On optimal associative recall by an incomplete key

A new association scheme is proposed. The fundamental principle of the conventional associative memory models is to solve the matrix equation which is made by the complete (memorized) keys and responses. Therefore, when an incomplete key pattern which is a fraction of memorized key is given to the models as a key, these models can not have an optimal association except for a special case. Analyzing the property of the incomplete key pattern, in this paper, we propose a new association model which behaves optimally for an incomplete key pattern. From the result of the computer simulation, we understand that this model has the expected ability.     

Structure-based design of pyridopyrimidinediones as dipeptidyl peptidase IV inhibitors

Dipeptidyl peptidase IV (DPP-4) inhibitors have been shown to enhance GLP-1 levels and thereby improve hyperglycemia in type II diabetes. From a small fragment hit, using structure-based design, we have discovered a new class of non-covalent, potent and selective DPP-4 inhibitors.     

Candidate Gene Identification for Systemic Lupus Erythematosus Using Network Centrality Measures and Gene Ontology

Systemic lupus erythematosus (SLE) commonly accredited as “the great imitator” is a highly complex disease involving multiple gene susceptibility with non-specific symptoms. Many experimental and computational approaches have been used to investigate the disease related candidate genes. But the limited knowledge of gene function and disease correlation and also lack of complete functional details about the majority of genes in susceptible locus, encumbrances the identification of SLE related candidate genes. In this paper, we have studied the human immunome network (undirected) using various graph theoretical centrality measures integrated with the gene ontology terms to predict the new candidate genes. As a result, we have identified 8 candidate genes, which may act as potential targets for SLE disease. We have also carried out the same analysis by replacing the human immunome network with human immunome signaling network (directed) and as an outcome we have obtained 5 candidate genes as potential targets for SLE disease. From the comparison study, we have found these two approaches are complementary in nature.     

Analysis of suppressor mutations of spoIVCA mutations: occurrence of DNA rearrangement in the absence of site-specific DNA recombinase SpoIVCA in Bacillus subtilis.

The spoIVCA gene of Bacillus subtilis encodes a site-specific recombinase, which excises a 48-kb skin element from the chromosomal DNA by DNA rearrangement and creates a new composite gene, sigK, on the chromosome. From spoIVCA mutants, we have isolated Spo+ revertants which have no skin element but have an intact sigK gene. This result suggests that the DNA rearrangement can occur in the absence of spoIVCA.     

Autopoietic and (M,R) systems

From the many attempts to produce a conceptual framework for the organization of living systems, the notions of (M,R) systems and Autopoiesis stand out for their rigor, their presupposition of the circularity of metabolism, and the new epistemologies that they imply. From their inceptions, these two notions have been essentially disconnected because each has defined its own language and tools. Here we demonstrate the existence of a deep conceptual link between (M,R) systems and Autopoietic systems. This relationship permits us to posit that Autopoietic systems, which have been advanced as capturing the central aspects of living systems, are a subset of (M,R) systems. This result, in conjunction with previous theorems proved by Rosen, can be used to outline a demonstration that the operation of Autopoietic systems cannot be simulated by Turing machines. This powerful result shows the potential of linking these two models. Finally, we suggest that the formalism of (M,R) systems could be used to model the circularity of metabolism.     

Implementation of liquid-based cytology in the screening programme against cervical cancer in the County of Funen, Denmark, and status for the first year

As one of the first laboratories in Denmark (and Scandinavia), we have gradually implemented liquid-based cytology into the screening programme against cervical cancer in the County of Funen since 1 June 2001. This paper describes the course of the implementation period in the different steps in the screening programme, and the preliminary results obtained after the first year. We conclude that the new technique has improved the specimen and diagnostic quality. As a result of the reduction of the screening time, the workload in the laboratory is in balance although we have introduced a rapid review as a quality control. Besides, the reduction in the number of repeated cytological tests and follow-up visits at the gynaecologist means a saving for the screening programme as a whole. From our point of view the implementation of ThinPrep method is economically neutral.     

Linear diterpenoids from Cystoseira balearica

From the brown alga Cystoseira balearica we have isolated, in addition to previously reported acyclic diterpenoids, two new compounds (eleganonal and iso-eleganonal). Their structures have been elucidated by spectral analysis and chemical correlation.     

Novel chlorinated dibenzofurans isolated from the cellular slime mold,Polysphondylium filamentosum,and their biological activities

Cellular slime molds are expected to have the huge potential for producing secondary metabolites including polyketides, and we have studied the diversity of secondary metabolites of cellular slime molds for their potential utilization as new biological resources for natural product chemistry. From the methanol extract of fruiting bodies of Polysphondylium filamentosum, we obtained new chlorinated benzofurans Pf-1 (4) and Pf-2 (5) which display multiple biological activities; these include stalk cell differentiation-inducing activity in the well-studied cellular slime mold, Dictyostelium discoideum, and inhibitory activities on cell proliferation in mammalian cells and gene expression in Drosophila melanogaster.     

用野生醋栗花粉匀浆诱导栽培番茄变异的初步研究

实验以79286栽培番茄品种为受体,用野生醋栗花粉匀浆物质处理该受体植株柱头再对其授粉。从诱导后代中获得了结果习性、果肩色等具有某些醋栗性状的变异,并从中选育出一个耐储性好、多果型的番茄新品系．其受体番茄由聚伞花序转化为总状花序型的频率为7．8－23％．每穗结果数由4－5个增加至6－8个。果大小介于供体与受体两者之间．     

A second DNA polymerase activity in yeast mitochondria

In eukaryotic cells, there is much evidence to indicate that the replication of the mitochondrial genome is carried out by a specific DNA polymerase named DNA polymerase gamma. In theyeast S, cerevisiae, a DNA polymerase gamma has been partially purified and the gene encoding the catalytic subunit identified. The characteristics of this enzyme are the same as those found in higher eukaryotes, except for the requirement for a higher magnesium concentration. During a purification procedure of yeast mitochondrial DNA polymerase, we have isolated a second DNA polymerase activity. Using different approaches we have ruled out the possibility of nuclear contamination oraproductofproteolysis. From its properties, this new DNA polymerase activity seems to be different from any yeast DNA polymerase. This new mitochondrial DNA polymerase activity provides evidence that the animal model of mitochondrial DNA replication cannot be generalized. The presence of two DNA polymerases in yeast mitochondria could reflect a different replication or repair mechanism.     

Approaches to library screening

Fuelled by the drive to complete the Human Genome Project, many laboratories have developed new methods of screening clone libraries. From PCR-based strategies to pooling schemes and increased automation, the tedious task of library screening has become less labour-intensive and more cost-efficient. Currently, two main screening methods dominate: hybridization and polymerase chain reaction (PCR). In the following article, we present a brief overview of hybridization and PCR-based screening of yeast and bacterial libraries. Multi-faceted approaches combining different techniques, as well as less frequently employed methods such as fingerprinting are also described.     

Generalized method for probability-based peptide and protein identification from tandem mass spectrometry data and sequence database searching

Tandem mass spectrometry-based proteomics is currently in great demand of computational methods that facilitate the elimination of likely false positives in peptide and protein identification. In the last few years, a number of new peptide identification programs have been described, but scores or other significance measures reported by these programs cannot always be directly translated into an easy to interpret error rate measurement such as the false discovery rate. In this work we used generalized lambda distributions to model frequency distributions of database search scores computed by MASCOT, X!TANDEM with k-score plug-in, OMSSA, and InsPecT. From these distributions, we could successfully estimate p values and false discovery rates with high accuracy. From the set of peptide assignments reported by any of these engines, we also defined a generic protein scoring scheme that enabled accurate estimation of protein-level p values by simulation of random score distributions that was also found to yield good estimates of protein-level false discovery rate. The performance of these methods was evaluated by searching four freely available data sets ranging from 40,000 to 285,000 MS/MS spectra.     

Working in the real and the imaginary

The science we practice is shaped by our interactions with people; the enthusiastic teachers, the fascinating mentors, the inspiring colleagues, and the inquisitive students. The science we enjoy takes us into areas we couldn''t have anticipated. From time to time, we come back to reality and try to find ways to share our new explorations with our friends and relatives and to convert our insights into collective progress. What could be a better job?     

Simulium spp. control program in Rio Grande do Sul, Brazil

Insects of the Simuliidae family have been the object of control in Rio Grande do Sul since the 70s. Their constant attacks became a social-economical problem as well as a problem of Public Health, with serious consequences to men and to the economy of the areas in which the insects develop. At first, the control was done with a chemical larvicide Themephos ABATE 500 E, but an imperfect measuring of outflow to determine the quantity of the product made Simulium spp. resistant to it. From 1983 on, following a study of a new method for the outflow measuring, we started to use a biological larvicide Bacillus thuringiensis serovar israelensis based. The biological control uses the new method in 36.4% of the state area, assisting about 3,500,000 inhabitants.     

RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies

Understanding the 3D structural properties of RNAs will play a critical role in identifying their functional characteristics and designing new RNAs for RNA-based therapeutics and nanotechnology. While several existing computational methods can help in the analysis of RNA properties by recognizing structural motifs, they do not provide the means to compare and contrast those motifs extensively. We have developed a new method, RNAMotifContrast, which focuses on analyzing the similarities and variations of RNA structural motif characteristics. In this method, a graph is formed to represent the similarities among motifs, and a new traversal algorithm is applied to generate visualizations of their structural properties. Analyzing the structural features among motifs, we have recognized and generalized the concept of motif subfamilies. To asses its effectiveness, we have applied RNAMotifContrast on a dataset of known RNA structural motif families. From the results, we observed that the derived subfamilies possess unique structural variations while holding standard features of the families. Overall, the visualization approach of this method presents a new perspective to observe the relation among motifs more closely, and the discovered subfamilies provide opportunities to achieve valuable insights into RNA’s diverse roles.     

Isolation of a natural sterol and an aliphatic acid from Vernonia cinerea

From the roots of Vernonia cinerea a new natural sterol and a new aliphatic acid characterized as stigmast-5,17(20)-dien-3β-ol and 26-methylheptacosanoic acid, respectively, have been isolated together with stigmasterol and sitosterol.     

抗菌肽的结构分析、抗菌机制及改造应用的研究进展

细菌感染已成为威胁人类健康的重要公共卫生问题之一,而抗生素的滥用又加快了细菌耐药性的进程。抗菌肽因其广谱抗菌活性、快速杀菌作用、低毒性和不易产生耐药性等特点受到了广泛关注。然而,抗菌肽的天然结构也预示了其应用存在一些限制,如易降解、不稳定、低渗透和高成本等。如何改良抗菌肽仍是需要解决的难题。本文从抗菌肽的来源和结构特征出发,分析了与抗菌相关的空间结构及其所对应的抗菌机制,总结了现有抗菌肽的改良策略,为寻求新型改良方案奠定基础。希望为今后抗菌肽的改造与临床应用提供新的思路和方向。     

利用电磁脉冲提高抗癌药物治疗肿瘤细胞疗效的实验研究

本文采用一种新的方法——电穿孔结合化学药物进行肿瘤治疗的电化学疗法。电穿孔由于能使细胞膜出现瞬时微孔,从而能大大提高癌细胞对药物的吸收率、促进了药物等大分子进入细胞。这里利用电穿孔现象结合抗癌药物治疗昆明小鼠身上的S-180肉瘤,从实验数据可看出,这种方法取得了很好的效果。这种癌症治疗新技术具有易于控制、便于操作等优点,特别适用浅表肿瘤的治疗,为临床治疗肿瘤提供了一条新的途径。     

Betacyanins of some chenopodiaceae

Four species of the Chenopodiaceae have been investigated for their betacyanin content. From the leaves of Suaeda fruticosa a new acylated pigment has been isolated and identified as citryl-celosianin.