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.     

Contribution of buried seeds to revegetation after eruptions of the volcano Usu,Northern Japan

Soon after the 1977–78 eruptions of the volcano Usu, there were created many gullies in which former topsoil, i.e., well-developed soil accumulated before the eruptions, was eroded in the crater basin, whereas the outside of the gully was covered with thick volcanic deposits. The short-dispersal-seed plants were the most abundant in the inside of gully where the former topsoil was exposed, however, they have not immigrated from external environments. The germination tests of the seeds extracted from the former topsoil demonstrated that viable seeds were buried at 1683.3/m² for 9 years after the eruptions. At least, 12 herbaceous species, e.g.,Rumex obtusifolius, Geum macrophyllum var.sachalinense andPoa annua, were derived from the buried seeds in the former topsoil. Their contribution to revegetation was estimated to be 40.0% in the inside of gully where the former topsoil was exposed in 1983, suggesting that buried seeds are one of the most important seed source for revegetation even in the case of a volcano which produced pumice and ash by eruption.     

A note on the present situation of the primate fauna found from south-eastern Cameroon to northern Congo

Brief results of a survey are reported for the primate fauna in south-eastern Cameroon and northern Congo. The survey was carried over the period from October 1988 to January 1989. I confirmed the occurrence ofMandrillus sphinx in the south-eastern part of Cameroon, viz. the south bank of the Dja river, the occurrence ofCercocebus albigena in almost all the survey areas, the occurrence ofCercopithecus cephus, C. nictitans, C. pogonias, andGorilla g. gorilla throughout the areas, and the occurrence ofCercopithecus neglectus andColobus badius near Bomassa, 70 km north of Ouesso, in Congo. I also confirmedColobus polykomos satanas in some parts of Cameroon, but this species is declining. Local people provided information onCercocebus galeritus agilis, Colobus guereza, andPan troglodytes in almost all the areas, in some of which I confirmed the animals directly. They also provided information aboutCercocebus torquatus on the north bank of the Dja river in Cameroon andMiopithecus talapoin in Sembe in Congo, although I could not confirm these species myself. Human activities had begun reducing the populations of the above primates, particularly those ofMandrillus sphinx, Colobus polykomos satanas, andGorilla g. gorilla, in south-eastern Cameroon and in northern Congo despite the low density of the human populations.     

Plant succession in areas of scorched and blown-down forest after the 1980 eruption of Mount St. Helens,Washington

Abstract. Patterns of plant succession were studied in areas of scorched and blown-down forest resulting from the 1980 eruption of Mount St. Helens, Washington. Changes in species abundance were observed for 7 years in permanent sample plots representing four post-disturbance habitats, or site types. Total plant cover and species richness increased with time on all site types. In blown-down forests supporting snowpack at the time of eruption, understory recovery was dominated by the vegetative regeneration of species persisting through disturbance. In forests without snowpacks, plant survival was poorer. Increases in cover and diversity were dominated first by introduced grasses, then by colonizing forbs characteristic of early successional sites. Epilo-bium angustifolium and Anaphalis margaritacea showed widespread recruitment and clonal expansion throughout the devastated area. As a result, species composition on previously forested sites converged toward that on formerly clearcut sites, where early serai forbs resprouted vigorously from beneath the tephra. Total plant cover and species diversity were poorly correlated with post-disturbance habitat and general site characteristics (e.g. distance from the crater, elevation, slope, and aspect). However, distributions of several life-forms (e.g. low sub-shrubs and tall shrubs) were strongly correlated with depth of burial by tephra and with cover of tree rootwads. Thus, early community recovery may reflect microsite variation or chance survival and recruitment rather than broad-scale gradients in environment or disturbance. Recovery of pre-disturbance composition and structure will undoubtedly be much slower than after other types of catastrophic disturbance. The rate and direction of community recovery will largely depend on the degree to which original understory species survived the eruption.     

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。     

中国生态环境过渡的一个重要地带

本文揭示沿腾冲－黑河联线的地带不仅如胡焕庸早年提出是一条人口地理界线,而且是一条生态环境界线,更重要的是,腾冲－黑河线表征的方向,在历史时期表现为全球变化的特征方向。     

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.