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.     

Line and crossing effects in a diallel mating system with highly inbred lines of White Leghorn chickens

Summary Seven highly inbred lines of White Leghorn chickens were used in a near complete diallel mating plan during eight years. The lines originated from three different base populations selected for egg weight. Average inbreeding coefficients of parents of chicks hatching in successive years were 0.75, 0.80, 0.84, 0.86, 0.89, 0.91, 0.93 and 0.94. The composition of line, specific combining ability and reciprocal effects and their estimated values are given. These effects were estimated for age at first egg (AFE), average weight of all eggs laid to 40 weeks (EW40), body weight at 40 weeks (BW40), number of eggs to 40 weeks (EP40) and number of eggs between 41 and 60 weeks (EP60). Records of 3247 hens surviving to 40 weeks and of 3133 birds to 60 weeks could be used. Large differences between line effects could be found in all traits. They were only partly due to the preceding selection in the base populations. All specific combining effects were in the expected direction, negative for AFE and positive for EW40, BW40, EP40 and EP60. Recovery of inbreeding depression inflated these effects rather substancially. Average heterosis, defined as the relative superiority of a line combination over the mid parent value, was –11.3%, 5.8%, 7.8%, 45.1% and 35.8% for AFE, EW40, BW40, EP40 and EP60 respectively. One line showed a relative superiority in AFE of -19.3% compared to about –7.9% for all other combinations. Reciprocal or sex-linked effects were generally smaller in all traits than specific combining effects, they were considerably smaller in AFE, EP40 and EP60. General reciprocal effects could be found for several lines in one or more traits. Offspring of two lines, when used as sire lines, showed a negative correlation between reciprocal effects of egg weight and body weight.     

杨树苗期合理密度与合理密度线研究

 本文以加杨(Populus Canadensis),I—214(Populus euramericana(Dode)Guinier CV—214),中保14等杨树密度试验(1988—1991)为依据,分析了初植密度、竞争对生长的抑制作用,阐述了合理密度、合理密度范围、缓冲作用、上限合理密度线的形成过程。指出在双对数图上,上限合理密度线遵从Logistic分布(1nw=K/1+e(0.732·lnN-2.429),呈左侧伸展的S型曲线。该曲线可划分为近似于lnw一lnN直线的上中下三部分,其中间部分直线式的斜率为-1.5左右,称作合理密度直线式。对密度与生长的动态作了分析、概述与讨论。     

Host-attacking behavior of a eulophid parasite,Kratochviliana sp., to the leaf mining host,Phytomyza ranunculi (Diptera: Agromyzidae) during its stay on the leaf

The present paper studies how the female parasite of Kratochviliana sp. visits and attacks its host larvae of Ranunculus leaf mining fly, P. ranunculi at a single leaf visit. The parasite visited its hosts at random on the leaf. The frequency of host visits was independent of the host density and the proportion of hosts survived from the parasite attack, in a leaf and its distribution was expressed as a single straight line. It almost always attacked living hosts at the first host visit after isolated from them for one day but with the rate of about 0.5 at the subsequent visits. In consequence, the relationships of the number of host attacks and killed hosts to the host density drew satulated curves in each. A model of host attack by this parasite at its single leaf visit was formulated by modifyingBakker et al.'s model (1972) basing upon these observations and the attack avoidance by the parasite to already attacked hosts previously reported.     

Vegetation dynamics in Brittany heathlands after fire

The vegetation dynamics of heathlands in Brittany have been followed for three years in areas subject to fire in August 1976. The pre-fire vegetation had been analysed and mapped before its destruction. The structure of the community and the processes taking place in it (in terms of biomass, primary productivity, phenology, mineral nutrition and food value) had been examined. The redevelopment of the canopy was studied by the point-contact method along permanent line transects. This semi-quantitative study permits calculation of the relative frequency of each species and, from this, its cover. The growth form of each species and the stratification of the community are also indicated by this method. Permanent plots were also used to record changes in the vegetation, by means of a census of individuals and records of the development and growth strategy of each species. The plots were located in homogeneous areas, or on bare soil around seed parents in order to examine seed dispersal and seedling establishment. These two methods yielded detailed information on the nature of the secondary successions following fire in the heathlands of Brittany.

     

Prediction of mean and variance of hybrids and of lines that can be derived from a random mating population

Summary A method is presented to estimate, from a two-factor crossing design including self-fertilization, mean and variance of lines and hybrids that can be derived from a random mating population. The derivation is only valid in the absence of epistasis. From such an estimation, it is possible to derive the expected value of the best lines and of the best hybrids that can be derived from a population.     

A new method of sequential sampling to obtain the population estimates with a fixed level of precision

A simple method of sequential sampling is developed which would make it automatically possible to secure, without excess sampling, a predetermined level of precision for a series of population estimates being required. It appears to have wide application to sampling field populations under various situations since it is simply based upon the relationship of variance to mean for which a comprehensive formula deduced for biological populations from the linearity in the regression of mean crowding on mean density could be adopted. Some problems that may arise in practical application of the method are also discussed.     

At Palmyra Atoll,the fish-community environmental DNA signal changes across habitats but not with tides

At Palmyra Atoll, the environmental DNA (eDNA) signal on tidal sand flats was associated with fish biomass density and captured 98%–100% of the expected species diversity there. Although eDNA spilled over across habitats, species associated with reef habitat contributed more eDNA to reef sites than to sand-flat sites, and species associated with sand-flat habitat contributed more eDNA to sand-flat sites than to reef sites. Tides did not disrupt the sand-flat habitat signal. At least 25 samples give a coverage >97.5% at this diverse, tropical, marine system.