bluuebunny/crossref_metadata_2025 huggingface dataset:
Linking perceptions of neighbourhood to health in Hamilton, Canada
Authors: Wilson K , Elliott S , Law M , Eyles J , Jerrett M , Keller-Olaman S
Published: February 2004

Study objective:To investigate the association between perceptions of neighbourhood physical and social characteristics and three health outcomes (self assessed health status, chronic conditions, and emotional distress).

Design:Cross sectional survey data analysed in small neighbourhoods.

Setting:Hamilton, Ontario, Canada, a medium sized industrial city, located at the western end of Lake Ontario (population at the time of the study about 380 000).

Participants:Random sample of 1504 adults aged 18 years and older residing in four contrasting neighbourhoods.

Main results:Significant differences across the four neighbourhoods are apparent in self assessed health status and emotional distress, but not in chronic conditions. Neighbourhoods with lower SES reported poorer health and more emotional distress. Perceptions of the physical environment dominated social concerns in all neighbourhoods. For all three health outcomes, individual risk factors followed expectations, with measures of poverty, age, and lifestyle all significantly associated with poor health outcomes. Physical environmental problems were positively and significantly associated with poor physical and emotional health. Specifically, people reporting they dislike aspects of their neighbourhood’s physical environment are 1.5 times more likely to report chronic health conditions (OR 1.56, 95% CI 1.19 to 2.05), while those reporting physical likes with their neighbourhood are less likely to report fair/poor health (OR 0.50, 95% CI 0.28 to 0.90) or emotional distress (OR 0.45, 95% CI 0.26 to 0.80).

Conclusions:These results demonstrate the importance of neighbourhood perceptions as a determinant of health, as well as conventional factors such as low income, lifestyle, and age. The dominance of physical environmental concerns may have arisen from the industrial nature of Hamilton, but this result merits further investigation.
Modelling potential responses to severe acute respiratory syndrome in Japan: the role of initial attack size, precaution, and quarantine
Authors: Nishiura H , Patanarapelert K , Sriprom M , Sarakorn W , Sriyab S , Ming Tang I
Published: February 2004

Background:There has been an outbreak of the severe acute respiratory syndrome (SARS) worldwide. With the use of detailed epidemiological data from other countries, this article describes the possible reason for the SARS epidemic not appearing in Japan, and simulates the impact of different control strategies that can break the transmission cycle of SARS associated coronavirus.

Method:Mathematical modelling is used for predicting the epidemiological outcome and simultaneously for evaluating the effect of interventions on SARS. The study estimates the initial attack size that would result in failed invasion. Three different interventions have been incorporated into the public health response policies; precautionary public health measures, isolation of infected people, and quarantine of exposed humans.

Results:The maximum number of humans newly infected could be roughly estimated on the basis of the initial attack size, using simple formulas. It is seen that the introduction of only a few cases into certain communities would not lead easily to an epidemic. The possible trajectories of SARS epidemic depend on the levels of public health interventions as quarantine and precautionary public health measures greatly affected the transmissibility of the disease. It is shown that there exist threshold levels of interventions at which the SARS epidemic settles down.

Conclusion:Initial attack size is one of the determinants of whether SARS can successfully invade the community or not. Two of the most effective policy procedures to prevent new infections would be to apply stringent precautionary measures and to impose quicker and more effective quarantine of the exposed populace.
The role of individual and contextual socioeconomic circumstances on mortality: analysis of time variations in a city of north west Italy
Authors: Marinacci C , Spadea T , Biggeri A , Demaria M , Caiazzo A , Costa G
Published: February 2004

Study objective:To evaluate the independent and mutual effects of neighbourhood deprivation and of individual socioeconomic conditions on mortality and to assess the trends over the past 30 years and the residual neighbourhood heterogeneity.

Design:General and cause specific mortality was analysed as a function of time period, highest educational level achieved, housing conditions, and neighbourhood deprivation, using multilevel Poisson models stratified by gender and age class.

Setting:The study was conducted in Turin, a city in north west Italy with nearly one million inhabitants and consisting of 23 neighbourhoods.

Participants:The study population included three cohorts of persons aged 15 years or older, recorded in the censuses of 1971, 1981, and 1991 and followed up for 10 years after each census.

Main results:Individual and contextual socioeconomic conditions showed an independent and significant impact on mortality, both among men and women, with significantly higher risks for coronary heart and respiratory diseases among people, aged less than 65 years, residing in deprived neighbourhoods (9% and 15% excess for coronary heart diseases, 20% and 24% for respiratory diseases, respectively for men and women living in deprived neighbourhoods compared with rich). The decreasing time trend in general mortality was less pronounced among men with lower education and poorer housing conditions, compared with their more advantaged counterparts; the same was found in less educated women aged less than 65 years.

Conclusions:These results and further developments in the evaluation of impact and mechanisms of other contextual effects can provide information for both health and non-health oriented urban policies.
Provenance of Jurassic sedimentary rocks of south-central Quesnellia, British Columbia: implications for paleogeography
Authors: Petersen Nathan T , Smith Paul L , Mortensen James K , Creaser Robert A , Tipper Howard W
Published: February 2004

Jurassic sedimentary rocks of southern to central Quesnellia record the history of the Quesnellian magmatic arc and reflect increasing continental influence throughout the Jurassic history of the terrane. Standard petrographic point counts, geochemistry, SmNd isotopes and detrital zircon geochronology, were employed to study provenance of rocks obtained from three areas of the terrane. Lower Jurassic sedimentary rocks, classified by inferred proximity to their source areas as proximal or proximal basin are derived from an arc source area. Sandstones of this age are immature. The rocks are geochemically and isotopically primitive. Detrital zircon populations, based on a limited number of analyses, have homogeneous Late Triassic or Early Jurassic ages, reflecting local derivation from Quesnellian arc sources. Middle Jurassic proximal and proximal basin sedimentary rocks show a trend toward more evolved mature sediments and evolved geochemical characteristics. The sandstones show a change to more mature grain components when compared with Lower Jurassic sedimentary rocks. There is a decrease in εNdT values of the sedimentary rocks and Proterozoic detrital zircon grains are present. This change is probably due to a combination of two factors: (1) pre-Middle Jurassic erosion of the Late Triassic  Early Jurassic arc of Quesnellia, making it a less dominant source, and (2) the increase in importance of the eastern parts of Quesnellia and the pericratonic terranes, such as Kootenay Terrane, both with characteristically more evolved isotopic values. Basin shale environments throughout the Jurassic show continental influence that is reflected in the evolved geochemistry and SmNd isotopes of the sedimentary rocks. The data suggest southern Quesnellia received material from the North American continent throughout the Jurassic but that this continental influence was diluted by proximal arc sources in the rocks of proximal derivation. The presence of continent-derived material in the distal sedimentary rocks of this study suggests that southern Quesnellia is comparable to known pericratonic terranes.
Geodynamic evolution of the Pan-African belt in central Africa with special reference to Cameroon
Authors: Toteu Sadrack Félix , Penaye Joseph , Djomani Yvette Poudjom
Published: February 2004

The Pan-African belt in central Africa has benefited from the many petrographic, structural, and geochronological studies in the recent years that have improved our understanding of the belt. However, those studies have also produced various and often divergent evolutionary models for the belt, some of which do not even involve well-defined cratons. Following a review of the available data in Cameroon, we propose a model of continentcontinent collision that involved the Congo craton and the north-central Cameroon active margin showing Archean to Paleoproterozoic inheritances. This model is based, among others, on (i) the prominent role of the Congo craton as demonstrated by the regional extension of external nappes on its northern edge and the concomitant exhumation of the 620 Ma granulitic rocks believed to have formed at the root of the collision zone, and (ii) the late development of a strike slip fault system in central Cameroon as the result of horizontal movement following the multistage collision. In the general framework of the Pan-Africano  Brasiliano belt, a comparison of the kinematic and age of deformation north of the Congo craton to that east of the West African craton, suggests that the overall tectonic evolution of the mobile domain between both cratons is controlled by their relative motion.
Early juvenile pterosaurs (Pterodactyloidea:Pterodaustro guinazui) from the Lower Cretaceous of central Argentina
Authors: Codorniú Laura , Chiappe Luis M
Published: February 2004

We report on two juvenile specimens of Pterodaustro guinazui, a medium-sized, filter-feeding pterodactyloid pterosaur from the Lower Cretaceous (Albian) lacustrine deposits of the Lagarcito Formation of central Argentina (Sierra de Las Quijadas, San Luis Province). Both specimens lack the skull, but one is otherwise nearly complete and articulated, and the other is more fragmentary. Their small size (~300 mm of wingspan), the lack of fusion of several postcranial bones, the minimal epiphyseal ossification, and the porous appearance of the periosteal surfaces indicate the specimens died at a very early stage of postnatal development. The presence of derived characters unique, within Pterodactyloidea, to P. guinazui (e.g., caudal vertebrae exceeding 16 elements) supports the proposed specific identification of the specimens. The new material provides anatomical information previously unknown for P. guinazui and sheds light on allometric transformations during the growth of this pterosaur. Comparisons with more mature and much larger individuals support two major allometric trends: (i) the negative allometric growth of the proximal portion of the forelimb, and (ii) the positive allometric growth of the metacarpal IV.
New reptile material from the Lower Triassic of Madagascar: implications for the PermianTriassic extinction event
Authors: Ketchum Hilary F , Barrett Paul M
Published: February 2004

Recently discovered reptile specimens from the "Eotriassic" deposits of Madagascar (Lower Triassic) are reported, adding valuable information to our knowledge of Malagasy faunas and providing additional data on tetrapod survivorship across the PermianTriassic (PT) boundary. Four specimens are attributable to the terrestrial procolophonoid Barasaurus besairiei Piveteau 1955, whereas the remainder are referable to the aquatic younginiform family Tangasauridae, including some individuals identifiable as Hovasaurus boulei Piveteau 1926. These specimens represent the geologically youngest tangasaurid and Barasaurus specimens to be described from Madagascar and suggest that these small reptiles passed unaffected through the end Permian mass extinction event, when ~78% of amniote families disappeared.
Early Tertiary Anaconda Metamorphic Core Complex, southwestern Montana
Authors: O'Neill J Michael , Lonn Jeff D , Lageson David R , Kunk Michael J
Published: February 2004

A sinuous zone of gently southeast-dipping low-angle Tertiary normal faults is exposed for 100 km along the eastern margins of the Anaconda and Flint Creek ranges in southwest Montana. Faults in the zone variously place Mesoproterozoic through Paleozoic sedimentary rocks on younger Tertiary granitic rocks or on sedimentary rocks older than the overlying detached rocks. Lower plate rocks are lineated and mylonitic at the main fault and, below the mylonitic front, are cut by mylonitic mesoscopic to microscopic shear zones. The upper plate consists of an imbricate stack of younger-on-older sedimentary rocks that are locally mylonitic at the main, lowermost detachment fault but are characteristically strongly brecciated or broken. Kinematic indicators in the lineated mylonite indicate tectonic transport to the east-southeast. Syntectonic sedimentary breccia and coarse conglomerate derived solely from upper plate rocks were deposited locally on top of hanging-wall rocks in low-lying areas between fault blocks and breccia zones. Muscovite occurs locally as mica fish in mylonitic quartzites at or near the main detachment. The 40Ar/39Ar age spectrum obtained from muscovite in one mylonitic quartzite yielded an age of 47.2 + 0.14 Ma, interpreted to be the age of mylonitization. The fault zone is interpreted as a detachment fault that bounds a metamorphic core complex, here termed the Anaconda metamorphic core complex, similar in age and character to the Bitterroot mylonite that bounds the Bitterroot metamorphic core complex along the Idaho-Montana state line 100 km to the west. The Bitterroot and Anaconda core complexes are likely components of a continuous, tectonically integrated system. Recognition of this core complex expands the region of known early Tertiary brittle-ductile crustal extension eastward into areas of profound Late Cretaceous contractile deformation characterized by complex structural interactions between the overthrust belt and Laramide basement uplifts, overprinted by late Tertiary Basin and Range faulting.
Emplacement, rapid burial, and exhumation of 90-Ma plutons in southeastern Alaska
Authors: Himmelberg Glen R , Haeussler Peter J , Brew David A
Published: February 2004

In southeastern Alaska, granodioritetonalite plutons of the AdmiraltyRevillagigedo belt intruded the JurassicCretaceous Gravina belt along the eastern side of the Alexander terrane around 90 Ma. These plutons postdate some deformation related to a major contractional event between the previously amalgamated Wrangellia and Alexander terranes and the previously accreted terranes of the North American margin. We studied the aureole mineral assemblages of these plutons near Petersburg, Alaska, determined pressure and temperature of equilibration, and examined structures that developed within and adjacent to these plutons. Parallelism of magmatic and submagmatic fabrics with fabrics in the country rock indicates synchroneity of pluton emplacement with regional deformation and suggests that magma transport to higher crustal levels was assisted by regional deformation. Replacement of andalusite by kyanite or sillimanite indicates crustal thickening soon after pluton emplacement. Regional structural analysis indicates the crustal thickening was accomplished by thrust burial. Thermobarometric analyses indicate the aureoles reached near-peak temperatures of 525 to 635 °C at pressures of 570 to 630 MPa. Consideration of the rate of thermal decay of the aureoles suggests that burial was rapid and occurred at rates around 5 to 8 mm/year. Structural observations indicate there was contractional deformation before, during, and after emplacement of the 90-Ma plutons. Initial exhumation of the AdmiraltyRevillagigedo belt in the Petersburg area may have occurred along a thrust west of the pluton belt within the Gravina belt.
Assembly Dynamics of the Bacterial Cell Division Protein FtsZ: Poised at the Edge of Stability
Authors: Romberg Laura , Levin Petra Anne
Published: February 2004

▪ Abstract  FtsZ is a prokaryotic tubulin homolog that assembles into a ring at the future site of cell division. The resulting “Z ring” forms the framework for the division apparatus, and its assembly is regulated throughout the bacterial cell cycle. A highly dynamic structure, the Z ring exhibits continual subunit turnover and the ability to rapidly assemble, disassemble, and, under certain circumstances, relocalize. These in vivo properties are ultimately due to FtsZ's capacity for guanosine triphosphate (GTP)-dependent, reversible polymerization. FtsZ polymer stability appears to be fine-tuned such that subtle changes in its assembly kinetics result in large changes in the Z ring structure. Thus, regulatory proteins that modulate FtsZ's assembly dynamics can cause the ring to rapidly remodel in response to developmental and environmental cues.
Archaeal DNA Replication: Eukaryal Proteins in a Bacterial Context
Authors: Grabowski Beatrice , Kelman Zvi
Published: February 2004

▪ Abstract  Genome sequences of a number of archaea have revealed an apparent paradox in the phylogenies of the bacteria, archaea, and eukarya, as well as an intriguing set of problems to be resolved in the study of DNA replication. The archaea, long thought to be bacteria, are not only different enough to merit their own domain but also appear to be an interesting mosaic of bacterial, eukaryal, and unique features. Most archaeal proteins participating in DNA replication are more similar in sequence to those found in eukarya than to analogous replication proteins in bacteria. However, archaea have only a subset of the eukaryal replication machinery, apparently needing fewer polypeptides and structurally simpler complexes. The archaeal replication apparatus also contains features not found in other organisms owing, in part, to the broad range of environmental conditions, some extreme, in which members of this domain thrive. In this review the current knowledge of the mechanisms governing DNA replication in archaea is summarized and the similarities and differences of those of bacteria and eukarya are highlighted.
Bacterial Biofilms: An Emerging Link to Disease Pathogenesis
Authors: Parsek Matthew R. , Singh Pradeep K.
Published: February 2004

▪ Abstract  The role of biofilms in the pathogenesis of some chronic human infections is now widely accepted. However, the criteria used to determine whether a given infection is caused by biofilms remain unclear. In this chapter we discuss three infections that are caused by biofilms—infectious kidney stones, bacterial endocarditis, and cystic fibrosis lung infections—and focus on the role of the biofilm in disease pathogenesis. Biofilms are also important as environmental reservoirs for pathogens, and the biofilm growth mode may provide organisms with survival advantages in natural environments and increase their virulence. The consequences of pathogens living in environmental biofilms and an analysis of some specific environmental biofilm systems are presented.
The Uncultured Microbial Majority
Authors: Rappé Michael S. , Giovannoni Stephen J.
Published: February 2004

▪ Abstract  Since the delineation of 12 bacterial phyla by comparative phylogenetic analyses of 16S ribosomal RNA in 1987 knowledge of microbial diversity has expanded dramatically owing to the sequencing of ribosomal RNA genes cloned from environmental DNA. Currently, only 26 of the approximately 52 identifiable major lineages, or phyla, within the domain Bacteria have cultivated representatives. Evidence from field studies indicates that many of the uncultivated phyla are found in diverse habitats, and some are extraordinarily abundant. In some important environments, including seawater, freshwater, and soil, many biologically and geochemically important organisms are at best only remotely related to any strain that has been characterized by phenotype or by genome sequencing. Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory.
Gene Organization: Selection, Selfishness, and Serendipity
Authors: Lawrence Jeffrey G.
Published: February 2004

▪ Abstract  The apparati behind the replication, transcription, and translation of prokaryotic and eukaryotic genes are quite different. Yet in both classes of organisms, genes may be organized in their respective chromosomes in similar ways by virtue of similarly acting selective forces. In addition, some gene organizations reflect biology unique to each class of organisms. Levels of organization are more complex than those of the simple operon. Multiple transcription units may be organized into larger units, local control regions may act over large chromosomal regions in eukaryotic chromosomes, and cis-acting genes may control the expression of downstream genes in all classes of organisms. All these mechanisms lead to genomes being far more organized, in both prokaryotes and eukaryotes, than hitherto imagined.
Kaposi's Sarcoma–Associated Herpesvirus Immunoevasion and Tumorigenesis: Two Sides of the Same Coin?
Authors: Moore Patrick S. , Chang Yuan
Published: February 2004

▪ Abstract  Kaposi's sarcoma–associated herpesvirus (KSHV) [or human herpesvirus 8 (HHV-8)] is the most frequent cause of malignancy among AIDS patients. KSHV and related herpesviruses have extensively pirated cellular cDNAs from the host genome, providing a unique opportunity to examine the range of viral mechanisms for controlling cell proliferation. Many of the viral regulatory homologs encode proteins that directly inhibit host adaptive and innate immunity. Other viral proteins target retinoblastoma protein and p53 control of tumor suppressor pathways, which also play key effector roles in intracellular immune responses. The immune evasion strategies employed by KSHV, by targeting tumor suppressor pathways activated during immune system signaling, may lead to inadvertent cell proliferation and tumorigenesis in susceptible hosts.
Measles Virus 1998–2002: Progress and Controversy
Authors: Rall Glenn F.
Published: February 2004

▪ Abstract  Despite the extensive media exposure that viruses such as West Nile, Norwalk, and Ebola have received lately, and the emerging threat that old pathogens may reappear as new agents of terrorism, measles virus (MV) persists as one of the leading causes of death by infectious agents worldwide, approaching the annual mortality rate of human immunodeficiency virus (HIV)-1. For most MV victims, fatality is indirect: Virus-induced transient immunosuppression predisposes the individual to opportunistic infections that, left untreated, can result in mortality. In rare cases, MV may also cause progressive neurodegenerative disease. During the past five years (1998–2002), development of animal models and the application of reverse genetics and immunological assays have collectively contributed to major progress in our understanding of MV biology and pathogenesis. Nevertheless, questions and controversies remain that are the basis for future research. In this review, major advances and current debates are discussed, including MV receptor usage, the cellular basis of immunosuppression, the suspected role of MV in “nonviral” diseases such as multiple sclerosis and Paget's disease, and the controversy surrounding MV vaccine safety.
Bacterial Membrane Lipids: Where Do We Stand?
Authors: Cronan John E.
Published: February 2004

▪ Abstract  Phospholipids play multiple roles in bacterial cells. These are the establishment of the permeability barrier, provision of the environment for many enzyme and transporter proteins, and they influence membrane-related processes such as protein export and DNA replication. The lipid synthetic pathway also provides precursors for protein modification and for the synthesis of other molecules. This review concentrates on the phospholipid synthetic pathway and discusses recent data on the synthesis and function of phospholipids mainly in the bacterium Escherichia coli.
Natural Selection and the Emergence of a Mutation Phenotype: An Update of the Evolutionary Synthesis Considering Mechanisms that Affect Genome Variation
Authors: Caporale Lynn Helena
Published: February 2004

▪ Abstract  Most descriptions of evolution assume that all mutations are completely random with respect to their potential effects on survival. However, much like other phenotypic variations that affect the survival of the descendants, intrinsic variations in the probability, type, and location of genetic change can feel the pressure of natural selection. From site-specific recombination to changes in polymerase fidelity and repair of DNA damage, an organism's gene products affect what genetic changes occur in its genome. Through the action of natural selection on these gene products, potentially favorable mutations can become more probable than random. With examples from variation in bacterial surface proteins to the vertebrate immune response, it is clear that a great deal of genetic change is better than “random” with respect to its potential effect on survival. Indeed, some potentially useful mutations are so probable that they can be viewed as being encoded implicitly in the genome. An updated evolutionary theory includes emergence, under selective pressure, of genomic information that affects the probability of different classes of mutation, with consequences for genome survival.
Molecular Genetics ofMycobacterium tuberculosisPathogenesis
Authors: Clark-Curtiss Josephine E. , Haydel Shelley E.
Published: February 2004

▪ Abstract  Tuberculosis (TB) has afflicted humankind throughout history. Approximately one third of the world's population is currently infected with Mycobacterium tuberculosis and nearly two million people die of TB annually. Although much has been learned about the structure of the tubercle bacillus, the epidemiology of TB, the physiological and immunological responses of the host to infection, and the physiology of M. tuberculosis in laboratory broth cultures, much of the basic biology of M. tuberculosis in its natural setting (the infected human) remains to be elucidated. Within the past decade, there have been remarkable advances in the development of genetic and molecular biological tools with which to study M. tuberculosis. This review discusses the approaches that have been employed and the progress that has been made in discovering how M. tuberculosis has achieved its prowess as a successful pathogen.
Molecular Pathogenicity of the Oral Opportunistic PathogenActinobacillus actinomycetemcomitans
Authors: Henderson Brian , Nair Sean P. , Ward John M. , Wilson Michael
Published: February 2004

▪ Abstract  Periodontitis is mankind's most common chronic inflammatory disease. One severe form of periodontitis is localized aggressive periodontitis (LAP), a condition to which individuals of African origin demonstrate an increased susceptibility. The main causative organism of this disease is Actinobacillus actinomycetemcomitans. A member of the Pasteurellaceae, A. actinomycetemcomitans produces a number of interesting putative virulence factors including (a) an RTX leukotoxin that targets only neutrophils and monocytes and whose action is influenced by a novel type IV secretion system involved in bacterial adhesion; (b) the newly discovered toxin, cytolethal distending toxin (CDT); and (c) a secreted chaperonin 60 with potent leukocyte-activating and bone resorbing activities. This organism also produces a plethora of proteins able to inhibit eukaryotic cell cycle progression and proteins and peptides that can induce distinct forms of proinflammatory cytokine networks. A range of other proteins interacting with the host is currently being uncovered. In addition to these secreted factors, A. actinomycetemcomitans is invasive with an unusual mechanism for entering, and traveling within, eukaryotic cells. This review focuses on recent advances in our understanding of the molecular and cellular pathogenicity of this fascinating oral bacterium.
Multiple Sigma Subunits and the Partitioning of Bacterial Transcription Space
Authors: Gruber Tanja M. , Gross Carol A.
Published: February 2004

▪ Abstract  Promoter recognition in eubacteria is carried out by the initiation factor sigma, which binds RNA polymerase and initiates transcription. Cells have one housekeeping factor and a variable number of alternative sigma factors that possess different promoter-recognition properties. The cell can choose from its repertoire of sigmas to alter its transcriptional program in response to stress. Recent structural information illuminates the process of initiation and also shows that the two key sigma domains are structurally conserved, even among diverse family members. We use the sigma repertoire of Escherichia coli, Bacillus subtilis, Streptomyces coelicolor, and cyanobacteria to illustrate the different strategies utilized to organize transcriptional space using multiple sigma factors.
Pathways of Oxidative Damage
Authors: Imlay James A.
Published: February 2004

▪ Abstract  The phenomenon of oxygen toxicity is universal, but only recently have we begun to understand its basis in molecular terms. Redox enzymes are notoriously nonspecific, transferring electrons to any good acceptor with which they make electronic contact. This poses a problem for aerobic organisms, since molecular oxygen is small enough to penetrate all but the most shielded active sites of redox enzymes. Adventitious electron transfers to oxygen create superoxide and hydrogen peroxide, which are partially reduced species that can oxidize biomolecules with which oxygen itself reacts poorly. This review attempts to present our still-incomplete understanding of how reactive oxygen species are formed inside cells and the mechanisms by which they damage specific target molecules. The vulnerability of cells to oxidation lies at the root of obligate anaerobiosis, spontaneous mutagenesis, and the use of oxidative stress as a biological weapon.
Bacteriophage-Induced Modifications of Host RNA Polymerase
Authors: Nechaev Sergei , Severinov Konstantin
Published: February 2004

▪ Abstract  Bacteriophages have developed an impressive array of ingenious mechanisms to modify bacterial host RNA polymerase to make it serve viral needs. In this review we summarize the current knowledge about two types of host RNA polymerase modifications induced by double-stranded DNA phages: covalent modifications and modifications through RNA polymerase-binding proteins. We interpret the biochemical and genetic data within the framework of a structure-function model of bacterial RNA polymerase and viral biology.
Gathering No Moss
Authors: Davies Julian
Published: February 2004

I never imagined that I would be asked to write an autobiography in a microbiology tome. For that matter, little did I think that I would consider microbiology the most intriguing subject in the life sciences and the only field I wanted to study. My formal scientific training was in chemistry. This is a recounting of my conversion and the opportunities I have had to work in the microbial sciences with some of the major figures (and characters) during a period of marvelous intensity and productivity. I want to recognize and thank my many distinguished colleagues for the ways in which they have helped me to experience a fruitful and stimulating life as a microbiologist.
On the Trail of a Cereal Killer: Exploring the Biology ofMagnaporthe grisea
Authors: Talbot Nicholas J.
Published: February 2004

▪ Abstract  The blast fungus Magnaporthe grisea causes a serious disease on a wide variety of grasses including rice, wheat, and barley. Rice blast is the most serious disease of cultivated rice and therefore poses a threat to the world's most important food security crop. Here, I review recent progress toward understanding the molecular biology of plant infection by M. grisea, which involves development of a specialized cell, the appressorium. This dome-shaped cell generates enormous turgor pressure and physical force, allowing the fungus to breach the host cuticle and invade plant tissue. The review also considers the role of avirulence genes in M. grisea and the mechanisms by which resistant rice cultivars are able to perceive the fungus and defend themselves. Finally, the likely mechanisms that promote genetic diversity in M. grisea and our current understanding of the population structure of the blast fungus are evaluated.
Spatial and Temporal Control of Differentiation and Cell Cycle Progression in Caulobacter crescentus
Authors: Ausmees Nora , Jacobs-Wagner Christine
Published: February 2004

▪ Abstract  The dimorphic and intrinsically asymmetric bacterium Caulobacter crescentus has become an important model organism to study the bacterial cell cycle, cell polarity, and polar differentiation. A multifaceted regulatory network orchestrates the precise coordination between the development of polar organelles and the cell cycle. One master response regulator, CtrA, directly controls the initiation of chromosome replication as well as several aspects of polar morphogenesis and cell division. CtrA activity is temporally and spatially regulated by multiple partially redundant control mechanisms, such as transcription, phosphorylation, and targeted proteolysis. A multicomponent signal transduction network upstream CtrA, containing histidine kinases CckA, PleC, DivJ, and DivL and the essential response regulator DivK, contributes to the control of CtrA activity in response to cell cycle and developmental cues. An intriguing feature of this signaling network is the dynamic cell cycle–dependent polar localization of its components, which is believed to have a novel regulatory function.
Bacterial Motility on a Surface: Many Ways to a Common Goal
Authors: Harshey Rasika M.
Published: February 2004

▪ Abstract  When free-living bacteria colonize biotic or abiotic surfaces, the resultant changes in physiology and morphology have important consequences on their growth, development, and survival. Surface motility, biofilm formation, fruiting body development, and host invasion are some of the manifestations of functional responses to surface colonization. Bacteria may sense the growth surface either directly through physical contact or indirectly by sensing the proximity of fellow bacteria. Extracellular signals that elicit new gene expression include autoinducers, amino acids, peptides, proteins, and carbohydrates. This review focuses mainly on surface motility and makes comparisons to features shared by other surface phenomenon.
Transposable Elements in Filamentous Fungi
Authors: Daboussi Marie-Josée , Capy Pierre
Published: February 2004

▪ Abstract  The past 10 years have been productive in the characterization of fungal transposable elements (TEs). All eukaryotic TEs described are found including an extraordinary prevalence of active members of the pogo family. The role of TEs in mutation and genome organization is well documented, leading to significant advances in our perception of the mechanisms underlying genetic changes in these organisms. TE-mediated changes, associated with transposition and recombination, provide a broad range of genetic variation, which is useful for natural populations in their adaptation to environmental constraints, especially for those lacking the sexual stage. Interestingly, some fungal species have evolved distinct silencing mechanisms that are regarded as host defense systems against TEs. The examination of forces acting on the evolutionary dynamics of TEs should provide important insights into the interactions between TEs and the fungal genome. Another issue of major significance is the practical applications of TEs in gene tagging and population analysis, which will undoubtedly facilitate research in systematic biology and functional genomics.
The Secret Lives of the Pathogenic Mycobacteria
Authors: Cosma Christine L. , Sherman David R. , Ramakrishnan Lalita
Published: February 2004

▪ Abstract  Pathogenic mycobacteria, including the causative agents of tuberculosis and leprosy, are responsible for considerable morbidity and mortality worldwide. A hallmark of these pathogens is their tendency to establish chronic infections that produce similar pathologies in a variety of hosts. During infection, mycobacteria reside in macrophages and induce the formation of granulomas, organized immune complexes of differentiated macrophages, lymphocytes, and other cells. This review summarizes our understanding of Mycobacterium–host cell interactions, the bacterial-granuloma interface, and mechanisms of bacterial virulence and persistence. In addition, we highlight current controversies and unanswered questions in these areas.
Vaccinia Virus Motility
Authors: Smith Geoffrey L. , Murphy Brendan J. , Law Mansun
Published: February 2004

▪ Abstract  Vaccinia virus (VV), the virus smallpox vaccine, replicates in the cytoplasm of infected cells. The intracellular movement of this large virus would be inefficient without specific transport mechanisms; therefore, VV uses microtubules for movement during both entry and egress. In addition, the dissemination of virus from infected cells to adjacent cells is promoted by the polymerization of actin beneath cell surface virions to drive virus particles away from the cell. Last, the roles of different VV particles in virus movement within and between hosts are discussed.
Genomic characterization and expression analysis of the first nonmammalian renin genes from zebrafish and pufferfish
Authors: Liang Ping , Jones Craig A. , Bisgrove Brent W. , Song Lei , Glenn Sean T. , Yost H. Joseph , Gross Kenneth W.
Published: February 2004

Liang, Ping, Craig A. Jones, Brent W. Bisgrove, Lei Song, Sean T. Glenn, H. Joseph Yost, and Kenneth W. Gross. Genomic characterization and expression analysis of the first nonmammalian renin genes from zebrafish and pufferfish. Physiol Genomics 16: 314–322, 2004. First published November 25, 2003; 10.1152/physiol-genomics. 00012.2003.—Renin is a key enzyme in the renin-angiotensin system (RAS), a pathway which plays an important physiological role in blood pressure and electrolyte homeostasis. The origin of the RAS is believed to have accompanied early evolution of vertebrates. However, renin genes have so far only been unequivocally identified in mammals. Whether or not a bona fide renin gene exists in nonmammalian vertebrates has been an intriguing question of physiological and evolutionary interest. Using a genomic analytical approach, we identified renin genes in two nonmammalian vertebrates, zebrafish ( Danio rerio) and pufferfish ( Takifugu rubripes). Phylogenetic analysis demonstrates that the predicted fish renins cluster together with mammalian renins to form a distinct subclass of vertebrate aspartyl proteases. RT-PCR results confirm generation of the predicted zebrafish mRNA and its expression in association with the opisthonephric kidney of adult zebrafish. Comparative in situ hybridization analysis of wild-type and developmental mutants indicates that renin expression is first detected bilaterally in cells of the interrenal primordia at 24 h postfertilization, which subsequently migrate to lie adjacent to, but distinct from, the glomerulus of the developing pronephric kidney. Our report provides the first molecular evidence for the existence of renin genes in lower vertebrates. The observation that the earliest renin-expressing cells, arising during ontogeny of this teleost vertebrate, are of adrenocortical lineage raises an interesting hypothesis as regards the origin of renin-expressing cells in the metanephric kidney of higher vertebrates.
INS VNTR is a QTL for the insulin response to oral glucose in obese children
Authors: Dos Santos Christine , Fallin Daniele , Le Stunff Catherine , LeFur Sophie , Bougnères Pierre
Published: February 2004

Dos Santos, Christine, Daniele Fallin, Catherine Le Stunff, Sophie LeFur, and Pierre Bougnères. INS VNTR is a QTL for the insulin response to oral glucose in obese children. Physiol Genomics 16: 309-313, 2004. First published December 2, 2003; 10.1152/ physiolgenomics.00024.2003.— We performed a genotype-phenotype association study to examine whether the insulin VNTR ( INS VNTR) polymorphism located in the insulin gene promoter was associated with changes in insulin response to oral glucose. Two classes of INS VNTR alleles are observed in Caucasians, the “short” class I and the “long” class III. Plasma insulin and glucose concentrations and indices of insulin secretion (IGI) and sensitivity (ISI) were measured using an oral glucose tolerance test (OGTT) in 387 obese children aged 12 ± 0.1 yr with a mean body mass index (BMI) of 30.6 kg/m2 (161% of the normal mean). During OGTT, plasma insulin and IGI were 20–30% higher in I/I obese children vs. III carriers ( P < 0.01). A general linear model adjusting for age, sex, and puberty was also used to evaluate the influence of the VNTR genotype on the BMI-IGI ( P = 0.07) and the BMI-ISI ( P < 0.006) relationships. The INS VNTR can therefore be considered a quantitative trait locus influencing glucose-stimulated insulin physiology in obese juveniles.
Mouse cardiac surgery: comprehensive techniques for the generation of mouse models of human diseases and their application for genomic studies
Authors: Tarnavski Oleg , McMullen Julie R. , Schinke Martina , Nie Qing , Kong Sekwon , Izumo Seigo
Published: February 2004

Mouse models mimicking human diseases are important tools in trying to understand the underlying mechanisms of many disease states. Several surgical models have been described that mimic human myocardial infarction (MI) and pressure-overload-induced cardiac hypertrophy. However, there are very few detailed descriptions for performing these surgical techniques in mice. Consequently, the number of laboratories that are proficient in performing cardiac surgical procedures in mice has been limited. Microarray technologies measure the expression of thousands of genes simultaneously, allowing for the identification of genes and pathways that may potentially be involved in the disease process. The statistical analysis of microarray experiments is highly influenced by the amount of variability in the experiment. To keep the number of required independent biological replicates and the associated costs of the study to a minimum, it is critical to minimize experimental variability by optimizing the surgical procedures. The aim of this publication was to provide a detailed description of techniques required to perform mouse cardiac surgery, such that these models can be utilized for genomic studies. A description of three major surgical procedures has been provided: 1) aortic constriction, 2) pulmonary artery banding, 3) MI (including ischemia-reperfusion). Emphasis has been placed on technical procedures with the inclusion of thorough descriptions of all equipment and devices employed in surgery, as well as the application of such techniques for expression profiling studies. The cardiac surgical techniques described have been, and will continue to be, important for elucidating the molecular mechanisms of cardiac hypertrophy and failure with high-throughput technology.
A comparison of oligonucleotide and cDNA-based microarray systems
Authors: Mah Nancy , Thelin Anders , Lu Tim , Nikolaus Susanna , Kühbacher Tanja , Gurbuz Yesim , Eickhoff Holger , Klöppel Günther , Lehrach Hans , Mellgård Björn , Costello Christine M. , Schreiber Stefan
Published: February 2004

Large-scale public data mining will become more common as public release of microarray data sets becomes a corequisite for publication. Therefore, there is an urgent need to clarify whether data from different microarray platforms are comparable. To assess the compatibility of microarray data, results were compared from the two main types of high-throughput microarray expression technologies, namely, an oligonucleotide-based and a cDNA-based platform, using RNA obtained from complex tissue (human colonic mucosa) of five individuals. From 715 sequence-verified genes represented on both platforms, 64% of the genes matched in “present” or “absent” calls made by both platforms. Calls were influenced by spurious signals caused by Alu repeats in cDNA clones, clone annotation errors, or matched probes that were designed to different regions of the gene; however, these factors could not completely account for the level of call discordance observed. Expression levels in sequence-verified, platform-overlapping genes were not related, as demonstrated by weakly positive rank order correlation. This study demonstrates that there is only moderate overlap in the results from the two array systems. This fact should be carefully considered when performing large-scale analyses on data originating from different microarray platforms.
Temporal patterns of gene expression in murine cutaneous burn wound healing
Authors: Feezor Robert J. , Paddock Heather N. , Baker Henry V. , Varela Juan C. , Barreda Joyce , Moldawer Lyle L. , Schultz Gregory S. , Mozingo David W.
Published: February 2004

The global changes in gene expression in injured murine skin were characterized following a second-degree scald burn. Dorsal skin was harvested from uninjured and from burned mice at 2 h and at 3 and 14 days following immersion in 65°C water for 45 s. Gene expression was surveyed using an Affymetrix U74Av2 GeneChip, and patterns of gene expression were analyzed using hierarchical clustering and supervised analysis. Burn injury produced significant alterations in the expression of a number of genes, with the greatest changes seen 3 and 14 days after the scald burn. Using a supervised analysis with a false discovery rate of 1% or 5%, differences in the expression of 192 or 1,116 genes, respectively, discriminated among the unburned skin and the three time points after the burn injury. Gene expression was primarily a transient and time-dependent upregulation. The expression of only 24 of the 192 discriminating genes was downregulated after the burn injury. No gene exhibited a sustained increase in expression over the entire 14 days following the burn injury. Gene ontologies revealed an integrated upregulation of inflammatory and protease genes at acute time intervals, and a diminution of cytoskeletal and muscle contractile genes at 3 or 14 days after the injury. Following a second-degree scald burn, global patterns of gene expression in the burn wound change dramatically over several weeks in a time-dependent manner, and these changes can be categorized based on the biological relevance of the genes.