bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

SUMMARY

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

SUMMARY
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

SUMMARYIn 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

SUMMARYThe 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

SUMMARYCaspases 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

SUMMARYBiofilms 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.
Dimerization of Incomplete Cuboidal Mo3S4 Units via α,ω-Dicarboxylates, and Their Supramolecular Architectures through Intermolecular S···S and C–H···S Interactions
Authors: Tang Yanhong , Yao Yuangen , Wu Ling , Qin Yeyan , Kang Yao , Li Zhaoji 
Published: January 2003

Abstract
Two novel hexanuclear molybdenum cluster compounds [Mo3S4(dtp)3(L)]2[η2-μ-OOC(CH2)nCOO-μ-η2] (n = 4, L = DMF for 1; n = 3, L = DMSO for 2) have been synthesized by reaction of Mo3S4(dtp)3(ClCH2COO)(Py) with α,ω-dicarboxylates. Intermolecular S···S and C–H···S interactions are observed, yielding two different two-dimensional supramolecular structures.
A minimal axisymmetric hurricane model
Authors: Mai Nguyen Chi , Smith Roger K. , Zhu Hongyan , Ulrich Wolfgang 
Published: January 2003

AbstractSolutions of an axisymmetric version of the minimal three‐dimensional numerical model of a tropical cyclone developed by Zhu et al. (2001) are described and compared with those of the three‐dimensional model. Vortex evolution is similar in the two models during the early stages of intensification, but the period of rapid intensification occurs earlier in the axisymmetric model due to the higher effective resolution obtained using a staggered grid. There are marked differences at later times, when, in the three‐dimensional model, asymmetric structures develop. The findings are compared with those of an earlier study by Anthes (1972).The axisymmetric model is used to investigate certain fundamental aspects of tropical‐cyclone dynamics, including the emergence of a region of supergradient winds in the boundary layer and the evolution of regions satisfying necessary conditions for inertial and barotropic instability. Supergradient winds develop in the boundary layer within a radius of about 100 km of the vortex axis at an early stage of evolution and appear to be a natural feature of the vortex boundary layer. The development of flow regions satisfying necessary conditions for inertial and barotropic instability occur later, and may be attributed inter alia to the upward transfer of air with relatively high angular momentum, from the boundary layer to the middle and upper layers, by the secondary circulation of the vortex, and the downward transfer of air with relatively low angular momentum to the middle layer. A linear analysis of a two‐layer slab‐symmetric flow suggests why inertial instability does not occur in the axisymmetric model. Barotropic instability does not appear to be the mechanism responsible for the growth of asymmetries in the calculations using the three‐dimensional version of the model. Copyright © 2002 Royal Meteorological Society.
Order‐based fitness functions for genetic algorithms applied to relevance feedback
Authors: López‐Pujalte Cristina , Guerrero‐Bote Vicente P. , de Moya‐Anegón Félix 
Published: January 2003

AbstractRecently there have been appearing new applications of genetic algorithms to information retrieval, most of them specifically to relevance feedback. The evolution of the possible solutions are guided by fitness functions that are designed as measures of the goodness of the solutions. These functions are naturally the key to achieving a reasonable improvement, and which function is chosen most distinguishes one experiment from another. In previous work, we found that, among the functions implemented in the literature, the ones that yield the best results are those that take into account not only when documents are retrieved, but also the order in which they are retrieved. Here, we therefore evaluate the efficacy of a genetic algorithm with various order‐based fitness functions for relevance feedback (some of them of our own design), and compare the results with the Ide dec‐hi method, one of the best traditional methods.
A profile of faculty reading and information‐use behaviors on the cusp of the electronic age
Authors: Belefant‐Miller Helen , King Donald W. 
Published: January 2003

AbstractThe majority of a university faculty's work deals with information or knowledge—finding, getting, reading, and using it. We analyzed the demographic portion of a library use survey given to faculty and staff of the University of Tennessee at Knoxville (UTK) to obtain a profile of information‐related activities carried out by university faculty. Journal articles were the predominant document type that faculty both read and authored. Faculty averaged 4.2 journal subscriptions per person, of which 84% were paid for personally. Twenty‐five percent of the faculty had obtained some funds for information products and of those funded, the median amount provided was $500. Faculty spent 24 minutes per day using e‐mail and 78 minutes per week using non‐e‐mail computer network. Faculty reported publishing 3.0 journal articles per year and 31% of the faculty had won an award for professional contributions in the previous 2 years.
Informational environments: Organizational contexts of online information use
Authors: Lamb Roberta , King John Leslie , Kling Rob 
Published: January 2003

AbstractBefore the Web, the story of online information services was largely one of over‐estimates and unmet expectations. This study examines sustained use and non‐use of online services within organizations in a way that overcomes limitations of the traditional approaches that repeatedly led to exuberant usage projections. By adopting an open‐systems view, we see that firms in highly technical and highly institutional environments have many more incentives to gather data and go online than do firms in low‐tech, unregulated industries. But firms make important choices about partnering and outsourcing that can shift informational activities across organizational boundaries. Our analysis focuses on the informational environments of firms in three industries: law, real estate and biotech/pharmaceuticals. This environmental model provides richer conceptualizations about the use of information and communication technologies, including Internet technologies, and better projections about future use. In support of our analysis, we briefly discuss insights from an ongoing intranets study informed by an informational environments perspective.
NLPIR: A theoretical framework for applying natural language processing to information retrieval
Authors: Zhou Lina , Zhang Dongsong 
Published: January 2003

AbstractThe role of information retrieval (IR) in support of decision making and knowledge management has become increasingly significant. Confronted by various problems in traditional keyword‐based IR, many researchers have been investigating the potential of natural language processing (NLP) technologies. Despite widespread application of NLP in IR and high expectations that NLP can address the problems of traditional IR, research and development of an NLP component for an IR system still lacks support and guidance from a cohesive framework. In this paper, we propose a theoretical framework called NLPIR that aims at integrating NLP into IR and at generalizing broad application of NLP in IR. Some existing NLP techniques are described to validate the framework, which not only can be applied to current research, but is also envisioned to support future research and development in IR that involve NLP.
Maillard reactions and increased enzyme inactivation during oligosaccharide synthesis by a hyperthermophilic glycosidase
Authors: Bruins M. E. , Van Hellemond E. W. , Janssen A. E. M. , Boom R. M. 
Published: January 2003

AbstractThe thermostable Pyrococcus furiosus β‐glycosidase was used for oligosaccharide production from lactose in a kinetically controlled reaction. Our experiments showed that higher temperatures are beneficial for the absolute as well as relative oligosaccharide yield. However, at reaction temperatures of 80°C and higher, the inactivation rate of the enzyme in the presence of sugars was increased by a factor of 2 compared to the inactivation rate in the absence of sugars. This increased enzyme inactivation was caused by the occurrence of Maillard reactions between the sugar and the enzyme. The browning of our reaction mixture due to Maillard reactions was modeled by a cascade of a zeroth‐ and first‐order reaction and related to enzyme inactivation. From these results we conclude that modification of only a small number of amino groups already gives complete inactivation of the enzyme. © 2003 Wiley Periodicals. Biotechnol Bioeng 81:546–552, 2003.
Simulation of growth and detachment in biofilm systems under defined hydrodynamic conditions
Authors: Horn Harald , Reiff Helmut , Morgenroth Eberhard 
Published: January 2003

AbstractDetachment from biofilms was evaluated using a mixed culture biofilm grown on primary wastewater in a tube reactor. The growth of biofilms and the detachment of biomass from biofilms are strongly influenced by hydrodynamic conditions. In a long‐term study, three biofilms were cultivated in a biofilm tube reactor. The conducted experiments of biofilm growth and detachment can be divided into three phases: 1) an exponential phase with a rapid increase of the biofilm thickness, 2) a quasi‐steady‐state with spontaneous fluctuation of the biofilm thickness between 500 and 1,200 μm in the investigated biofilm systems, and 3) a washout experiment with increased shear stress in three to four steps after several weeks of quasi‐steady‐state. Whereas the biofilm thickness during the homogeneous growth phase can be regarded constant throughout the reactor, it was found to be very heterogeneous during the quasi‐steady‐state and the washout experiments. Growth and detachment during all three phases was simulated with the same one‐dimensional biofilm model. For each of the three phases, a different detachment rate model was used. During the homogeneous growth phase, detachment was modeled proportional to the biofilm growth rate. During the quasi‐steady‐state phase, detachment was described by random detachment events assuming a base biofilm thickness. Finally, the washout experiment was simulated with detachment being a function of the biofilm thickness before the increase of the shear stress. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 607–617, 2003.
Anisotropic stretch‐induced hypertrophy in neonatal ventricular myocytes micropatterned on deformable elastomers
Authors: Gopalan Sindhu M. , Flaim Chris , Bhatia Sangeeta N. , Hoshijima Masahiko , Knoell Ralph , Chien Kenneth R. , Omens Jeffrey H. , McCulloch Andrew D. 
Published: January 2003

AbstractBecause cell shape and alignment, cell–matrix adhesion, and cell–cell contact can all affect growth, and because mechanical strains in vivo are multiaxial and anisotropic, we developed an in vitro system for engineering aligned, rod‐shaped, neonatal cardiac myocyte cultures. Photolithographic and microfluidic techniques were used to micropattern extracellular matrices in parallel lines on deformable silicone elastomers. Confluent, elongated, aligned myocytes were produced by varying the micropattern line width and collagen density. An elliptical cell stretcher applied 2:1 anisotropic strain statically to the elastic substrate, with the axis of greatest stretch (10%) either parallel or transverse to the myofibrils. After 24 h, the principal strain parallel to myocytes did not significantly alter myofibril accumulation or expression of atrial natriuretic factor (ANF), connexin‐43 (Cx‐43), or N‐cadherin (by indirect immunofluorescent antibody labeling and immunoblotting) compared with unstretched controls. In contrast, 10% transverse principal strain resulted in continuous staining of actin filaments (rhodamine phalloidin); increased immunofluorescent labeling of ANF, Cx‐43, and N‐cadherin; and upregulation of protein signal intensity by western blotting. By using microfabrication and microfluidics to control cell shape and alignment on an elastic substrate, we found greater effects for transverse than for longitudinal stretch in regulating sarcomere organization, hypertrophy, and cell‐to‐cell junctions. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 578–587, 2003.