bluuebunny/crossref_metadata_2025 huggingface dataset:
Acetylation of Histones and Transcription-Related Factors
Authors: Sterner David E. , Berger Shelley L.
Published: January 2003

The state of chromatin (the packaging of DNA in eukaryotes) has long been recognized to have major effects on levels of gene expression, and numerous chromatin-altering strategies—including ATP-dependent remodeling and histone modification—are employed in the cell to bring about transcriptional regulation. Of these, histone acetylation is one of the best characterized, as recent years have seen the identification and further study of many histone acetyltransferase (HAT) proteins and their associated complexes. Interestingly, most of these proteins were previously shown to have coactivator or other transcription-related functions. Confirmed and putative HAT proteins have been identified from various organisms from yeast to humans, and they include Gcn5-related N-acetyltransferase (GNAT) superfamily members Gcn5, PCAF, Elp3, Hpa2, and Hat1: MYST proteins Sas2, Sas3, Esa1, MOF, Tip60, MOZ, MORF, and HBO1; global coactivators p300 and CREB-binding protein; nuclear receptor coactivators SRC-1, ACTR, and TIF2; TATA-binding protein-associated factor TAF
II
250 and its homologs; and subunits of RNA polymerase III general factor TFIIIC. The acetylation and transcriptional functions of these HATs and the native complexes containing them (such as yeast SAGA, NuA4, and possibly analogous human complexes) are discussed. In addition, some of these HATs are also known to modify certain nonhistone transcription-related proteins, including high-mobility-group chromatin proteins, activators such as p53, coactivators, and general factors. Thus, we also detail these known factor acetyltransferase (FAT) substrates and the demonstrated or potential roles of their acetylation in transcriptional processes.
Thermophilic Fungi: Their Physiology and Enzymes
Authors: Maheshwari Ramesh , Bharadwaj Girish , Bhat Mahalingeshwara K.
Published: January 2003

Thermophilic fungi are a small assemblage in mycota that have a minimum temperature of growth at or above 20°C and a maximum temperature of growth extending up to 60 to 62°C. As the only representatives of eukaryotic organisms that can grow at temperatures above 45°C, the thermophilic fungi are valuable experimental systems for investigations of mechanisms that allow growth at moderately high temperature yet limit their growth beyond 60 to 62°C. Although widespread in terrestrial habitats, they have remained underexplored compared to thermophilic species of eubacteria and archaea. However, thermophilic fungi are potential sources of enzymes with scientific and commercial interests. This review, for the first time, compiles information on the physiology and enzymes of thermophilic fungi. Thermophilic fungi can be grown in minimal media with metabolic rates and growth yields comparable to those of mesophilic fungi. Studies of their growth kinetics, respiration, mixed-substrate utilization, nutrient uptake, and protein breakdown rate have provided some basic information not only on thermophilic fungi but also on filamentous fungi in general. Some species have the ability to grow at ambient temperatures if cultures are initiated with germinated spores or mycelial inoculum or if a nutritionally rich medium is used. Thermophilic fungi have a powerful ability to degrade polysaccharide constituents of biomass. The properties of their enzymes show differences not only among species but also among strains of the same species. Their extracellular enzymes display temperature optima for activity that are close to or above the optimum temperature for the growth of organism and, in general, are more heat stable than those of the mesophilic fungi. Some extracellular enzymes from thermophilic fungi are being produced commercially, and a few others have commercial prospects. Genes of thermophilic fungi encoding lipase, protease, xylanase, and cellulase have been cloned and overexpressed in heterologous fungi, and pure crystalline proteins have been obtained for elucidation of the mechanisms of their intrinsic thermostability and catalysis. By contrast, the thermal stability of the few intracellular enzymes that have been purified is comparable to or, in some cases, lower than that of enzymes from the mesophilic fungi. Although rigorous data are lacking, it appears that eukaryotic thermophily involves several mechanisms of stabilization of enzymes or optimization of their activity, with different mechanisms operating for different enzymes.
Molecular Genetics of Heterokaryon Incompatibility in Filamentous Ascomycetes
Authors: Saupe Sven J.
Published: January 2003

Filamentous fungi spontaneously undergo vegetative cell fusion events within but also between individuals. These cell fusions (anastomoses) lead to cytoplasmic mixing and to the formation of vegetative heterokaryons (i.e., cells containing different nuclear types). The viability of these heterokaryons is genetically controlled by specific loci termed het loci (for heterokaryon incompatibility). Heterokaryotic cells formed between individuals of unlike het genotypes undergo a characteristic cell death reaction or else are severely inhibited in their growth. The biological significance of this phenomenon remains a puzzle. Heterokaryon incompatibility genes have been proposed to represent a vegetative self/nonself recognition system preventing heterokaryon formation between unlike individuals to limit horizontal transfer of cytoplasmic infectious elements. Molecular characterization of het genes and of genes participating in the incompatibility reaction has been achieved for two ascomycetes, Neurospora crassa and Podospora anserina. These analyses have shown that het genes are diverse in sequence and do not belong to a gene family and that at least some of them perform cellular functions in addition to their role in incompatibility. Divergence between the different allelic forms of a het gene is generally extensive, but single-amino-acid differences can be sufficient to trigger incompatibility. In some instances het gene evolution appears to be driven by positive selection, which suggests that the het genes indeed represent recognition systems. However, work on nonallelic incompatibility systems in P. anserina suggests that incompatibility might represent an accidental activation of a cellular system controlling adaptation to starvation.
Programmed Death in Bacteria
Authors: Lewis Kim
Published: January 2003

Programmed cell death (PCD) in bacteria plays an important role in developmental processes, such as lysis of the mother cell during sporulation of Bacillus subtilis and lysis of vegetative cells in fruiting body formation of Myxococcus xanthus. The signal transduction pathway leading to autolysis of the mother cell includes the terminal sporulation sigma factor Eς
K
, which induces the synthesis of autolysins CwlC and CwlH. An activator of autolysin in this and other PCD processes is yet to be identified. Autolysis plays a role in genetic exchange in Streptococcus pneumoniae, and the gene for the major autolysin, lytA, is located in the same operon with recA. DNA from lysed cells is picked up by their neighbors and recombined into the chromosome by RecA. LytA requires an unknown activator controlled by a sensory kinase, VncS. Deletion of vncS inhibits autolysis and also decreases killing by unrelated antibiotics. This observation suggests that PCD in bacteria serves to eliminate damaged cells, similar to apoptosis of defective cells in metazoa. The presence of genes affecting survival without changing growth sensitivity to antibiotics (vncS, lytA, hipAB, sulA, and mar) indicates that bacteria are able to control their fate. Elimination of defective cells could limit the spread of a viral infection and donate nutrients to healthy kin cells. An altruistic suicide would be challenged by the appearance of asocial mutants without PCD and by the possibility of maladaptive total suicide in response to a uniformly present lethal factor or nutrient depletion. It is proposed that a low rate of mutation serves to decrease the probability that asocial mutants without PCD will take over the population. It is suggested that PCD is disabled in persistors, rare cells that are resistant to killing, to ensure population survival. It is suggested that lack of nutrients leads to the stringent response that suppresses PCD, producing a state of tolerance to antibiotics, allowing cells to discriminate between nutrient deprivation and unrepairable damage. High levels of persistors are apparently responsible for the extraordinary survival properties of bacterial biofilms, and genes affecting persistence appear to be promising targets for development of drugs aimed at eradicating recalcitrant infections. PCD in unicellular eukaryotes is also considered, including aging in Saccharomyces cerevisiae. Apoptosis-like elimination of defective cells in S. cerevisiae and protozoa suggests that all unicellular life forms evolved altruistic programmed death that serves a variety of useful functions.
Signal Peptide-Dependent Protein Transport in
Bacillus subtilis
: a Genome-Based Survey of the Secretome
Authors: Tjalsma Harold , Bolhuis Albert , Jongbloed Jan D. H. , Bron Sierd , van Dijl Jan Maarten
Published: January 2003

One of the most salient features of Bacillus subtilis and related bacilli is their natural capacity to secrete a variety of proteins into their environment, frequently to high concentrations. This has led to the commercial exploitation of bacilli as major “cell factories” for secreted enzymes. The recent sequencing of the genome of B. subtilis has provided major new impulse for analysis of the molecular mechanisms underlying protein secretion by this organism. Most importantly, the genome sequence has allowed predictions about the composition of the secretome, which includes both the pathways for protein transport and the secreted proteins. The present survey of the secretome describes four distinct pathways for protein export from the cytoplasm and approximately 300 proteins with the potential to be exported. By far the largest number of exported proteins are predicted to follow the major “Sec” pathway for protein secretion. In contrast, the twin-arginine translocation “Tat” pathway, a type IV prepilin-like export pathway for competence development, and ATP-binding cassette transporters can be regarded as “special-purpose” pathways, through which only a few proteins are transported. The properties of distinct classes of amino-terminal signal peptides, directing proteins into the various protein transport pathways, as well as the major components of each pathway are discussed. The predictions and comparisons in this review pinpoint important differences as well as similarities between protein transport systems in B. subtilis and other well-studied organisms, such as Escherichia coli and the yeast Saccharomyces cerevisiae. Thus, they may serve as a lead for future research and applications.
Resistance ofBacillusEndospores to Extreme Terrestrial and Extraterrestrial Environments
Authors: Nicholson Wayne L. , Munakata Nobuo , Horneck Gerda , Melosh Henry J. , Setlow Peter
Published: January 2003

Endospores of Bacillus spp., especially Bacillus subtilis, have served as experimental models for exploring the molecular mechanisms underlying the incredible longevity of spores and their resistance to environmental insults. In this review we summarize the molecular laboratory model of spore resistance mechanisms and attempt to use the model as a basis for exploration of the resistance of spores to environmental extremes both on Earth and during postulated interplanetary transfer through space as a result of natural impact processes.
Search and Discovery Strategies for Biotechnology: the Paradigm Shift
Authors: Bull Alan T. , Ward Alan C. , Goodfellow Michael
Published: January 2003

Profound changes are occurring in the strategies that biotechnology-based industries are deploying in the search for exploitable biology and to discover new products and develop new or improved processes. The advances that have been made in the past decade in areas such as combinatorial chemistry, combinatorial biosynthesis, metabolic pathway engineering, gene shuffling, and directed evolution of proteins have caused some companies to consider withdrawing from natural product screening. In this review we examine the paradigm shift from traditional biology to bioinformatics that is revolutionizing exploitable biology. We conclude that the reinvigorated means of detecting novel organisms, novel chemical structures, and novel biocatalytic activities will ensure that natural products will continue to be a primary resource for biotechnology. The paradigm shift has been driven by a convergence of complementary technologies, exemplified by DNA sequencing and amplification, genome sequencing and annotation, proteome analysis, and phenotypic inventorying, resulting in the establishment of huge databases that can be mined in order to generate useful knowledge such as the identity and characterization of organisms and the identity of biotechnology targets. Concurrently there have been major advances in understanding the extent of microbial diversity, how uncultured organisms might be grown, and how expression of the metabolic potential of microorganisms can be maximized. The integration of information from complementary databases presents a significant challenge. Such integration should facilitate answers to complex questions involving sequence, biochemical, physiological, taxonomic, and ecological information of the sort posed in exploitable biology. The paradigm shift which we discuss is not absolute in the sense that it will replace established microbiology; rather, it reinforces our view that innovative microbiology is essential for releasing the potential of microbial diversity for biotechnology penetration throughout industry. Various of these issues are considered with reference to deep-sea microbiology and biotechnology.
Lytic Cycle ofToxoplasma gondii
Authors: Black Michael W. , Boothroyd John C.
Published: January 2003

Toxoplasma gondii is an obligate intracellular pathogen within the phylum Apicomplexa. This protozoan parasite is one of the most widespread, with a broad host range including many birds and mammals and a geographic range that is nearly worldwide. While infection of healthy adults is usually relatively mild, serious disease can result in utero or when the host is immunocompromised. This sophisticated eukaryote has many specialized features that make it well suited to its intracellular lifestyle. In this review, we describe the current knowledge of how the asexual tachyzoite stage of Toxoplasma attaches to, invades, replicates in, and exits the host cell. Since this process is closely analogous to the way in which viruses reproduce, we refer to it as the Toxoplasma “lytic cycle.”
Bacteria in the Leaf Ecosystem with Emphasis onPseudomonas syringae—a Pathogen, Ice Nucleus, and Epiphyte
Authors: Hirano Susan S. , Upper Christen D.
Published: January 2003

The extremely large number of leaves produced by terrestrial and aquatic plants provide habitats for colonization by a diversity of microorganisms. This review focuses on the bacterial component of leaf microbial communities, with emphasis on Pseudomonas syringae—a species that participates in leaf ecosystems as a pathogen, ice nucleus, and epiphyte. Among the diversity of bacteria that colonize leaves, none has received wider attention than P. syringae, as it gained notoriety for being the first recombinant organism (Ice−P. syringae) to be deliberately introduced into the environment. We focus on P. syringae to illustrate the attractiveness and somewhat unique opportunities provided by leaf ecosystems for addressing fundamental questions of microbial population dynamics and mechanisms of plant-bacterium interactions. Leaf ecosystems are dynamic and ephemeral. The physical environment surrounding phyllosphere microbes changes continuously with daily cycles in temperature, radiation, relative humidity, wind velocity, and leaf wetness. Slightly longer-term changes occur as weather systems pass. Seasonal climatic changes impose still a longer cycle. The physical and physiological characteristics of leaves change as they expand, mature, and senesce and as host phenology changes. Many of these factors influence the development of populations of P. syringae upon populations of leaves. P. syringae was first studied for its ability to cause disease on plants. However, disease causation is but one aspect of its life strategy. The bacterium can be found in association with healthy leaves, growing and surviving for many generations on the surfaces of leaves as an epiphyte. A number of genes and traits have been identified that contribute to the fitness of P. syringae in the phyllosphere. While still in their infancy, such research efforts demonstrate that the P. syringae-leaf ecosystem is a particularly attractive system with which to bridge the gap between what is known about the molecular biology of genes linked to pathogenicity and the ecology and epidemiology of associated diseases as they occur in natural settings, the field.
Probiotic Bacteria as Biological Control Agents in Aquaculture
Authors: Verschuere Laurent , Rombaut Geert , Sorgeloos Patrick , Verstraete Willy
Published: January 2003

There is an urgent need in aquaculture to develop microbial control strategies, since disease outbreaks are recognized as important constraints to aquaculture production and trade and since the development of antibiotic resistance has become a matter of growing concern. One of the alternatives to antimicrobials in disease control could be the use of probiotic bacteria as microbial control agents. This review describes the state of the art of probiotic research in the culture of fish, crustaceans, mollusks, and live food, with an evaluation of the results obtained so far. A new definition of probiotics, also applicable to aquatic environments, is proposed, and a detailed description is given of their possible modes of action, i.e., production of compounds that are inhibitory toward pathogens, competition with harmful microorganisms for nutrients and energy, competition with deleterious species for adhesion sites, enhancement of the immune response of the animal, improvement of water quality, and interaction with phytoplankton. A rationale is proposed for the multistep and multidisciplinary process required for the development of effective and safe probiotics for commercial application in aquaculture. Finally, directions for further research are discussed.
Molecular Properties of Bacterial Multidrug Transporters
Authors: Putman Monique , van Veen Hendrik W. , Konings Wil N.
Published: January 2003

One of the mechanisms that bacteria utilize to evade the toxic effects of antibiotics is the active extrusion of structurally unrelated drugs from the cell. Both intrinsic and acquired multidrug transporters play an important role in antibiotic resistance of several pathogens, including Neisseria gonorrhoeae, Mycobacterium tuberculosis, Staphylococcus aureus, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Vibrio cholerae. Detailed knowledge of the molecular basis of drug recognition and transport by multidrug transport systems is required for the development of new antibiotics that are not extruded or of inhibitors which block the multidrug transporter and allow traditional antibiotics to be effective. This review gives an extensive overview of the currently known multidrug transporters in bacteria. Based on energetics and structural characteristics, the bacterial multidrug transporters can be classified into five distinct families. Functional reconstitution in liposomes of purified multidrug transport proteins from four families revealed that these proteins are capable of mediating the export of structurally unrelated drugs independent of accessory proteins or cytoplasmic components. On the basis of (i) mutations that affect the activity or the substrate specificity of multidrug transporters and (ii) the three-dimensional structure of the drug-binding domain of the regulatory protein BmrR, the substrate-binding site for cationic drugs is predicted to consist of a hydrophobic pocket with a buried negatively charged residue that interacts electrostatically with the positively charged substrate. The aromatic and hydrophobic amino acid residues which form the drug-binding pocket impose restrictions on the shape and size of the substrates. Kinetic analysis of drug transport by multidrug transporters provided evidence that these proteins may contain multiple substrate-binding sites.
Coupling of Flagellar Gene Expression to Flagellar Assembly in
Salmonella enterica
Serovar Typhimurium and
Escherichia coli
Authors: Chilcott Gavin S. , Hughes Kelly T.
Published: January 2003

How do organisms assess the degree of completion of a large structure, especially an extracellular structure such as a flagellum? Bacteria can do this. Mutants that lack key components needed early in assembly fail to express proteins that would normally be added at later assembly stages. In some cases, the regulatory circuitry is able to sense completion of structures beyond the cell surface, such as completion of the external hook structure. In Salmonella and Escherichia coli, regulation occurs at both transcriptional and posttranscriptional levels. One transcriptional regulatory mechanism involves a regulatory protein, FlgM, that escapes from the cell (and thus can no longer act) through a complete flagellum and is held inside when the structure has not reached a later stage of completion. FlgM prevents late flagellar gene transcription by binding the flagellum-specific transcription factor ς
28
. FlgM is itself regulated in response to the assembly of an incomplete flagellum known as the hook-basal body intermediate structure. Upon completion of the hook-basal body structure, FlgM is exported through this structure out of the cell. Inhibition of ς
28
-dependent transcription is relieved, and genes required for the later assembly stages are expressed, allowing completion of the flagellar organelle. Distinct posttranscriptional regulatory mechanisms occur in response to assembly of the flagellar type III secretion apparatus and of ring structures in the peptidoglycan and lipopolysaccharide layers. The entire flagellar regulatory pathway is regulated in response to environmental cues. Cell cycle control and flagellar development are codependent. We discuss how all these levels of regulation ensure efficient assembly of the flagellum in response to environmental stimuli.
Cytopathogenesis and Inhibition of Host Gene Expression by RNA Viruses
Authors: Lyles Douglas S.
Published: January 2003

Many viruses interfere with host cell function in ways that are harmful or pathological. This often results in changes in cell morphology referred to as cytopathic effects. However, pathogenesis of virus infections also involves inhibition of host cell gene expression. Thus the term “cytopathogenesis,” or pathogenesis at the cellular level, is meant to be broader than the term “cytopathic effects” and includes other cellular changes that contribute to viral pathogenesis in addition to those changes that are visible at the microscopic level. The goal of this review is to place recent work on the inhibition of host gene expression by RNA viruses in the context of the pathogenesis of virus infections. Three different RNA virus families, picornaviruses, influenza viruses, and rhabdoviruses, are used to illustrate common principles involved in cytopathogenesis. These examples were chosen because viral gene products responsible for inhibiting host gene expression have been identified, as have some of the molecular targets of the host. The argument is made that the role of the virus-induced inhibition of host gene expression is to inhibit the host antiviral response, such as the response to double-stranded RNA. Viral cytopathogenesis is presented as a balance between the host antiviral response and the ability of viruses to inhibit that response through the overall inhibition of host gene expression. This balance is a major determinant of viral tissue tropism in infections of intact animals.
Positive and Negative Aspects of the Human Immunodeficiency Virus Protease: Development of Inhibitors versus Its Role in AIDS Pathogenesis
Authors: Ikuta Kazuyoshi , Suzuki Satoko , Horikoshi Haruko , Mukai Tetsu , Luftig Ronald B.
Published: January 2003

In this review we summarize multiple aspects of the human immunodeficiency virus (HIV) protease from both structural and functional viewpoints. After an introductory overview, we provide an up-to-date status report on protease inhibitors (PI). This proceeds from a discussion of PI structural design, to how PI are optimally utilized in highly active antiretroviral triple therapy (one PI along with two reverse transcriptase inhibitors), the emergence of PI resistance, and the natural role of secretory leukocyte PI. Then we switch to another focus: the interaction of HIV protease with other genes in acute and persistent infection, which in turn may have an effect on AIDS pathogenesis. We conclude with a discussion on future directions in HIV treatment, involving multiple-target anti-HIV therapy, vaccine development, and novel reactivation-inhibitory reagents.
Origin and Evolution of the Mitochondrial Proteome
Authors: Kurland C. G. , Andersson S. G. E.
Published: January 2003

The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral α-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from α-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the α-proteobacterial endosymbiont is unclear, but there is no indication that it was an autotroph. There are no indications of a specific α-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph.
Proteases for Cell Suicide: Functions and Regulation of Caspases
Authors: Chang Howard Y. , Yang Xiaolu
Published: January 2003

Caspases are a large family of evolutionarily conserved proteases found from Caenorhabditis elegans to humans. Although the first caspase was identified as a processing enzyme for interleukin-1β, genetic and biochemical data have converged to reveal that many caspases are key mediators of apoptosis, the intrinsic cell suicide program essential for development and tissue homeostasis. Each caspase is a cysteine aspartase; it employs a nucleophilic cysteine in its active site to cleave aspartic acid peptide bonds within proteins. Caspases are synthesized as inactive precursors termed procaspases; proteolytic processing of procaspase generates the tetrameric active caspase enzyme, composed of two repeating heterotypic subunits. Based on kinetic data, substrate specificity, and procaspase structure, caspases have been conceptually divided into initiators and effectors. Initiator caspases activate effector caspases in response to specific cell death signals, and effector caspases cleave various cellular proteins to trigger apoptosis. Adapter protein-mediated oligomerization of procaspases is now recognized as a universal mechanism of initiator caspase activation and underlies the control of both cell surface death receptor and mitochondrial cytochrome c-Apaf-1 apoptosis pathways. Caspase substrates have bene identified that induce each of the classic features of apoptosis, including membrane blebbing, cell body shrinkage, and DNA fragmentation. Mice deficient for caspase genes have highlighted tissue- and signal-specific pathways for apoptosis and demonstrated an independent function for caspase-1 and -11 in cytokine processing. Dysregulation of caspases features prominently in many human diseases, including cancer, autoimmunity, and neurodegenerative disorders, and increasing evidence shows that altering caspase activity can confer therapeutic benefits.
Microbial Biofilms: from Ecology to Molecular Genetics
Authors: Davey Mary Ellen , O'toole George A.
Published: January 2003

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.
A TABULAR LEARNING STRUCTURE WITH AN ADAPTABLE k-d TREE FOR RELAXATION OF THE CURSE OF DIMENSIONALITY
Authors: CHENG YI-HSUN ETHAN , LIN CHUN-SHIN
Published: January 2003

Memory-based learning schemes are characterized by their memorization of observed events. A memory-based learning scheme either memorizes the collected data directly or reorganizes such information and stores it distributively into a tabular memory. For the tabular type, the system requires a training process to determine the contents of the associative memory. This training process helps filter out zero-mean noise. Since the stored data are associated to pre-assigned input locations, memory management and data retrieval are easier and more efficient. Despite these merits, a drawback of tabular schemes is the difficulty in applying it to high-dimensional problems due to the curse of dimensionality. As the input dimensionality increases, the number of quantized elements in the input space increases at an exponential rate and that causes a huge demand of memory. In this paper, a dynamic tabular structure is proposed for possible relaxation of such a demand. The memorized data are organized as part of a k-d tree. Nodes in the tree, called vertices, correspond to some regularly assigned input points. Memory resource is allocated only at locations where it is needed. Being able to easily compute the vertex positions helps reduce the searching cost in data retrieval. In addition, the learning process is able to expand the tree structure into one covering the problem domain. With memory allocated based on demand, memory consumption becomes closely related to task complexity instead of input dimensionality, and is minimized. Algorithms for structure construction and training are presented in this paper. Simulation results demonstrate that the memory can be efficiently utilized. The developed scheme offers a solution for high-dimensional learning problems with a manageable size of effective input domain.
POSE ESTIMATION IN AUTOMATED VISUAL INSPECTION USING ANN
Authors: HATI S. , SENGUPTA S.
Published: January 2003

In this paper, we present an accurate and robust pose estimator of rigid, polyhedral objects, based on Artificial Neural Networks (ANN), as suitable for Automated Visual Inspection (AVI) applications. The estimator is novel in the sense that it is trained with different poses of the objects having dimensional deviations within its tolerance range and is therefore robust with respect to within tolerance dimensional errors. The estimation accuracy is scalable and our computer simulation experiments in the existing configurations of ANNs have shown an accuracy better than 4% of the placement error. The ANN based pose estimator offers several advantages over the classical implementations.
INCREMENTAL LEARNING IN BIOLOGICAL AND MACHINE LEARNING SYSTEMS
Authors: CHALUP STEPHAN K.
Published: January 2003

Incremental learning concepts are reviewed in machine learning and neurobiology. They are identified in evolution, neurodevelopment and learning. A timeline of qualitative axon, neuron and synapse development summarizes the review on neurodevelopment. A discussion of experimental results on data incremental learning with recurrent artificial neural networks reveals that incremental learning often seems to be more efficient or powerful than standard learning but can produce unexpected side effects. A characterization of incremental learning is proposed which takes the elaborated biological and machine learning concepts into account.
DECISION MAKING USING HYBRID ROUGH SETS AND NEURAL NETWORKS
Authors: HASSAN YASSER , TAZAKI EIICHIRO , EGAWA SHIN , SUYAMA KAZUHO
Published: January 2003

A methodology for using rough sets theory for preference modeling in decision problem is presented in this paper. We will introduce a new method where neural network systems and rough sets theory are completely integrated into a hybrid system and are used cooperatively for decision and classification support. At the first glance, the two methods we discuss have not much in common. But, in spite of the differences between them, it is interesting to try to incorporate both into one combined system, and apply it in the building of a decision support system.
USING WEIGHTED FIXED NEURAL NETWORKS FOR UNSUPERVISED FUZZY CLUSTERING
Authors: HAMID MUHAMMED HAMED
Published: January 2003

A novel algorithm for unsupervised fuzzy clustering is introduced. The algorithm uses a so-called Weighted Fixed Neural Network (WFNN) to store important and useful information about the topological relations in a given data set. The algorithm produces a weighted connected net, of weighted nodes connected by weighted edges, which reflects and preserves the topology of the input data set. The weights of the nodes and the edges in the resulting net are proportional to the local densities of data samples in input space. The connectedness of the net can be changed, and the higher the connectedness of the net is chosen, the fuzzier the system becomes. The new algorithm is computationally efficient when compared to other existing methods for clustering multi-dimensional data, such as color images.
RECONFIGURABLE CONTROL SYSTEM DESIGN FOR FAULT DIAGNOSIS AND ACCOMMODATION
Authors: HO LIANG-WEI , YEN GARY G.
Published: January 2003

The growing demand in system reliability and survivability under failures has urged ever-increasing research effort on the development of fault diagnosis and accommodation. In this paper, the on-line fault tolerant control problem for dynamic systems under unanticipated failures is investigated from a realistic point of view without any specific assumption on the type of system dynamical structure or failure scenarios. The sufficient conditions for system on-line stability under catastrophic failures have been derived using the discrete-time Lyapunov stability theory. Based upon the existing control theory and the modern computational intelligence techniques, an on-line fault accommodation control strategy is proposed to deal with the desired trajectory-tracking problems for systems suffering from various unknown and unanticipated catastrophic component failures. Theoretical analysis indicates that the control problem of interest can be solved on-line without a complete realization of the unknown failure dynamics provided an on-line estimator satisfies certain conditions. Through the on-line estimator, effective control signals to accommodate the dynamic failures can be computed using only the partially available information of the faults. Several on-line simulation studies have been presented to demonstrate the effectiveness of the proposed strategy. To investigate the feasibility of using the developed technique for unanticipated fault accommodation in hardware under the real-time environment, an on-line fault tolerant control test bed has been constructed to validate the proposed technology. Both on-line simulations and the real-time experiment show encouraging results and promising futures of on-line real-time fault tolerant control based solely upon insufficient information of the system dynamics and the failure dynamics.
EXPONENTIAL INTEGRABILITY FOR IMAGES OF ORNSTEIN–UHLENBECK OPERATORS ACTING ON CYLINDER FUNCTIONS ON LOOP SPACES
Authors: GONG FUZHOU
Published: January 2003

Let E be the loop space over a compact connected Riemannian manifold with a torsion skew symmetric (TSS) connection. Let L be the Ornstein–Uhlenbeck (O-U) operator on the loop space E, and f be a cylinder function on E. We first extend the expression of Lf, proved by Enchev and Stroock for the Levi–Cività connection, to a general TSS connection, and then prove that if [Formula: see text], ε |Lf|2 is exponential integrable for some constant ε := ε (f)>0.
MARKOV MODELS OF LITERARY STYLE FOR AUTHORSHIP IDENTIFICATION
Authors: RAND WILLIAM
Published: January 2003

The author introduces a statistical model of literary style that allows for the authorship question to be examined. This model uses Markov modeling to examine underlying patterns in pieces of literature. Different methods for comparing these models are examined. The methods are then applied to an experiment involving the authorship of 16th century sonnets. Finally suggestions for improving on this technique are discussed.
AN APPROACH TO EXPLAIN NEURAL NETWORKS USING SYMBOLIC ALGORITHMS
Authors: MILARÉ CLAUDIA R. , DE L. F. DE CARVALHO ANDRÉ C. P. , MONARD MARIA C.
Published: January 2003

Although Artificial Neural Networks have been satisfactorily employed in several problems, such as clustering, pattern recognition, dynamic systems control and prediction, they still suffer from significant limitations. One of them is that the induced concept representation is not usually comprehensible to humans. Several techniques have been suggested to extract meaningful knowledge from trained networks. This paper proposes the use of symbolic learning algorithms, commonly used by the Machine Learning community, such as C4.5, C4.5rules and CN2, to extract symbolic representations from trained networks. The approach proposed is similar to that used by the Trepan algorithm, which extracts symbolic representations, expressed as decision trees, from trained networks. Experimental results are presented and discussed in order to compare the knowledge extracted from Artificial Neural Networks using the proposed approach and the Trepan approach. Results are compared regarding two aspects: fidelity and comprehensibility.
SEGMENTATION VERSUS NON-SEGMENTATION BASED NEURAL TECHNIQUES FOR CURSIVE WORD RECOGNITION: AN EXPERIMENTAL ANALYSIS
Authors: FAN XIAOLONG , VERMA BRIJESH
Published: January 2003

This paper presents a comparative analysis of segmentation and non-segmentation based techniques for cursive handwritten word recognition. In our segmentation based technique, every word is segmented into characters, the chain code features are extracted from segmented characters, the features are fed to neural network classifier and finally the words are constructed using a string compare algorithm. In our non-segmentation based technique, the chain code features are extracted directly from words and the words are fed to a neural network classifier to classify them into word classes. To make a fair comparison, a CEDAR benchmark database is used, and the parameters such as the number of words, thresholding, resizing, feature extraction techniques, etc. are kept same for both the techniques. The experimental results and analysis show that the non-segmentation technique achieves higher recognition rate than the segmentation based technique.
KNOWLEDGE ACQUISITION AND STRATEGY GENERATION WITH LG WARGAMING TOOLS
Authors: STILMAN BORIS , YAKHNIS VLADIMIR , UMANSKIY OLEG
Published: January 2003

This paper describes a wargaming software kit, which includes two software tools, LG-CONSTRUCTOR and LG-STRATEGIST. Both are based on the new type of game theory called Linguistic Geometry (LG) for solving higher-dimensional Abstract Board Games (ABG). LG-CONSTRUCTOR will supply warfighters at all levels with the patterns of war games. With LG-CONSTRUCTOR, a warfighter will be able to consider and visualize the most viable patterns and quickly convert them into the LG hypergame, most adequate to the current mission. The adequacy of construction will be tested on the "fly" by playing and re-playing semi-finished hypergames. Employing this hypergame, LG-STRATEGIST will generate the best strategies for the military operation for all the contesting sides of the conflict. It will plan the entire operation, assess possible courses of actions (COA) for all sides, select counteractions, control operation by re-planning in real time, and play and re-play various "what-if" scenarios.
NO FREE LUNCHES IN MULTI-AGENT SYSTEMS
Authors: JOHANSSON STEFAN J.
Published: January 2003

We introduce the notion of Characteristic Distributions which is a way of representing information about the payoffs of different behaviors in a Multi-Agent System. We discuss how they can be used to simplify and structure the analysis of strategies and prove the existence of optimal environments, given a certain behavior, and that all behaviors payoff equally, when taken over all possible environments (no free lunch theorem for strategies).
TOWARDS A HIGH RELIABILITY OF THE PCR AMPLIFICATION PROCESS IN DNA COMPUTING
Authors: NAKATSUGAWA MASASHI , KASHIWAMURA SATOSHI , OHUCHI AZUMA , YAMAMOTO MASAHITO , SHIBA TOSHIKAZU
Published: January 2003

Polymerase Chain Reaction (PCR) is the most important experimental technique in DNA computing. When a concentration of DNA sequence is too small to investigate, PCR amplifies the DNA sequence by the addition of a polymerase. PCR is frequently used in DNA computing, because the calculation result is usually represented by a small concentration of DNA sequence. Therefore, PCR has a crucial influence on the calculation result. The reliability of PCR needs to be improved for DNA computing. In this paper, the reliability of PCR is defined by the reproducibility of the amplified concentration of DNA sequence. The PCR protocol is adjusted to improve the reliability. Quality Engineering efficiently supports this adjustment.
CONSTRUCTION AND ANALYSIS OF STOCK MARKET MODEL USING ADG: AUTOMATICALLY DEFINED GROUPS
Authors: HARA AKIRA , NAGAO TOMOHARU
Published: January 2003

In real market, the squares of stock price change rates have high autocorrelation, and the change rates show high peak and fat tail distribution. With the aim of analyzing the mechanism of the stock price change, we construct an artificial stock market composed of multiple agents whose investment strategies are represented by tree-shaped programs. The market is optimized by using a Genetic Programming so that the change of its stock price resembles that of "real" stock market statistically. In order to perform an efficient optimization and to analyze agents' behavior easily, we use ADG; Automatically Defined Groups previously proposed by authors. We show experimentally that complex changes such as real market appear in the proposed artificial market. Moreover we analyze the interaction of agents which causes realistic stock price changes.
LOCAL SEARCH BY CONCENTRATION-CONTROLLED DNA COMPUTING
Authors: YAMAMOTO MASAHITO , KAWAZOE YUMI , OHUCHI AZUMA , KAMEDA ATSUSHI , MATSUURA NOBUO , SHIBA TOSHIKAZU
Published: January 2003

Concentration-controlled DNA computing is presented for accomplishing a local search for the solution of a shortest path problem. In this method, the concentrations of DNA representing edges are determined according to the costs on edges, and then the hybridization process is performed. Since the concentrations of hopeless candidate solutions tend to be small after the hybridization process, a local search by concentration-controlled DNA computing is a promising approach. In order to discuss about the relationship between given costs on edges in the graph and concentrations of generated DNA paths, a simulation model of the hybridization process is used and the results of a laboratory experiment are shown.
MACROSCOPIC QUANTITATIVE OBSERVATION OF MULTI-ROBOT BEHAVIOR
Authors: KINOSHITA M. , YOKOI HIROSHI , KAKAZU YUKINORI , WATANABE MICHIKO , KAWAKAMI TAKASHI
Published: January 2003

In observing behavior of multiple autonomous robots, a microscopic observation expressed by dynamic equations is usually used. However, it is very difficult to estimate behavior of robots or mutual interactions among them in real time. Furthermore, it is hard to realize the observed system by taking consideration in all the factors of the system. On the other hand, a macroscopic observation defined by state equations is efficient for recognizing behavior of multiple robots. In this study, a quantitative observation approach is proposed on behavior of multiple robots. This approach introduces macroscopic state quantities in thermodynamics into expression of the multiple robots system. The advantage of this approach is that observation on the behavior of autonomous robots in real world can be mapped to characteristic quantities in another conceptual state space. At first, the state quantities of multiple robots system are defined and their physical meaning is discussed regarding it as quantitative observation of multiple robots. The macroscopic state quantities in thermodynamics, such as temperature, pressure and entropy, are introduced into mobile robots system. Each mobile robot is regarded as a particle in term of thermodynamic systems. Experiments show that the states of robots system can be classified from a viewpoint of the macroscopic state quantities in thermodynamics. This verifies that the macroscopic quantitative observation is efficient and applicable to controlling multiple robots system.