some minima can vanish and/or new minima can appear). In particular, the transition from one conformation to another one may happen due to rearrangement.     

Immunological studies of ferredoxin-nitrite reductases and ferredoxin-glutamate synthases from photosynthetic organisms

Polyclonal antiserum specific for ferredoxin-nitrite reductase (EC 1.7.7.1) from the green alga Chlamydomonas reinhardii recognized the nitrite reductase from other green algae, but did not cross-react with the corresponding enzyme from different cyanobacteria or higher plant leaves. An analogous situation was also found for ferredoxin-glutamate synthase (EC 1.4.7.1), using its specific antiserum. Besides, the antibodies raised against C. reinhardii ferredoxin-glutamate synthase were able to inactivate the ferredoxin-dependent activity of nitrite reductase from green algae.These results suggest that there exist similar domains in ferredoxin-nitrite reductases and ferredoxin-glutamate synthases from green algae. In addition, both types of enzymes share common antigenic determinants, probably located at the ferredoxin-binding domain. In spite of their physicochemical resemblances, no apparent antigenic correlation exists between the corresponding enzymes from green algae and those from higher plant leaves or cyanobacteria.Abbreviations Fd ferredoxin - GOGAT glutamate synthase - MV⁺ reduced methyl viologen (radical cation) - NiR nitrite reductase - PMSF phenylmethylsulphonyl fluoride - SDS sodium dodecyl sulfate     

Degradation of 3-chlorobiphenyl by in vivo constructed hybrid pseudomonads

Abstract 3-Chlorobiphenyl-degrading bacteria were obtained from the mating between Pseudomonas putida strain BN10 and Pseudomonas sp. strain B13. Strains such as BN210 resulted from the transfer of the genes coding the enzyme sequence for the degradation of chlorocatechols from B13 into BN10, whereas B13 derivatives such as B131 have acquired the biphenyl degradation sequence from BN10. During growth of the hybrid strains on 3-chlorobiphenyl 90% chloride was released. Activities of phenylcatechol 2,3-dioxygenase, benzoate dioxygenase, catechol 1,2-dioxygenase, chloromuconate cyloisomerase and 4-carboxymethyl-enebut-2-en-4-olide hydrolase were found in 3-chlorobiphenyl-grown cells. The hybrid strains were found to convert some congeners of the Aroclor 1221 mixture such as mono- and dichloro-substituted biphenyls.     

Succession of sessile organisms on experimental plates immersed in Nabeta Bay,Izu Peninsula,Japan V. An integrated consideration on the definition and prediction of succession

Successional changes of sessile organisms over about 3 years on concrete plates immersed at depths of 1.0, 2.5, 4.0 and 5.5 m in Nabeta Bay, Shimoda, Pacific coast of Japan, were investigated from their species composition, percentage cover, and the structure, metabolism, biomass and maturity of the community for the purpose of verifying the hypothesis of succession by Margalef (1968) and Odum (1969). The process of succession was divided into five stages from a cluster analysis based on Horn's (1966) similarity in community structure. The five stages were characterized from dominant, species and 18 community attributes in terms of structure, metabolism, biomass and maturity. With the advance of stages, two large-sized, long-lived species, the kelpEisenia bicyclis and the oysterCrassostrea nippona, dominated; 18 community attributes showed a directional succession ending in a constant community structure, low community metabolism, accumulation of community biomass except chlorophylla and an enhanced degree of community maturity. This directionality in succession of community attributes was valid for the prediction of Margalef and Odum, despite a tendency for estimated daily energy budget to be more heterotrophic in such an open system. From these results, it was suggested that the definition of succession by Odum (1969) should be interpreted as the regularity in shift of dominant species, not individual species, and as the control of system by feedback mechanism developing with succession rather than community-controlled mechanism.