bluuebunny/crossref_metadata_2025 huggingface dataset:
Reductive Dehalogenation of Brominated Phenolic Compounds by Microorganisms Associated with the Marine Sponge
Aplysina aerophoba
Authors: Ahn Young-Beom , Rhee Sung-Keun , Fennell Donna E. , Kerkhof Lee J. , Hentschel Ute , Häggblom Max M.
Published: July 2003

Marine sponges are natural sources of brominated organic compounds, including bromoindoles, bromophenols, and bromopyrroles, that may comprise up to 12% of the sponge dry weight.
Aplysina aerophoba
sponges harbor large numbers of bacteria that can amount to 40% of the biomass of the animal. We postulated that there might be mechanisms for microbially mediated degradation of these halogenated chemicals within the sponges. The capability of anaerobic microorganisms associated with the marine sponge to transform haloaromatic compounds was tested under different electron-accepting conditions (i.e., denitrifying, sulfidogenic, and methanogenic). We observed dehalogenation activity of sponge-associated microorganisms with various haloaromatics. 2-Bromo-, 3-bromo-, 4-bromo-, 2,6-dibromo-, and 2,4,6-tribromophenol, and 3,5-dibromo-4-hydroxybenzoate were reductively debrominated under methanogenic and sulfidogenic conditions with no activity observed in the presence of nitrate. Monochlorinated phenols were not transformed over a period of 1 year. Debromination of 2,4,6-tribromophenol, and 2,6-dibromophenol to 2-bromophenol was more rapid than the debromination of the monobrominated phenols. Ampicillin and chloramphenicol inhibited activity, suggesting that dehalogenation was mediated by bacteria. Characterization of the debrominating methanogenic consortia by using terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis analysis indicated that different 16S ribosomal DNA (rDNA) phylotypes were enriched on the different halogenated substrates. Sponge-associated microorganisms enriched on organobromine compounds had distinct 16S rDNA TRFLP patterns and were most closely related to the δ subgroup of the proteobacteria. The presence of homologous reductive dehalogenase gene motifs in the sponge-associated microorganisms suggested that reductive dehalogenation might be coupled to dehalorespiration.
Single-Cell Protein Profiling of Wastewater Enterobacterial Communities Predicts Disinfection Efficiency
Authors: Ponniah Gomathinayagam , Chen Han , Michielutti Ronda , Salonen Nancy , Blum Paul
Published: July 2003

The efficiency of enterobacterial disinfection is dependent largely on enterobacterial community physiology. However, the relationship between enterobacterial community physiology and wastewater processing is unclear. The purpose of this study was to investigate this relationship. The influence of wastewater treatment processes on enterobacterial community physiology was examined at the single-cell level by using culture-independent methods. Intracellular concentrations of two conserved proteins, the growth-related protein Fis and the stationary-phase protein Dps, were analyzed by epifluoresence microscopy of uncultivated cells by using enterobacterial group-specific polyclonal fluorochrome-coupled antibodies. Enterobacterial single-cell community protein profiles were distinct for different types of biological treatment. The differences were not apparent when bulk methods of protein analysis were used. Trickling filter wastewater yielded Fis-enriched communities compared to the communities in submerged aeration basin wastewater. Community differences in Fis and Dps contents were used to predict disinfection efficiency. Disinfection of community samples by heat exposure combined with cultivation in selective media confirmed that enterobacterial communities exhibited significant differences in sensitivity to disinfection. These findings provide strategies that can be used to increase treatment plant performance, reduce the enterobacterial content in municipal wastewater, and minimize the release of disinfection by-products into receiving water.
Catabolism of Arylboronic Acids by
Arthrobacter nicotinovorans
Strain PBA
Authors: Negrete-Raymond Ana C. , Weder Barbara , Wackett Lawrence P.
Published: July 2003

Arthrobacter
sp. strain PBA metabolized phenylboronic acid to phenol. The oxygen atom in phenol was shown to be derived from the atmosphere using
18
O
2
. 1-Naphthalene-, 2-naphthalene-, 3-cyanophenyl-, 2,5-fluorophenyl-, and 3-thiophene-boronic acids were also transformed to monooxygenated products. The oxygen atom in the product was bonded to the ring carbon atom originally bearing the boronic acid substituent with all the substrates tested.
Some Observational Aspects of Stellar Evolution
Authors: Eggen Olin J.
Published: July 2003

The interplay between theory and observation in astronomy has nowhere been more successful than in the field of stellar evolution. Modern theories of stellar evolution have been, in outline, firmly fixed for more than ten years, and the observations upon which they were based, as well as some derivative observations and suggested alterations in the theories, have been described in detail by Sandage (1) and Burbidge (2). The general ideas so well entrenched that any discrepant result of a fundamental kind must stand the most careful scrutiny. Because the field of stellar evolution is too large to cover completely in a short article, only a few topics of current interest to the writer are discussed.
Stellar Pulsations Across the HR Diagram: Part 1
Authors: Gautschy Alfred , Saio Hideyuki
Published: July 2003

Stellar pulsations, either as radial or nonradial dynamical variabilities, are found in many phases of stellar evolution, and these variable stars occupy vastly differing regions on the Hertzsprung-Russell diagram. The diagnostic potential of such oscillations is considerable and its importance will grow in the future when smaller and smaller amplitude variabilities can be monitored as a matter of routine. This review of the theoretical aspects of stellar pulsations appears in two parts. The first part introduces the theoretical concepts and the physical mechanisms involved in stellar pulsations and reviews recent advances therein. Applications of the theory to model neutron-star oscillations and the pulsations of hydrogen-deficient stars are also reviewed.
Magnetohydrodynamic Turbulence in the Solar Wind
Authors: Goldstein M. L. , Roberts D. A. , Matthaeus W. H.
Published: July 2003

The fluctuations in magnetic field and plasma velocity in the solar wind possess many features expected of fully developed magnetohydrodynamic turbulence. Understanding this nonlinear system is complicated by the dynamical effects of velocity shear between fast and slow solar wind streams, by the spherical expansion of the solar wind, and by its compressibility. Direct spacecraft observations from 0.3 to over 20 AU, radio scintillation observations of plasmas near the Sun, numerical simulations, and various models provide complementary methods that have shown convincingly that the fluctuations in the wind parameters undergo significant dynamical evolution independent of whatever turbulence might exist in the solar photosphere and corona. This rich area of study allows one to test theories of turbulence against direct observation, and to use observations to guide and motivate development of turbulence theories. The solar wind thus provides an excellent laboratory for studying many fundamental questions about turbulent plasmas.
An Anthropological Odyssey
Authors: Bernardi Bernardo
Published: July 2003

My anthropological experience may be described as a long and inspiring journey across the seas of the human condition. I have always been struck by what I call the paradox of human reality: Born to live, we are destined to die; ready to enjoy life, we must struggle to avoid discomfort and disease; conscious of individuality, we are still unavoidably bound from birth to a social group; claiming to be equal, we nevertheless differ both as individuals and groups.

Whenever it seemed I had a comprehensive view of human nature, I was led to a reorienting perspective. I regret none of the various phases of my long journey. Each has contributed to the evolution of my anthropological approach to reality. The reverse is also true: My anthropological perspective has often brought changes in my life’s route. Indeed, the study of anthropology, which revealed the essence of the human condition, decisively led me to change my social and professional stations. I left the Catholic priesthood and its missionary activity, dedicating myself fully to the study of anthropology
Clocking the First Americans
Authors: Meltzer David J.
Published: July 2003

The antiquity of the first Americans is one of the most controversial issues in American archaeology, and it must be resolved to understand fully the adaptive radiation of Homo sapiens into the New World. Humans were in the Americas at least by Clovis times 11,200 years ago. Accepting that these were the first Americans, however, is complicated by claims of an even earlier presence, by the absence of a Clovis source (i.e. an Alaskan predecessor is lacking), and by the theoretical demands of explaining how or why Clovis groups apparently migrated rapidly through the hemisphere. New models from evolutionary ecology, along with possible changes in the Clovis chronology (resulting from improved radiocarbon calibration), may address some of these anomalies. But there still remains the possibility of an earlier (pre-Clovis) entry, supported by some mtDNA and archaeological evidence. The mtDNA evidence, however, is complicated by questions about the viability of the presumed founder effect (on which the mtDNA clock is based). Also, the several possible pre-Clovis archaeological sites have not yet been accepted. Resolution of the timing of the peopling of the Americas, on which several theoretical and methodological issues hinge, remains a question of developing archaeological evidence, resolving ambiguity in analytical techniques and dating methods (and rejecting ones that now appear critically flawed), and expanding search strategies. The Monte Verde site in Chile is the most viable pre-Clovis candidate, although for now neither it nor any other site resolves when and by which route humans first came to the Americas.
Literacy and Literacies
Authors: Collins James
Published: July 2003

This review explores questions of power, epistemology, cultural form, and historical process, as they are raised by and developed in studies of literacy. It begins by reviewing arguments for universalist vs situated accounts of literacy and literacies. Having discussed universalist claims and evidence, and having shown that they cannot withstand criticism, the review develops generalizations about the implications of plural literacies. It explores the relationship among modern state formation, educational systems, and official vs popular literacies, by drawingo n poststructuralist argumentsa bout the role of writing in social formations and on recent historical and ethnographic research on literacy. It analyzes the role of literacies in the formation of class, gender, and racial-ethnic identities, by focusing on the role of education in class stratification, the debate about public vs private in gender dynamics, and the volatile relations between oppressed nationalities and official literacies.
Ethnography in/of the World System: The Emergence of Multi-Sited Ethnography
Authors: Marcus George E.
Published: July 2003

This review surveys an emergent methodological trend in anthropological research that concerns the adaptation of long-standing modes of ethnographic practices to more complex objects of study. Ethnography moves from its conventional single-site location, contextualized by macro-constructions of a larger social order, such as the capitalist world system, to multiple sites of observation and participation that cross-cut dichotomies such as the “local” and the “global,” the “lifeworld” and the “system.” Resulting ethnographies are therefore both in and out of the world system. The anxieties to which this methodological shift gives rise are considered in terms of testing the limits of ethnography, attenuating the power of fieldwork, and losing the perspective of the subaltern. The emergence of multi-sited ethnography is located within new spheres of interdisciplinary work, including media studies, science and technology studies, and cultural studies broadly. Several “tracking” strategies that shape multi-sited ethnographic research are considered. The review concludes with observations about the reflexive persona of the ethnographer as “circumstantial activist” in which methodological discussions about multi-sited research in anthropology are now being developed.
Science as Culture, Cultures of Science
Authors: Franklin Sarah
Published: July 2003

Although controversial, science studies has emerged in the 1990s as a significant culture area within anthropology. Various histories inform the cultural analysis of science, both outside and within anthropology. A shift from the study of gender to the study of science, the influence of postcolonial critiques of the discipline, and the impact of cultural studies are discussed in terms of their influence upon the cultural analysis of science. New ethnographic methods, the question of “ethnosciences” and multiculturalism, and the implosion of informatics and biomedicine all comprise fields of recent scholarship in the anthropology of science. Debates over modernism and postmodernism, globalization and environment, and the status of the natural inform many of these discussions. The work of Escobar, Hess, Haraway, Martin, Rabinow, Rapp, and Strathern are used to highlight new directions within anthropology concerning both cultures of science and science as culture.
Advances in Maya Epigraphy
Authors: Bricker Victoria R.
Published: July 2003

During the past twenty years, significant progress has been made in determining the nature of the Maya script, the subjects covered in the monumental inscriptions, the grammatical structure of Maya writing, and the astronomical content of hieroglyphic texts on the monuments and in the codices. The script is unequivocally logosyllabic in nature, consisting of a mixture of logographic, syllabic, and semantic signs. The monumental texts are primarily concerned with dynastic history, including references to the births, marriages, military exploits, accessions to office, and deaths of rulers and their families, as well as the rituals that they performed. The grammar of hieroglyphic texts corresponds closely in structure to that of the Cholan and Yucatecan languages that were spoken in the region where hieroglyphs occur. And the pre-Columbian Maya were accomplished astronomers who produced complex tables for predicting solar and lunar eclipses, the stations of Venus and Mars, and solstices and equinoxes.
Language Acquisition in Crosslinguistic Perspective
Authors: Bavin E. L.
Published: July 2003

This review examines crosslinguistic research that has increased our understanding of the acquisition process over the past 15 years. It begins by outlining different aspects of the study of first language acquisition, for example, infants’ preverbal attention to language and strategies in segmenting language input. A major section of the review stresses the importance of ethnographic studies because acquisition must be considered in relation to language socialization patterns in the particular culture in which the language is acquired. Another section examines crosslinguistic research and the impact of Slobin’s work, as well as factors that seem to influence the child’s mastery of formfunction mappings in spatial, temporal, and gender domains. Examples from diverse languages are used to illustrate that children use different clues, depending on the system being acquired. The final section of the review examines findings of a crosslinguistic research project designed to collect and analyze narrative data; only through an examination of a particular language’s discourse data can we study the full range of its structure’s functions. The review concludes by stressing the need to consider the interaction between linguistic factors and the cultural context of acquisition.
Osteoporosis in Biocultural Perspective
Authors: Stini William A.
Published: July 2003

Osteoporosis is a condition in which loss of bone density leads to increased risk of fracture. This condition is increasing in frequency in most parts of the world and has become a major cause of medical expenditures in the United States, where it is estimated to cost nearly $10 billion per year. European countries report similar increases in the proportion of their medical costs attributable to osteoporosis. In most cases, osteoporosis, which occurs earlier and more frequently in women, is associated with age-related endocrine changes, especially the decline in estrogen production occurring at menopause. However, earlier occurrence resulting from factors such as inactivity, low bone peak density in early adulthood, low calcium intake, and a variety of dietary and lifestyle factors can lead to high risk of fracture before menopause. This is because bone is in a continual state of turnover, and the balance between bone formation and resorption can be upset by a number of endogenous and exogenous factors. Relatively inefficient intestinal absorption of calcium, which can increase the risk of osteoporosis, is probably an adaptation that avoids the necessity of excessive kidney excretion of calcium. Modern lifestyles and increased life expectancies are exposing the biological cost of this adaptation.
Tasmanian Archaeology: Establishing the Sequences
Authors: Jones Rhys
Published: July 2003

The past thirty years have seen a transformation of Tasmanian prehistoric research. Analysis of shell middens established a sequence documenting coastal adaptation over the past 8 kyr. Fishing ceased in mid-Holocene times, and explanations for this as being due either to the effects of isolation on Tasmanian Aboriginal society or to a structural reorganization of coastal economic strategies have caused considerable debate. From the early 1980s excavations in limestone caves within wilderness valleys in the southwest have shown that this region was occupied throughout the Last Glacial Maximum, back to 35 kyr B.P. The technological, subsistence, and symbolic systems of these southern Ice Age hunters is linked to paleoenvironmental conditions when Tasmania was joined to the mainland by the low-sea Bassian landbridge. The Aborigines of Tasmania, long constructed as an abstract frozen metaphor for Paleolithic man, are now seen as the inheritors of a deep real past.
The Mexican-US Border: The Making of an Anthropology of Borderlands
Authors: Alvarez Robert R.
Published: July 2003

This review traces the development of an anthropology of borderlands. The ideas of early ethnography and applied anthropology about border regions are considered along with contemporary perspectives on reterritorialized communities and practices illustrated specifically by Mexican migration and transborder processes. The argument is made that the conceptual parameters of borderlands, borders, and their crossings, stemming from work done on the Mexican-US border, in particular, illustrate the contradiction, paradox, difference, and conflict of power and domination in contemporary global capitalism and the nation-state, especially as manifested in local-level practices. Furthermore, the borderlands genre is a basis upon which to redraw our conceptual frameworks of community and culture area.
The Local and the Global: The Anthropology of Globalization and Transnationalism
Authors: Kearney M.
Published: July 2003

This review examines current anthropological literature concerned with migration and other forms of population movement, and with the movement of information, symbols, capital, and commodities in global and transnational spaces. Special attention is given to the significance of contemporary increases in the volume and velocity of such flows for the dynamics of communities and for the identity of their members. Also examined are innovations in anthropological theory and forms of representation that are responses to such nonlocal contexts and influences.
Hormones, Sex, and Gender
Authors: Worthman Carol M.
Published: July 2003

Anthropologists study human diversity but are sharply divided over the roles of culture and biology in that diversity. The division is clearly represented in distinctions between sex and gender as biological and cultural categories, respectively. The disciplinary divide is further reflected in the contrast between the study of sex differences and hormones by biological anthropologists and the critique by cultural anthropologists of the value of biological approaches to sex or gender differences. This review considers anthropological ideas and debates about sex, gender, and hormones and about the relationships among them. The rationale for such a review is that divisions over conceptualization and study of sex, gender, and sex or gender differences are partly grounded in misunderstanding or ignorance of current biological understandings of sex differentiation in particular and individual differences in general.
A Long View of Nitrogen Metabolism
Authors: Ratner Sarah
Published: July 2003

The invitation of the Editorial Committee to write a prefatory chapter deeply affirms my long commitment to biochemistry. I feel honored to be the first woman, I trust the first in a long succession, to be so chosen. My preoccupations with the intermediary metabolism of amino acids and proteins began in 1937 when research laboratories in this country were occupied with the chemistry of amino acids and with nutritional studies. Major contributions were being made on the functional role of vitamins in nutrition and in elucidation of the chemical structure of vitamins. In the field of sterols, activity was reflected in major contributions to the nature of vitamin D and to the structure and action of the estrogenic hormones. Not until I became thoroughly immersed in research on amino acid metabolism did I catch up with the biochemical developments in European and English laboratories emerging from the elucidation of the function of vitamins as cofactors in enzymatic catalysis, thus stimulating and making possible the pursuit of in vitro approaches to oxidative metabolism that was soon to follow.
A Pursuit of a Hobby
Authors: Ochoa Severo
Published: July 2003

One evening in the late nineteen forties my wife and I were at a party given in honor of Otto Loewi and Sir Henry Dale, corecipients of the 1936 Nobel Prize in Medicine for their discovery of the chemical transmission of the nerve impulse. We were all asked to sign the guest book and state our hobby and I did this as Sir Henry looked over my shoulder. As I put down my hobby as Biochemistry he roared with laughter. At that time I was Professor of Pharmacology and Chairman of the Department at the New York University School of Medicine and Sir Henry said, “now that he is a pharmacologist, he has biochemistry as a hobby.” I tell this story to justify the title of this essay, because in my life biochemistry has been my only and real hobby.
THEN AND NOW
Authors: Wood Harland G.
Published: July 2003

Scientists are among the fortunate few who earn their livelihood by pursuit of a hobby. This hobby sometimes consumes their every thought but usually it provides a deeply satisfying life. Some, I’m sure, and perhaps with reason, will not agree with this statement. In my case, in my seventy-seventh year, biochemistry is still exciting, just as it was 51 years ago when I published my first scientific paper. Throughout those years, with few exceptions, I have let my own curiosity guide my research efforts without much regard for where they would eventually lead or what practical value they might have. Some of the curiosity detours have been fruitless, but these frustrations have been surpassed by the satisfaction from experiments that went nicely or resulted in unexpected findings. Sharing these experiences with coworkers has made life in the laboratory very fulfilling.
THE ENVELOPE OF MYCOBACTERIA
Authors: Brennan Patrick J. , Nikaido Hiroshi
Published: July 2003

Mycobacteria, members of which cause tuberculosis and leprosy, produce cell walls of unusually low permeability, which contribute to their resistance to therapeutic agents. Their cell walls contain large amounts of C60-C90 fatty acids, mycolic acids, that are covalently linked to arabinogalactan. Recent studies clarified the unusual structures of arabinogalactan as well as of extractable cell wall lipids, such as trehalose-based lipooligosaccharides, phenolic glycolipids, and glycopeptidolipids. Most of the hydrocarbon chains of these lipids assemble to produce an asymmetric bilayer of exceptional thickness. Structural considerations suggest that the fluidity is exceptionally low in the innermost part of bilayer, gradually increasing toward the outer surface. Differences in mycolic acid structure may affect the fluidity and permeability of the bilayer, and may explain the different sensitivity levels of various mycobacterial species to lipophilic inhibitors. Hydrophilic nutrients and inhibitors, in contrast, traverse the cell wall presumably through channels of recently discovered porins.
THE ROLES OF RETINOIDS IN VERTEBRATE DEVELOPMENT
Authors: Means Anna L. , Gudas Lorraine J.
Published: July 2003

Several lines of experimentation suggest that endogenous retinoids, metabolites of vitamin A, play a role in the anterior/posterior development of the central body axis and the limbs of vertebrates. High levels of endogenous retinoids have been detected in proximity to these developing axes in a variety of vertebrate fetuses. Teratogenesis studies suggest that both retinoid excess and deficiency are capable of disrupting the development of these axes. Finally, retinoic acid receptors regulate many developmental control genes, including homeobox genes and growth factor genes.
MOLECULAR BIOLOGY OF MAMMALIAN AMINO ACID TRANSPORTERS
Authors: Malandro Marc S. , Kilberg Michael S.
Published: July 2003

Recently a number of α-amino acid transport proteins and corresponding cDNA clones have been isolated and categorized into gene families. The “CAT family” contains two members that mediate high-affinity Na+-independent transport of cationic amino acids in many tissues, and a third member that encodes a liver-specific low-affinity activity. The “glutamate transporter family” contains at least four members that mediate Na+-dependent glutamate/aspartate uptake and two members that are selective for neutral amino acids. The glutamate transporters are expressed at high levels in both glia and neurons of the central nervous system. The Na+/Cl--dependent proline transporter (PROT) belongs to a large superfamily of neurotransmitter transporters and is expressed in regions of the brain that contain glutamanergic neurons. All four glycine transporters of the “GLYT family” also belong to the neurotransmitter superfamily and exhibit the greatest expression in the central nervous system. The “rBAT/4F2hc family” of proteins induce both neutral and cationic amino acid uptake when expressed in Xenopus oocytes. Cystinuria is linked to specific mutations in the rBAT sequence.
THE STRUCTURE AND FUNCTION OF PROTEINS INVOLVED IN MAMMALIAN PRE-mRNA SPLICING
Authors: Krämer Angela
Published: July 2003

Intervening sequences are removed from nuclear pre-mRNAs in a well-defined multi-step pathway. Small nuclear ribonucleoprotein particles (snRNPs) and numerous protein factors are essential for the formation of the active spliceosome in which intron excision proceeds in two successive transesterification reactions. Important elements for catalysis are the RNA moieties of the snRNPs that align the pre-mRNA splice sites in the active center of the spliceosome. Although pre-mRNA splicing is almost certainly RNA-mediated, both snRNA-associated proteins and non-snRNP splicing factors participate in each step of the splicing reaction. Splicing proteins exert auxiliary functions in the recognition, selection, and juxtaposition of the splice sites and drive conformational changes during spliceosome assembly and catalysis. Many splicing factors have been isolated in recent years and corresponding cDNAs have been cloned. This review summarizes the structure and function of mammalian proteins which are essential components of the constitutive splicing machinery.
MOLECULAR GENETICS OF SIGNAL TRANSDUCTION IN DICTYOSTELIUM
Authors: Parent Carole A. , Devreotes Peter N.
Published: July 2003

In conditions of starvation, the free living amoebae of Dictyostelium enter a developmental program: The cells aggregate by chemotaxis to form a multicellular structure that undergoes morphogenesis and cell-type differentiation. These processes are mediated by a family of cell surface CAMP receptors (CARS) that act on a specific heterotrimeric G protein to stimulate actin polymerization, activation of adenylyl and guanylyl cyclases, and a host of other responses. Most of the components in these pathways have mammalian counterparts. The accessible genetics of this unicellular organism facilitate structure-function analysis and enable the discovery of novel genes involved in the regulation of these important pathways.
STRUCTURAL BASIS OF LECTIN-CARBOHYDRATE RECOGNITION
Authors: Weis William I. , Drickamer Kurt
Published: July 2003

Lectins are responsible for cell surface sugar recognition in bacteria, animals, and plants. Examples include bacterial toxins; animal receptors that mediate cellcell interactions, uptake of glycoconjugates, and pathogen neutralization; and plant toxins and mitogens. The structural basis for selective sugar recognition by members of all of these groups has been investigated by x-ray crystallography. Mechanisms for sugar recognition have evolved independently in diverse protein structural frameworks, but share some key features. Relatively low affinity binding sites for monosaccharides are formed at shallow indentations on protein surfaces. Selectivity is achieved through a combination of hydrogen bonding to the sugar hydroxyl groups with van der Waals packing, often including packing of a hydrophobic sugar face against aromatic amino acid side chains. Higher selectivity of binding is achieved by extending binding sites through additional direct and water-mediated contacts between oligosaccharides and the protein surface. Dramatically increased affinity for oligosaccharides results from clustering of simple binding sites in oligomers of the lectin polypeptides. The geometry of such oligomers helps to establish the ability of the lectins to distinguish surface arrays of polysaccharides in some instances and to crosslink glycoconjugates in others.
CONNEXINS, CONNEXONS, AND INTERCELLULAR COMMUNICATION
Authors: Goodenough Daniel A , Goliger Jeffrey A. , Paul David L.
Published: July 2003

Cells in tissues share ions, second messengers, and small metabolites through clusters of intercellular channels called gap junctions. This type of intercellular communication permits coordinated cellular activity. Intercellular channels are formed from two oligomeric integral membrane protein assemblies, called connexons, which span two adjacent cells’ plasma membranes and join in a narrow, extracellular “gap.” Connexons are formed from connexins, a highly related multigene family consisting of at least 13 members. Since the cloning of the first connexin in 1986, considerable progress has been made in our understanding of the complex molecular switches that control the formation and permeability of the intercellular channels. Analysis of the mechanisms of channel assembly has revealed the selectivity of inter-connexin interactions and uncovered novel characteristics of the channel permeability and gating behavior. Structure-function studies provide a molecular understanding of the significance of connexin diversity and demonstrate the unique regulation of connexins by tyrosine kinases and oncogenes.
HEMATOPOIETIC RECEPTOR COMPLEXES
Authors: Wells James A. , de Vos Abraham M.
Published: July 2003

Hematopoietic hormones/cytokines and receptors regulate a wide variety of biological activities and are important in medicine. Through recent biochemical, biophysical, and structural studies we are beginning to understand how these molecules work at the molecular level. These extracellular hormones activate their transmembrane receptors by causing them to oligomerize. The receptor oligomers in turn activate intracellular tyrosine kinase molecules which then activate transcription factors (the JAK-STAT pathways). This review centers on the molecular basis for hormone-receptor binding, and how this information is useful in understanding protein-protein interactions and for the design of second generation molecules.
BIOCHEMISTRY AND STRUCTURAL BIOLOGY OF TRANSCRIPTION FACTOR IID (TFIID)
Authors: Burley S. K. , Roeder R. G.
Published: July 2003

Eukaryotes have three distinct RNA polymerases that catalyze transcription of nuclear genes. RNA polymerase II is responsible for transcribing nuclear genes encoding the messenger RNAs and several small nuclear RNAs. Like RNA polymerases I and III, pol II cannot recognize its target promoter directly and initiate transcription without accessory factors. Instead, this large multisubunit enzyme relies on both general transcription factors and transcriptional activators and coactivators to regulate transcription from class II promoters. At the center of this process is TFIID, a 700-kD complex composed of the TATA box binding protein (TBP) and a set of phylogenetically conserved, polymerase-specific TBP-associated factors or TAFns. Together, TBP and the TAFIIs direct assembly of the transcription machinery and play critical regulatory roles in eukaryotic gene expression.
With the Help of Giants
Authors: Fridovich Irwin
Published: July 2003

A childhood fascination with animals, plants, and insects was aided and abetted by many giants, beginning with my parents. The Bronx High School of Science and the City College of New York (CCNY) made a solid and priceless grounding in chemistry and biology available free of charge. Abe Mazur at CCNY revealed the wonders of biochemistry and illustrated that it was possible to pursue these wonders while being paid to do so. He also directed me to Duke University Medical School for PhD work under the tutelage of Phil Handler. With the exception of a sabbatical year at Harvard with Frank Westheimer, my entire career has been spent at Duke serving under three fine and supportive chairmen: Handler, Hill, and Raetz. The premier discoveries to emanate from my laboratory have been the sulfite oxidase, the several superoxide dismutases, the manganese catalase, and the catalase/peroxidase. Many other topics piqued my interest and resulted in ∼ 400 publications. Herein I have recounted some of the circumstances surrounding that work and named a few of the people involved. The first 20 years I worked happily at the bench and the next 35 years just as happily facilitating the work of younger people. It has been so rewarding that I wish for nothing more than to be allowed to keep at it.
Proteome Analysis by Mass Spectrometry
Authors: Ferguson P. Lee , Smith Richard D.
Published: July 2003

▪ Abstract  The coupling of high-performance mass spectrometry instrumentation with highly efficient chromatographic and electrophoretic separations has enabled rapid qualitative and quantitative analysis of thousands of proteins from minute samples of biological materials. Here, we review recent progress in the development and application of mass spectrometry–based techniques for the qualitative and quantitative analysis of global proteome samples derived from whole cells, tissues, or organisms. Techniques such as multidimensional peptide and protein separations coupled with mass spectrometry, accurate mass measurement of peptides from global proteome digests, and mass spectrometric characterization of intact proteins hold great promise for characterization of highly complex protein mixtures. Advances in chemical tagging and isotope labeling techniques have enabled quantitative analysis of proteomes, and highly specific isolation strategies have been developed aimed at selective analysis of posttranslationally modified proteins.
Structure and Function of Natural Killer Cell Surface Receptors
Authors: Radaev Sergei , Sun Peter D.
Published: July 2003

▪ Abstract  Since mid-1990, with cloning and identification of several families of natural killer (NK) receptors, research on NK cells began to receive appreciable attention. Determination of structures of NK cell surface receptors and their ligand complexes led to a fast growth in our understanding of the activation and ligand recognition by these receptors as well as their function in innate immunity. Functionally, NK cell surface receptors are divided into two groups, the inhibitory and the activating receptors. Structurally, they belong to either the immunoglobulin (Ig)-like receptor superfamily or the C-type lectin-like receptor (CTLR) superfamily. Their ligands are either members of class I major histocompatibility complexes (MHC) or homologs of class I MHC molecules. The inhibitory form of NK receptors provides the protective immunity through recognizing class I MHC molecules with self-peptides on healthy host cells. The activating, or the noninhibitory, NK receptors mediate the killing of tumor or virally infected cells through their specific ligand recognition. The structures of activating and inhibitory NK cell surface receptors and their complexes with the ligands determined to date, including killer immunoglobulin-like receptors (KIRs) and their complexes with HLA molecules, CD94, Ly49A, and its complex with H-2Dd, and NKG2D receptors and their complexes with class I MHC homologs, are reviewed here.
The State of Lipid Rafts: From Model Membranes to Cells
Authors: Edidin Michael
Published: July 2003

▪ Abstract  Lipid raft microdomains were conceived as part of a mechanism for the intracellular trafficking of lipids and lipid-anchored proteins. The raft hypothesis is based on the behavior of defined lipid mixtures in liposomes and other model membranes. Experiments in these well-characterized systems led to operational definitions for lipid rafts in cell membranes. These definitions, detergent solubility to define components of rafts, and sensitivity to cholesterol deprivation to define raft functions implicated sphingolipid- and cholesterol-rich lipid rafts in many cell functions. Despite extensive work, the basis for raft formation in cell membranes and the size of rafts and their stability are all uncertain. Recent work converges on very small rafts <10 nm in diameter that may enlarge and stabilize when their constituents are cross-linked.
Molecular Recognition and Docking Algorithms
Authors: Brooijmans Natasja , Kuntz Irwin D.
Published: July 2003

▪ Abstract  Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.
COPs Regulating Membrane Traffic
Authors: Kreis Thomas E. , Lowe Martin , Pepperkok Rainer
Published: July 2003

Cytosolic coat proteins (COPs) regulate membrane traffic in eukaryotic cells. Three classes of coat protein complexes have so far been identified: clathrin and its adaptor proteins, coalomer (COPI), and COPII. Coatomer (composed of seven different subunits) and ADP-ribosylation factor (ARF), which form the COPI coat, are required for budding of coated vesicles from membranes. COPI has been implicated in several steps of transport from the intermediate compartment to the cis-Golgi network, through cisternae of the Golgi stack, and is essential for retrieval to the endoplasmic reticulum (ER) of membrane proteins containing the carboxy-terminal dilysine ER-retention motif. A family of structurally and functionally related COPs may regulate all membrane traffic steps in eukaryotic cells.
Weighing Functions for Ozone Depletion and Greenhouse Gas Effects on Climate
Authors: Wuebbles Donald J.
Published: July 2003

Weighing functions are extremely useful tools for evaluating the relative effects of gases affecting global atmospheric ozone and climate. In particular. the concepts of Ozone Depletion Potentials (OOPs) and Global Warming Potentials (GWPs) are extensively used in policy consideration and scientific studies of the ozone and climate issues. OOPs provide a relative measure of the expected cumulative impact on stratospheric ozone from trace gas emissions, and are being used to examine the relative effects on ozone from CFCs, halons and other halocarbons currently being used and to evaluate the potential effects of possible replacement compounds. GWPs provide a means for comparing the relative effects on climate expected from various greenhouse gases. This chapter examines these weighing functions and other indices being used in evaluating concerns about global ozone and climate, discusses the science underlying these indices, and presents the current state-of-the-art for numerical indices and their uncertainties.
Yucca Mountain: A Crisis for Policy: Prospects for America's High-Level Nuclear Waste Program
Authors: Flynn James , Slovic Paul
Published: July 2003

The federal government's attempts to site a permanent high-level radioactive waste repository have been frustrating and so far unsuccessful. Many of the problems were recognized more than a decade ago. In 1982, the US Congress passed the Nuclear Waste Policy Act and established a program to site and develop an underground repository. By 1987, this program was widely considered to be a failure. It was plagued by public opposition, intergovernmental conflict, poor management, scientific questions and concerns, and substantial cost overruns. In December 1987 Congress amended the act and selected Yucca Mountain, Nevada, as the only location to be studied as a potential repository. This halted further work on other potential sites in the western US, the eastern US sites for a second repository, and the monitored retrievable system facility that the US Department of Energy (DOE) wanted to locate in Tennessee. These amendments did not address the basic causes for the fail ures between 1983 and 1987. As a result, although the program was greatly simplified with only one site, it was beset by the same problems that created the original collapse. Now there are new and widespread calls for a congressional review and restructuring of the program from federal, state, and local officials, government agencies, industry, and public groups. This article examines the lessons from these two failed attempts and makes recommendations for devising a new policy.
Extra-Oral Digestion in Predaceous Terrestrial Arthropoda
Authors: Cohen Allen Carson
Published: July 2003

At least 79% of predaceous land-dwelling arthropods use extra-oral digestion (EOD) as a means of utilizing relatively large prey with intractable cuticles. Through the injection of potent hydrolytic enzymes, either by refluxing or nonrefluxing application, these predators greatly increase the efficiency of prey extraction and nutrient concentration. The advantages of EOD are expressed ecologically as an abbreviation of handling time and an increase in the nutrient density of consumed food, allowing small predators to consume relatively large prey. The basis of EOD is a highly coordinated combination of biochemical, morphological, and behavioral adaptations that vary with different taxa.
Molecular Mechanisms of Action of Juvenile Hormone
Authors: Jones Grace
Published: July 2003

Determination of the molecular modes of action of juvenile hormone to regulate gene expression has remained an elusive goal. This review discusses how studies on JH action have been influenced by the perspectives based on the mode of action of vertebrate retinoid/steroid hormones. Also identified are assumptions implicit in the experimental approaches used thus far, as well as alternative perspectives from which to frame future hypotheses on JH action.
Control of Moth Pests by Mating Disruption: Successes and Constraints
Authors: Cardé Ring T. , Minks Albert K.
Published: July 2003

Male moths generally find their mates by following the females' pheromone plume to its source. A formulated copy of this message is used to regulate mating of many important pests, including the pink bollworm (Pectinophora gossypiella), the oriental fruit moth (Grapholita molesta), and the tomato pinworm (Keiferia lycopersicella). How synthetic disruptant interrupts normal orientation is uncertain, but the most probable mechanisms invoke adaptation and habituation, competition between point sources of formulation and females, and a camouflage of a female's pheromone plume by the formulation. The efficacy of this technology is related principally to the motility of mated females into the area to be managed, the initial population levels of the pest, and the release characteristics of the formulation. In most cases, implementation of this technology necessitates a sophisticated monitoring and management program. Area-wide management schemes are ideal vehicles for using disruptants. Future acceptance of this environmentally safe control method should increase, largely because of growing dissatisfaction with conventional pesticides.
The Role of Macroinvertebrates in Stream Ecosystem Function
Authors: Wallace J. Bruce , Webster Jackson R.
Published: July 2003

This review focuses on some of the roles of macroinvertebrate functional groups, i.e. grazers, shredders, gatherers, filterers, and predators, in stream-ecosystem processes. Many stream-dwelling insects exploit the physical characteristics of streams to obtain their foods. As consumers at intermediate trophic levels, macroinvertebrates are influenced by both bottom-up and top-down forces in streams and serve as the conduits by which these effects are propagated. Macroinvertebrates can have an important influence on nutrient cycles, primary productivity, decomposition, and translocation of materials. Interactions among macroinvertebrates and their food resources vary among functional groups. Macroinvertebrates constitute an important source of food for numerous fish, and unless outside energy subsidies are greater than in-stream food resources for fish, effective fisheries management must account for fish-invertebrate linkages and macroinvertebrate linkages with resources and habitats. Macroinvertebrates also serve as valuable indicators of stream degradation. The many roles performed by stream-dwelling macroinvertebrates underscore the importance of their conservation.
Evolution of Ticks
Authors: Klompen J. S. H. , Black W. C. , Keirans J. E. , Oliver J. H.
Published: July 2003

Evolutionary patterns in ticks have traditionally been cast in terms of host associations. Largely untested assumptions of cospeciation and observations of current host associations are used to estimate the age of different taxa. Several recent phylogenetic studies of supraspecific relationships in ticks, based on both morphological and DNA-sequence data, allow the first rigorous testing of these assumptions. Reanalysis of patterns of tick-host associations suggests that the perception of host specificity in ticks may be an artifact of incomplete sampling. An analysis of tick-host and -habitat associations and biogeographical patterns, in the context of the newly derived phylogenies, suggests that much of the existing host-association patterns may be explained as artifacts of biogeography and ecological specificity.