Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions

Systematic genetic interaction studies have illuminated many cellular processes. Here we quantitatively examine genetic interactions among 26 Saccharomyces cerevisiae genes conferring resistance to the DNA-damaging agent methyl methanesulfonate (MMS), as determined by chemogenomic fitness profiling of pooled deletion strains. We constructed 650 double-deletion strains, corresponding to all pairings of these 26 deletions. The fitness of single- and double-deletion strains were measured in the presence and absence of MMS. Genetic interactions were defined by combining principles from both statistical and classical genetics. The resulting network predicts that the Mph1 helicase has a role in resolving homologous recombination-derived DNA intermediates that is similar to (but distinct from) that of the Sgs1 helicase. Our results emphasize the utility of small molecules and multifactorial deletion mutants in uncovering functional relationships and pathway order.     

Cooperative Sensor Anomaly Detection Using Global Information

Sensor networks are deployed in many application areas nowadays ranging from environment monitoring, industrial monitoring, and agriculture monitoring to military battlefield sensing. The accuracy of sensor readings is without a doubt one of the most important measures to evaluate the quality of a sensor and its network. Therefore, this work is motivated to propose approaches that can detect and repair erroneous (i.e., dirty) data caused by inevitable system problems involving various hardware and software components of sensor networks. As information about a single event of interest in a sensor network is usually reflected in multiple measurement points, the inconsistency among multiple sensor measurements serves as an indicator for data quality problem. The focus of this paper is thus to study methods that can effectively detect and identify erroneous data among inconsistent observations based on the inherent structure of various sensor measurement series from a group of sensors. Particularly, we present three models to characterize the inherent data structures among sensor measurement traces and then apply these models individually to guide the error detection of a sensor network. First, we propose a multivariate Gaussian model which explores the correlated data changes of a group of sensors. Second, we present a Principal Component Analysis (PCA) model which captures the sparse geometric relationship among sensors in a network. The PCA model is motivated by the fact that not all sensor networks have clustered sensor deployment and clear data correlation structure. Further, if the sensor data show non-linear characteristic, a traditional PCA model can not capture the data attributes properly. Therefore, we propose a third model which utilizes kernel functions to map the original data into a high dimensional feature space and then apply PCA model on the mapped linearized data. All these three models serve the purpose of capturing the underlying phenomenon of a sensor network from its global view, and then guide the error detection to discover any anomaly observations. We conducted simulations for each of the proposed models, and evaluated the performance by deriving the Receiver Operating Characteristic (ROC) curves.     

Novel aspects of glypican glycobiology

Mutations in glypican genes cause dysmorphic and overgrowth syndromes in men and mice, abnormal development in flies and worms, and defective gastrulation in zebrafish and ascidians. All glypican core proteins share a characteristic pattern of 14 conserved cysteine residues. Upstream from the C-terminal membrane anchorage are 3–4 heparan sulfate attachment sites. Cysteines in glypican-1 can become nitrosylated by nitric oxide in a copper-dependent reaction. When glypican-1 is exposed to ascorbate, nitric oxide is released and participates in deaminative cleavage of heparan sulfate at sites where the glucosamines have a free amino group. This process takes place while glypican-1 recycles via a nonclassical, caveolin-1-associated route. Glypicans are involved in growth factor signalling and transport, e.g. of polyamines. Cargo can be unloaded from heparan sulfate by nitric oxide-dependent degradation. How glypican and its degradation products and the cargo exit from the recycling route is an enigma.Received 27 November 2003; received after revision 8 January 2004; accepted 13 January 2004     

P systems with array objects and array rewriting rules

Array P systems were introduced by Paun Gh. which is linking the two areas of membrane computing and picture grammars. Puzzle grammars were introduced by us for generating connected picture arrays in the two-dimensional plane, motivated by the problem of tiling the plane. On the other hand, incorporating into arrays the developmental type of generation used in the well-known biologically motivated L systems, Siromoney and Siromoney proposed a very general rectangular array generating model, called extended controlled tabled L array system (ECTLAS). In this paper we introduce two variations of the array P system, called BPG array P system and parallel array P system. The former has in the regions array objects and basic puzzle grammar rules (BPG), which are a specific kind of puzzle grammar rules. In the latter, the regions have rectangular array objects and tables of context-free rules. We examine these two types of P systems for their array generative power.     

P systems with array objects and array rewriting rules

Array P systems were introduced by Paun Gh. which is linking the two areas of membrane computing and picture grammars. Puzzle grammars were introduced by us for generating connected picture arrays in the two-dimensional plane, motivated by the problem of tiling the plane. On the other hand, incorporating into arrays the developmental type of generation used in the well-known biologically motivated L systems, Siromoney and Siromoney proposed a very general rectangular array generating model, called extended controlled tabled L array system (ECTLAS). In this paper we introduce two variations of the array P system, called BPG array P system and parallel array P system. The former has in the regions array objects and basic puzzle grammar rules (BPG), which are a specific kind of puzzle grammar rules. In the latter, the regions have rectangular array objects and tables of context-free rules. We examine these two types of P systems for their array generative power.     

CSE/H2S通路缺失影响小鼠肝脏胆固醇和脂肪酸代谢（英文）

肝脂质代谢异常导致过度肝脂肪沉积和脂肪变性是脂肪肝发展的关键环节.胱硫脒-伽马-裂解酶(CSE)是在肝脏中催化硫化氢(H2S)生成的酶之一.本研究的目的是研究CSE/H2S在调控肝脏胆固醇和脂肪酸代谢中的作用.用高脂饮食(HFD)喂食野生型(WT)和CSE敲除(KO)小鼠后,对小鼠肝形态学和生物化学变化进行了分析.与WT小鼠不同,HFD喂食显著增加CSE-KO小鼠的血浆和肝脏胆固醇水平以及肝和胆囊的大小.这些CSE-KO小鼠呈现典型的脂肪肝组织学和生物化学变化以及肝功能损害.血浆和肝脏甘油三酯水平也比HFD喂养WT小鼠显著降低.核受体转录因子LXRα以及它的靶基因,CYP7A1,在对照组和HFD组CSE-KO小鼠肝脏中的表达都低于相应WT小鼠的水平.这些异常阻碍胆固醇分解成胆汁并导致胆固醇蓄积在肝脏和胆囊.由于CSE/H2S通路缺失造成对HFD诱导的脂肪肝的高易感性,肝脏CSE/H2S通路可能是治疗脂肪肝损伤的一个新的靶向.     

The effects of continuous chloroform and halothane anesthesia on plasma prolactin levels in ovariectomized estrogen-treated rats

Summary In ovariectomized, estrogen-treated rats bearing indwelling aortic catheters, continuous inhalation of chloroform or halothane resulted in increases in plasma prolactin levels 10 min after the exposure to the anesthetics. The plasma prolactin levels over the subsequent 2 h, however, were not significantly different from that of the control animals.Supported by NSF Research Grant BMS 74-17332.The authors wish to express their appreciation to Mrs Cynthia Van De Walle for her outstanding assistance in the performance of the prolactin RIA and the art work.