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.     

On-Chip Endothelial Inflammatory Phenotyping

Atherogenesis is potentiated by metabolic abnormalities that contribute to a heightened state of systemic inflammation resulting in endothelial dysfunction. However, early functional changes in endothelium that signify an individual''s level of risk are not directly assessed clinically to help guide therapeutic strategy. Moreover, the regulation of inflammation by local hemodynamics contributes to the non-random spatial distribution of atherosclerosis, but the mechanisms are difficult to delineate in vivo. We describe a lab-on-a-chip based approach to quantitatively assay metabolic perturbation of inflammatory events in human endothelial cells (EC) and monocytes under precise flow conditions. Standard methods of soft lithography are used to microfabricate vascular mimetic microfluidic chambers (VMMC), which are bound directly to cultured EC monolayers.¹ These devices have the advantage of using small volumes of reagents while providing a platform for directly imaging the inflammatory events at the membrane of EC exposed to a well-defined shear field. We have successfully applied these devices to investigate cytokine-,² lipid-^{3, 4} and RAGE-induced⁵ inflammation in human aortic EC (HAEC). Here we document the use of the VMMC to assay monocytic cell (THP-1) rolling and arrest on HAEC monolayers that are conditioned under differential shear characteristics and activated by the inflammatory cytokine TNF-α. Studies such as these are providing mechanistic insight into atherosusceptibility under metabolic risk factors.     

The interactive effects of temperature,food level and maternal phenotype on offspring size in Daphnia magna

Invertebrate offspring are usually larger in colder environments. To test for possible effects of covariates (e.g. maternal phenotype and feeding conditions) on this pattern, we performed a laboratory experiment to look at the effect of temperature on newborn weight in the planktonic crustacean Daphnia magna. Three tempèratures (12°C, 16°C and 22°C) and two food levels (10,000 cells ml^–1 and 150,000 cells ml^–1) were used, and offspring were examined from the first five clutches of mothers that had been maintained under the constant experimental conditions for three generations. Preliminary analysis suggested that newborn weight was significantly affected by temperature although patterns in the data were not clear cut. In addition, the covariates mother weight and clutch size were positively and negatively correlated with newborn weight, respectively; and later clutches tended to contain heavier offspring. Therefore, in an effort to control for the effects of the covariates, repeated-measures analysis of covariance was performed using ratio values of newborn weight/mother weight (relative newborn weight) as the dependent variable, clutch size as the covariate and clutch number as the repeated measures term. Now, temperature as a main effect in an ANCOVA model did not significantly influence relative newborn weight. The repeatedmeasure term clutch number also became nonsignificant, indicating that when differences in mother weight due to age were accounted for there were no overall differences in relative newborn weight between clutches from a particular mother. Temperature effects on relative newborn weight were only significant as part of interaction terms with food concentration and with clutch number. Thus there were different weight responses to temperature within food levels, and between clutch numbers within food levels. Under the low-food conditions newborn were heaviest at 16°C, lightest at 12°C and intermediate at 22°C. Conversely, under the high-food condition newborn were lightest at 16°C, heaviest at 12°C and again intermediate at 22°C. However, newborn tended to be heavier under the low food condition, and food concentration was highly significant as a main effect. Mother growth rate showed no significant relationship with newborn weight. It is concluded that direct temperature effects on relative newborn weight are marginal and nonsignificant. Temperature effects through interactions with food concentration and clutch number are important determinants of newborn weight, but relatively speaking account for only a small proportion of observed variance in newborn weight (25%), compared with the direct effect of food concentration (67%).     

Characterization of Mendelian and Non-Mendelian Mutant Strains by Micronuclear Transplantation in Paramecium tetraurelia

ABSTRACT. Mutant strain d48 and d12 cannot express serotype A. In d48, the A i-antigen gene is present in the micronucleus, but not in the macronucleus. It has recently been shown that d12 contains the A gene in its micronucleus, but its macronucleus lacks the gene. Micronuclear transplantations into enucleated cells were performed to analyze those mutants. Reciprocal transplantation between wild type and d48 confirmed that d48 contains the A gene in the micronucleus and its cytoplasm is defective. Wild type 51 enucleated cells into which were transplanted d12 micronuclei could not express A. Amiccronucleate d12 cells into which were transplanted normal micronuclei from 51 or d48 showed no expression of A. These results show that even if the micronucleus of d12 contains the A gene, it must be abnormal, and its cytoplasm is also defective the same as d48. Genetic analysis showed that heterozygote of d12 and wild type 51 or d48 caused a cure of the cytoplasmic defect of d48 and d12 during the development of macronuclei.     

Size-scaling of zooplankton foraging in Arctic charr

Prey capture rate (number of prey s⁻¹) and the mode of feeding of Arctic charr Salvelinus alpinus were studied by performing foraging experiments with two sizes (1·1 and 1·8 mm) of Daphnia longispina prey. Arctic charr were particulate feeders at all densities tested. Adjusted for the effect of prey density, the capture rate showed a hump-shaped relationship with Arctic charr size for both sizes of D. longispina . Estimated attack rates ( a ) also tended to show a hump-shaped relationship with fish size. The estimated size-scaling exponent of the attack rate function, however, was relatively small, implying small changes in attack rate over fish sizes. Simultaneous estimations of a and handling time were used in combination with published data on fish metabolism and dry mass rations of prey to estimate maintenance resource density of prey as a function of Arctic charr mass. Maintenance resource densities increased monotonically with Arctic charr size, and rapidly as optimum fish size relative to attack rate on prey was passed.     

Expression of heterologous genes for wall teichoic acid in Bacillus subtilis 168

Summary A localized region of low DNA sequence homology was revealed in two strains of Bacillus subtilis by a specific 100-fold reduction in transformation by W23 DNA of the tag1 locus, a teichoic acid marker of strain 168. Fifty nine rare recombinants, hybrid at this locus, had all acquired donor-specific phage resistance characters, while losing those specific to the 168 recipient. Chemical analysis of isolated cell walls showed that these modifications are associated with major changes in the wall teichoic acids. Genetic analysis demonstrated that determinants for the ribitol phosphate polymer of strain W23 had been transferred to 168, replacing those for the glycerol phosphate polymer in the recipient. All W23 genes coding for poly(ribitol phosphate) in the hybrids and those specifying anionic wall polymers in strain 168 are clustered near hisA. In addition to tag1, the region exchanged extends just beyond gtaA in some hybrids, whereas in others it may include the more distant gtaB marker, encompassing a region sufficient to contain at least 20 average-sized genes. Surface growth, flagellation, transformability and sporulation all appeared normal in hybrids examined. Recombinants without a major wall teichoic acid from either strain were not found, suggesting that an integral transfer of genes for poly(ribitol phosphate) from W23 had occurred in all hybrids isolated. We interpret these results as indicating an essential role for anionic wall polymers in the growth of B. subtillis.     

The effect of the 4B chromosomes of hexaploid wheat on the growth and regeneration of callus cultures

Summary Calli were initiated from immature embryos of nine lines of hexaploid wheat (Triticum aestivum L. em. Thell). These were the euploid lines Chinese Spring and Cappelle-Desprez, a line of Chinese Spring ditelocentric for the long arm of 4B, four substitution lines of Chinese Spring in which chromosome 4B has been replaced by its homologues from different wheat varieties and substituted into Chinese Spring and a substitution line of Besostaya I 4B into Cappelle-Desprez. The calli from these lines were found to differ in their growth rates and morphogenic and regenerative activities. The substitution of different 4B chromosomes into Chinese Spring significantly increased morphogenesis and shoot regeneration from callus. The potential for developing wheat lines with improved culture characteristics is discussed.