Associating somatic mutation with clinical outcomes through kernel regression and optimal transport

Somatic mutations in cancer patients are inherently sparse and potentially high dimensional. Cancer patients may share the same set of deregulated biological processes perturbed by different sets of somatically mutated genes. Therefore, when assessing the associations between somatic mutations and clinical outcomes, gene-by-gene analysis is often under-powered because it does not capture the complex disease mechanisms shared across cancer patients. Rather than testing genes one by one, an intuitive approach is to aggregate somatic mutation data of multiple genes to assess their joint association with clinical outcomes. The challenge is how to aggregate such information. Building on the optimal transport method, we propose a principled approach to estimate the similarity of somatic mutation profiles of multiple genes between tumor samples, while accounting for gene–gene similarities defined by gene annotations or empirical mutational patterns. Using such similarities, we can assess the associations between somatic mutations and clinical outcomes by kernel regression. We have applied our method to analyze somatic mutation data of 17 cancer types and identified at least five cancer types, where somatic mutations are associated with overall survival, progression-free interval, or cytolytic activity.     

Induction of detoxification enzymes in phytophagous insects: Role of insecticide synergists,larval age,and species

Five insecticide synergists, all of which were either methylenedioxyphenyl compounds or analogs, were compared as to their effect on cytochrome P450 monooxygenase induction caused by an allelochemical in fall armyworm larvae. Feeding the synergists (piperonyl butoxide, safrole, isosafrole, MGK 264, and myristicin) individually to the larvae caused decreases in the microsomal aldrin epoxidase activities ranging from 38% to 74% when compared with controls. Feeding indole-3-carbinol resulted in a 4-fold increase in the microsomal epoxidase activity. However, cotreatment of any of the synergists and the inducer completely eliminated the induction. Sixth instar larvae were more inducible than second instar larvae with respect to microsomal epoxidase and glutathione transferase in the fall armyworm. Enzyme inducibility varied widely among the seven phytophagous Lepidoptera examined. When indole-3-carbinol was used as an inducer of microsomal epoxidase, the extent of inducibility of the enzyme was fall armyworm > velvetbean caterpillar > corn earworm > beet armyworm > tobacco budworm > cabbage looper > diamondback moth. When indole-3-acetonitrile was used as an inducer, the inducibility of glutathione transferase was fall armyworm > beet armyworm > corn earworm > cabbage looper > velvetbean caterpillar > tobacco budworm > diamondback moth. Inducibility of five microsomal oxidase systems also varied considerably in the corn earworm, indicating the multiplicity of cytochrome P450 in this species. Microsomal epoxidase and glutathione transferase were induced by cruciferous host plants such as cabbage and their allelochemicals in diamondback moth larve. © 1993 Wiley-Liss, Inc.     

环境温度影响蟾蜍卵母细胞成熟能力的机制之实验分析

长年饲养在高温(28—30℃)环境中雌性中华大蟾蜍,它们的卵母细胞可以长足,但经激素处理时,生发泡不破裂,仅显示成熟过程早期阶段的变化。值得注意的是,在孕酮刺激后的高温卵卵质中,出观了一种能诱发低温卵恢复减数分裂的物质,称作为“依赖冬眠因子的促成熟物质”(HF-MPS)。HF-MPS 与MPF 有不少相似之处,如孕酮处理后,它们在卵质中出现的时间相仿,它们的形成均不依赖于转录水平,而是依赖于翻译水平的蛋白质合成活动;但亦存在不同之处,如MPF 诱发低温卵GVBD 时程不受温度影响,而HF-MPS 在10℃环境中,诱发低温卵GVBD 的时间明显延缓;MPF 不仅能诱发低温卵GVBD,而且同样能诱发高温卵GVBD,然而,HF-MPS 只能诱发低温卵GVBD。由此表明,MPF 和HF-MPS 似乎是截然不同的两类活性蛋白质。高温卵缺少低温诱发产生的“冬眠因子”,所以不能恢复cdc 2基因的转录活动,不能实现MPF 自身催化扩增作用,不能保证孕酮处理后的卵母细胞完成正常成熟的全过程变化。足见,低温是中华大蟾蜍卵母细胞恢复减数分裂过程中的必要条件,是导致中华大蟾蜍现有区域分布的内在原因之一。     

Changing synaptic specificities in the nervous system of Caenorhabditis elegans: Differentiation of the DD motoneurons

During postembryonic development, the DD motoneurons in the nematode Caenorhabditis elegans completely reorganize their pattern of synapses. Ablation of a pair of embryonic precursors results in the absence of this entire class of motoneurons. In their absence animals exhibit two developmentally distinct locomotory defects. The transition period from one defect to the other is correlated with the synaptic reorganization of the DD mns. Mutations in a gene (unc-123) have been isolated that exhibit locomotory defects similar to those of the ablated adult animals. Genetic and cellular analyses of one of these alleles suggest that the unc-123 gene product may be involved in the reestablishment of functional synapses in these neurons. © 1993 John Wiley & Sons, Inc.     

染色体研究的进展与植物分类学(下)

染色体研究的进展与植物分类学（下）徐炳声,张芝玉,陈家宽,洪德元（中国科学院植物研究所系统与进化植物学开放研究实验室北京１０００９３）（上海第二军医大学药学院上海２００４３３）（武汉大学生命科学学院武汉４３００７２）ＡＤＶＡＮＣＥＳＩＮＣＨＲＯＭＯＳ...     

Multiplicity of brain cysteine sulfinic acid decarboxylase — Purification,characterization and subunit structure

Cysteine sulfinic acid decarboxylase (CSAD), the rate-limiting enzyme in taurine biosynthesis, appears to be present in the brain in multiple isoforms. Two distinct forms of CSAD, referred to as CSAD I and CSAD II, were obtained on Sephadex G-100 column. CSAD I and CSAD II differ in (1) the elution profile on Sephadex G-100 column; (2) the sensitivity towards Mn²⁺, methione, and other sulfur-containing amino acids and (3) their immunologic properties. CSAD II has been purified to about 2,500-fold by a combination of column chromatographies and polyacrylamide gel electrophoresis (PAGE). The purity of the enzyme preparation was established as judged from the following observations: (1) a single protein band was observed under various electrophoretic conditions, e.g., 5–20% nondenaturing PAGE, 7% nondenaturing PAGE and 10% SDS-PAGE and (2) in nondenaturing PAGE, the protein band comigrated with CSAD activity. CSAD II has a molecular weight of 90 kDa and is a homodimer consisting of two 43 ± 2 kDa subunits. CSAD appears to require Mn²⁺ for its maximum activity. Other divalent cations fail to replace Mn²⁺ in activation of CSAD activity. However, the precise role of Mn²⁺ in the action of CSAD remains to be determined.     

Effects of dehydration on the electron transport of Chlorella. An in vivo fluorescence study

Chlorella was used to study the effects of dehydration on photosynthetic activities. The use of unicellular green algae assured that the extent of dehydration was uniform throughout the whole cell population during the course of desiccation. Changes in the activities of the cells were monitored by measurements of fluorescence induction kinetics. It was found that inhibition of most of the photosynthetic activities started at a similar level of cellular water content. They included CO₂ fixation, photochemical activity of Photosystem II and electron transport through Photosystem I. The blockage of electron flow through Photosystem I was complete and the whole transition occurred within a relative short time of dehydration. On the other hand, the suppression of Photosystem II activity was incomplete and the transition took a longer time of dehydration. Upon rehydration, the inhibition of Photosystem II activity was fully reversible when samples were in the middle of the transition, but was not thereafter. The electron transport through Photosystem I was also reversible during the transition, but was only partially afterward.Abbreviations DCMU 3-(3,4-dichlorophenyl)-1,1-dimethyl urea - F_m maximum fluorescence yield - F₀ non-variable fluorescence level emitted when all PS II centers are open - F_v variable part of fluorescence - PS photosystem - Q_A primary quinone acceptor of Photosystem II     

Charge transfer photochemistry of quadruply bonded ditungsten halophosphine complexes

The quadruple metal-metal bonded complexes, W₂Cl₄(PR₃)₄ (PR₃ = PMe₃, PMe₂Ph, PBu₃), photoreact in dichloromethane with near-UV excitation (λ>375 nm) to yield a mixed valence W₂(II,III) photoproduct. Electronic absorption and EPR spectra of photolyzed solutions are identical to those obtained from the thermal oxidation of W₂Cl₄(PR₃)₄ by PhICI₂, which is known to yield W₂Cl₅(PR₃)₃. Subsequent reaction of the photolyzed solution yields the oxidized, confacial biotahedral W₂(III,III) halophosphine. Analysis of the organic photoproduct reveals that the halocarbon solvent is reduced by one electron to yield the chloromethyl radical. When the radical is produced in low yields, hydrogen abstraction from solvent appears to be sufficiently efficient to compete with dimerization and only chloromethane is observed; however, at higher concentrations, the chloromethyl radicals couple to produce dichloroethane. Photoreaction is observed only with near-UV excitation of the LMCT absorption manifold of W₂Cl₄(PR₃)₄. At lower energy wavelengths, transient absorption spectroscopy shows the production of the ¹δδ^* excited state, which decays to ground state over times commensurate with the decay of ¹δδ^* luminescence. In hydrocarbon solutions, no transient intermediate or photochemistry is observed, indicating that the LMCT excited state, although capable of reducing a C---X bond, cannot activate the stronger C---H bonds of hydrocarbons. The photochemistry and transient absorption spectroscopy results of the W₂Cl₄(PR₃)₄ complexes are compared to our previous studies of the homologs.     

Molecular Evolution and Phylogeny of Satellite RNA Associated with Bamboo Mosaic Potexvirus

Satellite RNA of bamboo mosaic potexvirus (satBaMV) is a linear RNA molecule which encodes a 20-kDa nonstructural protein. Sequences of seven different satBaMV isolates from bamboo hosts in three genera showed 0.7% to 7.5% base variation which spanned the whole RNA molecule. However, the putative 20-kDa open reading frame was all preserved in these isolates. The phylogenetic relationship based on the nucleotide sequence did not show particular grouping of satBaMV from the host in one genus; neither was the grouping of satBaMV evident by location of sampling. Putative secondary structures of the 3′ untranslated regions showed a basic pattern with conserved hexanucleotides (ACCUAA) and polyadenylation signal (AAUAAA) located in the loop regions. Although the satBaMV-encoded 20-kDa protein is a nonstructural protein, its predicted secondary structure contains eight-stranded β-sheets which may form ``jelly-roll' structure similar to that found in capsid protein encoded by satellite virus of panicum mosaic virus. Received: 26 June 1996 / Accepted: 9 September 1996