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  • Annual Reviews
  • 2005-2009  (3,514)
  • 1970-1974  (2,927)
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  • 1
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 67 (2005), S. 491-514 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Vision at absolute threshold is based on signals produced in a tiny fraction of the rod photoreceptors. This requires that the rods signal the absorption of single photons, and that the resulting signals are transmitted across the retina and encoded in the activity sent from the retina to the brain. Behavioral and ganglion cell sensitivity has often been interpreted to indicate that these biophysical events occur noiselessly, i.e., that vision reaches limits to sensitivity imposed by the division of light into discrete photons and occasional photon-like noise events generated in the rod photoreceptors. We argue that this interpretation is not unique and provide a more conservative view of the constraints behavior and ganglion cell experiments impose on phototransduction and retinal processing. We summarize what is known about how these constraints are met and identify some of the outstanding open issues.
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  • 2
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Physiology 68 (2006), S. 159-191 
    ISSN: 0066-4278
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Medicine , Biology
    Notes: Liver X receptors (LXRs) and farnesoid X receptor (FXR) are nuclear receptors that function as intracellular sensors for sterols and bile acids, respectively. In response to their ligands, these receptors induce transcriptional responses that maintain a balanced, finely tuned regulation of cholesterol and bile acid metabolism. LXRs also permit the efficient storage of carbohydrate- and fat-derived energy, whereas FXR activation results in an overall decrease in triglyceride levels and modulation of glucose metabolism. The elegant, dual interplay between these two receptor systems suggests that they coevolved to constitute a highly sensitive and efficient system for the maintenance of total body fat and cholesterol homeostasis. Emerging evidence suggests that the tissue-specific action of these receptors is also crucial for the proper function of the cardiovascular, immune, reproductive, endocrine pancreas, renal, and central nervous systems. Together, LXRs and FXR represent potential therapeutic targets for the treatment and prevention of numerous metabolic and lipid-related diseases.
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  • 3
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 2 (1973), S. 63-84 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 4
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 1 (1972), S. 27-54 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 5
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 1 (1972), S. 55-112 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 6
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 1 (1972), S. 247-270 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 7
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 1 (1972), S. 227-246 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 8
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 2 (1973), S. 127-136 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 9
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 269-291 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review proposes a model for analyzing the power of ideologies of communication in producing subjectivities, organizing them hierarchically, and recruiting people to occupy them. By way of illustration, it compares this productive capacity, which is herein termed communicability, with schemes of racialization and medicalization. The argument draws on critical discourse analysis, conversational analysis, post-Habermasian research on publics, Bakhtin, Bourdieu, Foucault, and work on language ideologies to synthesize a framework for studying spheres of communicability. The concept is then used in exploring how constructions of race and health intersect in some of the most powerful spheres of communicabilityĐ??those associated with colonial medicine, HIV/AIDS, severe accute respiratory syndrome (SARS), Alzheimer's, genetics, clinical trials, "race-based medicine," organ transplant, and biostatistics. The review attempts to connect linguistic anthropology and discourse analysis more productively to medical anthropology, the history of medicine and public health, medical sociology, public health, genetics, and science studies.
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  • 10
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 451-471 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Previous research has suggested that arctic populations have elevated metabolic rates in response to their cold, marginal climate. Recent studies of indigenous Siberian groups have confirmed these earlier findings and have shed light on the mechanisms through which northern populations adapt to their environments. Indigenous Siberians show significant elevations in basal metabolic rate compared with reference values. Total energy expenditure is variable across Siberian groups and is correlated with levels of acculturation. Siberian populations appear to have adapted to cold stress through both short-term acclimatization and genetic adaptations, with thyroid hormones playing an important role in shaping metabolic responses. Elevated metabolic rates also have important consequences for health and may contribute to the low serum lipid levels observed in Siberian groups. Further research is needed to elucidate the underlying mechanisms of metabolic adaptation and their implications for ongoing health changes among indigenous Siberians.
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  • 11
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 717-739 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Throughout the twentieth century, social and cultural policies toward indigenous peoples in Latin America have been closely related to indigenismo, an ideological movement that denounced the exploitation of aboriginal groups and strove for the cultural unity and the extension of citizenship through social integration and "acculturation." This review traces the colonial and nineteenth-century roots of indigenismo and places it in the context of the populist tendencies in most Latin American states from the 1920s to the 1970s, which favored economic protectionism and used agrarian reform and the provision of services as tools for governance and legitimacy. Also examined is the role of anthropological research in its relation to state hegemony as well as the denunciation of indigenista policies by ethnic intellectuals and organizations. In recent decades, the dismantling of populist policies has given rise to a new official "neoliberal" discourse that extols multiculturalism. However, the widespread demand for multicultural policies is also seen as the outcome of the fight by militant indigenous organizations for a new type of citizenship.
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  • 12
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 253-268 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review article addresses the following question: Given the transformed social, political, and intellectual conditions for ethnographic research among indigenous peoples in North America, what forms has such research come to take at the turn of the twenty-first century? The review considers significant trends and innovations in research sites and topics, research methodologies, theoretical orientations, and forms of representation. It also assesses the distinctive strengths and limitations posed by ethnographic research for scholars engaging with significant dimensions of contemporary indigenous life, including struggles for rights, resources, recognition, and language vitality in both the national and international arenas; the repatriation and sovereignty movements; the development of tribal casinos, tourist complexes, cultural centers, and media outlets; continued social and economic marginalization of many indigenous peoples; and challenges posed by neoliberalism and globalization to tribal governments and economies.
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  • 13
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 667-693 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Over the past several decades, global manifestations of racism have undergone significant transformations. The anticolonial struggle, the civil rights movement, and the antiapartheid offensive have challenged the former established racial regimes. But the consolidation of global capitalism has also created new forms of racialization. A variety of antiracist strategies and interventions have emerged to confront new racisms. Analyses of racism have sought to interrogate its history and contemporary manifestations, how it is maintained and reproduced, and to predict its future. Anthropologists and other social scientists are challenged to develop theoretical perspectives and methodological approaches to advance our understanding of these new manifestations of race and racism.
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  • 14
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 139-158 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Under the influence of phenomenological approaches, a semiotic perspective on the body is being replaced in archaeology by analysis of the production and experience of lived bodies in the past through the juxtaposition of traces of body practices, idealized representations, and evidence of the effects of habitual gestures, postures, and consumption practices on the corporal body. On the basis of a shared assumption that social understandings of the body were created and reproduced through associations with material culture, archaeology of the body has proceeded from two theoretical positions: the body as the scene of display and the body as artifact. Today, the body as a site of lived experience, a social body, and site of embodied agency, is replacing prior static conceptions of an archaeology of the body as a public, legible surface.
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  • 15
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 3 (1974), S. 21-56 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 16
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 3 (1974), S. 117-151 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 17
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 363-384 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review explores contemporary processes through which immigrants are categorized into shifting racial landscapes in the new Europe. Tracing the racial genealogy of the immigrant through European and Europeanist migration studies, the successive construction of overlapping tropes of the nomad, the laborer, the uprooted victim, the hybrid cosmopolite, and the (Muslim) transmigrant are examined. This history points to the perduring problematization of the immigrant as the object of national integration. If migration studies have effectively tended to racialize migrants into a new savage slot, recent ethnographies of the immigrant experience in Europe point to ways in which immigrant and diasporic groups cross racial frontiers and enact solidarity across class and cultural lines.
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  • 18
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    Annual Review of Anthropology 34 (2005), S. 575-598 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: A review of work on African Americans through archaeology takes place under diasporic studies and relies on literature that defines the North American black experience. The focus is on the establishment of freedom by the founding of maroon communities and independent settlements of free people, as well as on the use and interpretation of African diasporic history and theory, particularly by archaeologists using knowledge of the diaspora to effect modern political change.
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  • 19
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 231-252 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: The description and explanation of racial and ethnic health disparities are major initiatives of the public health research establishment. Black Americans suffer on nearly every measure of health in relation to white Americans. Five theoretical models have been proposed to explain these disparities: a racial-genetic model, a health-behavior model, a socioeconomic status model, a psychosocial stress model, and a structural-constructivist model. We selectively review literature on health disparities, emphasizing research on low birth weight and high blood pressure. The psychosocial stress model and the structural-constructivist model offer greatest promise to explain disparities. In future research, theoretical elaboration and operational specificity are needed to distinguish among three distinct factors: (a) genetic variants contributing to disease risk; (b) ethnoracial or folk racial categories masquerading as biology; and (c) ethnic group membership. Such elaboration is necessary to move beyond the conflation of these three distinct constructs that characterizes much of current research.
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  • 20
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 293-315 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Much attention has been focused on the survival of Indigenous languages in recent years. Many, particularly anthropologists and linguists, anticipate the demise of the majority of Indigenous languages within this century and have called on the need to arrest the loss of languages. Opinions vary concerning the loss of language; some regard it as a hopeless cause, and others see language revitalization as a major responsibility of linguistics and kindred disciplines. To that end, this review explores efforts in language revitalization and documentation and the engagement with Indigenous peoples. It remains unclear why some attempts at language revitalization succeed, whereas others fail. What is clear is that the process is profoundly political.
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  • 21
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 3 (1974), S. 279-299 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 22
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 3 (1974), S. 357-383 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
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  • 23
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 575-598 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: A review of work on African Americans through archaeology takes place under diasporic studies and relies on literature that defines the North American black experience. The focus is on the establishment of freedom by the founding of maroon communities and independent settlements of free people, as well as on the use and interpretation of African diasporic history and theory, particularly by archaeologists using knowledge of the diaspora to effect modern political change.
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  • 24
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 549-573 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review examines literature on indigenous movements in Latin America from 1992 to 2004. It addresses ethnic identity and ethnic activism, in particular the reindianization processes occurring in indigenous communities throughout the region. We explore the impact that states and indigenous mobilizing efforts have had on each other, as well as the role of transnational nongovernmental organizations and para-statal organizations, neoliberalism more broadly, and armed conflict. Shifts in ethnoracial, political, and cultural indigenous discourses are examined, special attention being paid to new deployments of rhetorics concerned with political imaginaries, customary law, culture, and identity. Self-representational strategies will be numerous and dynamic, identities themselves multiple, fluid, and abundantly positional. The challenges these dynamics present for anthropological field research and ethnographic writing are discussed, as is the dialogue between scholars, indigenous and not, and activists, indigenous and not. Conclusions suggest potentially fruitful research directions for the future.
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  • 25
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 269-291 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This review proposes a model for analyzing the power of ideologies of communication in producing subjectivities, organizing them hierarchically, and recruiting people to occupy them. By way of illustration, it compares this productive capacity, which is herein termed communicability, with schemes of racialization and medicalization. The argument draws on critical discourse analysis, conversational analysis, post-Habermasian research on publics, Bakhtin, Bourdieu, Foucault, and work on language ideologies to synthesize a framework for studying spheres of communicability. The concept is then used in exploring how constructions of race and health intersect in some of the most powerful spheres of communicabilityĐ??those associated with colonial medicine, HIV/AIDS, severe accute respiratory syndrome (SARS), Alzheimer's, genetics, clinical trials, "race-based medicine," organ transplant, and biostatistics. The review attempts to connect linguistic anthropology and discourse analysis more productively to medical anthropology, the history of medicine and public health, medical sociology, public health, genetics, and science studies.
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  • 26
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    Annual Review of Anthropology 34 (2005), S. 317-341 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: This essay reviews recent anthropological attention to the "beginnings" and "endings" of life. A large literature since the 1990s highlights the analytic trends and innovations that characterize anthropological attention to the cultural production of persons, the naturalization of life, and the emergence of new life forms. Part I of this essay outlines the coming-into-being, completion and attenuation of personhood and how life and death are attributed, contested, and enacted. Dominant themes include how connections are forged or severed between the living and the dead and the socio-politics of dead, dying, and decaying bodies. The culture of medicine is examined for its role in organizing and naming life and death. Part II is organized by the turn to biopolitical analyses stimulated by the work of Foucault. It encompasses the ways in which the biosciences and biotechnologies, along with state practices, govern forms of living and dying and new forms of life such as the stem cell, embryo, comatose, and brain dead, and it emphasizes the production of value. Much of this scholarship is informed by concepts of liminality (a period and state of being between social statuses) and subjectification (in which notions of self, citizenship, life and its management are linked to the production of knowledge and political forms of regulation).
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  • 27
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Anthropology 34 (2005), S. 105-120 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: To what extent are intellectuals artisans of nationalism? In this chapter we review past and present anthropological research that has helped to reveal the agency of intellectuals in the projects and operations of states and nations. If the intellectual has long been defined in the Marxian-Gramscian tradition as a social actor with a special praxical investment in ways and forms of knowing, then what we discuss as "intellectualism," the social formation of knowledge, should be understood as a central dimension of the (re)production of nations and nationalism both inside and outside of states. We suggest that further drawing anthropological attention to intellectuals and their knowledge practices (ranging from the poetic-literary to the technical-administrative) will help the anthropology of nations and nationalism to (a) locate the role of human agency in the creation, circulation, and contestation of national culture, (b) capture the intellectual work involved in nationalism and bureaucracy in its full diversity, and (c) imagine a new series of ethnographic access points among educated professionals for the study of nationalism in action.
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  • 28
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    Annual Review of Anthropology 34 (2005), S. 13 
    ISSN: 0084-6570
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Ethnic Sciences , Biology
    Notes: Scholarly interest in body size has increased in concert with recent efforts to shape and assess bodies in particular ways within industrialized social contexts. Attending to both overt and covert references to Eurocentric body projects, this chapter reviews literature in anthropology, sociology, and cultural studies that addresses the cultural politics of body size in various parts of the world. It begins with a discussion of biocultural paradigms, which accept certain biomedical categories even when challenging or reconfiguring their hegemonic power. Next is a survey of works analyzing body size within "non-Western" groups as well as European and North American subgroups. These studies often employ culturally powerful "Western" constructs as foils, an approach that risks cultural othering. The analysis then turns to the extensive literature that unpacks dominant Euro-American body practices and discourses. Here, diverse perspectives on several key concerns in sociocultural anthropology are considered; concepts of culture and power, theories of the body and embodiment, and understandings of human agency vary in instructive ways. The chapter concludes with a review of scholarship on postcolonial processes and representations that incorporates a critical perspective on Eurocentric preoccupations with body size.
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  • 29
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Earth and Planetary Sciences 1 (1973), S. 297-311 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Earth and Planetary Sciences 1 (1973), S. 39-61 
    ISSN: 0084-6597
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    Topics: Geosciences , Physics
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    Annual Review of Earth and Planetary Sciences 2 (1974), S. 101-150 
    ISSN: 0084-6597
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Earth and Planetary Sciences 2 (1974), S. 239-256 
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    Annual Review of Earth and Planetary Sciences 2 (1974), S. 333-367 
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 113-132 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Orogenic collapse is a process that transfers gravitational potential energy from regions of high potential energy to regions of lower potential energy. This transfer is classically considered to be accomplished by extension in the orogenic core and by synchronous shortening in foreland regions of the orogen. Not all extensional features in collisional mountain belts need, however, reflect orogenic collapse. Normal faulting, thrust faulting, and strike-slip faulting are all active in different parts of the Alps today and reflect complex local responses to ongoing Europe-Adria convergence. The Western Alps is the only area today where extension and shortening radial to orogen trend occur synchronously and where orogenic collapse may be an important process. Elsewhere in the Alps, normal faults are oriented at a high angle to orogen trend and were primarily active in Oligocene and Miocene time. Most present-day activity in the Central and Eastern Alps is on strike-slip faults that are accommodating lateral extrusion of material rather than orogenic collapse.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 163-193 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Weather and climate predictions are uncertain, because both forecast initial conditions and the computational representation of the known equations of motion are uncertain. Ensemble prediction systems provide the means to estimate the flow-dependent growth of uncertainty during a forecast. Sources of uncertainty must therefore be represented in such systems. In this paper, methods used to represent model uncertainty are discussed. It is argued that multimodel and related ensembles are vastly superior to corresponding single-model ensembles, but do not provide a comprehensive representation of model uncertainty. A relatively new paradigm is discussed, whereby unresolved processes are represented by computationally efficient stochastic-dynamic schemes.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 247-276 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Processes operating beneath glaciers can have a greater influence on flow dynamics than those operating within them. The variety and complexity of these processes, which involve interactions among ice, water, and geological solids, resist efforts to establish simple truths and can lead to surprising outcomes. Thermal conditions at the ice-bed interface (melting or nonmelting) and the mechanical properties of the glacier substrate (soft or hard) determine which processes can be activated. The warm-soft case supports the greatest variety of processes and is the most important for fast-flow dynamics and for the mobilization of subglacial sediment. Process interactions can lead to oscillations and spatio-temporal switching behavior in glaciers and ice sheets as well as to the generation of subglacial landforms.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 301-333 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: Microbes are recognized as important components of the Earth system, playing key roles in controlling the composition of the atmosphere and surface waters, forming the basis of the marine food web, and the cycling of chemicals in the ocean. A revolution in microbial ecology has occurred in the past 15Đ??20 years with the advent of rapid methods for discovering and sequencing the genes of uncultivated microbes from natural environments. Initially based on sequences from the 16S rRNA gene, this revolution made it possible to identify microorganisms without first cultivating them, to discover and characterize the immense previously unsuspected diversity of the microbial world, and to reconstruct the evolutionary relationships among microbes. Subsequent focus on functional genes, those that encode enzymes that catalyze biogeochemical transformations, and current work on larger DNA fragments and entire genomes make it possible to link microbial diversity to ecosystem function. These approaches have yielded insights into the regulation of microbial activity and proof of the microbial role in biogeochemical processes previously unknown. Questions raised by the molecular revolution, which are now the focus of microbial ecology research, include the significance of microbial diversity and redundancy to biogeochemical processes and ecosystem function.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 421-442 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: The Ediacara biota (575Đ??542 Ma) marks the first appearance of large, architecturally complex organisms in Earth history. Present evidence suggests that the Ediacara biota included a mixture of stem- and crown-group radial animals, stem-group bilaterian animals, "failed experiments" in animal evolution, and perhaps representatives of other eukaryotic kingdoms. These soft-bodied organisms were preserved under (or rarely within) event beds of sand or volcanic ash, and four distinct preservational styles (Flinders-, Fermeuse-, Conception-, and Nama-style) profoundly affected the types of organisms and features that could be preserved. Even the earliest Ediacaran communities (575Đ??565 Ma) show vertical and lateral niche subdivision of the sessile, benthic, filter-feeding organisms, which is strikingly like that of Phanerozoic and modern communities. Later biological and ecological innovations include mobility (〉555 Ma), calcification (550 Ma), and predation (〈549 Ma). The Ediacara biota abruptly disappeared 542 million years ago, probably as a consequence of mass extinction andor biological interactions with the rapidly evolving animals of the Cambrian explosion.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 531-570 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: The Earth has a radiogenic W-isotopic composition compared to chondrites, demonstrating that it formed while 182Hf (half-life 9 Myr) was extant in Earth and decaying to 182W. This implies that Earth underwent early and rapid accretion and core formation, with most of the accumulation occurring in Đ♯10 Myr, and concluding approximately 30 Myr after the origin of the Solar System. The Hf-W data for lunar samples can be reconciled with a major Moon-forming impact that terminated the terrestrial accretion process Đ♯30 Myr after the origin of the Solar System. The suggestion that the proto-Earth to impactor mass ratio was 7:3 and occurred during accretion is inconsistent with the W isotope data. The W isotope data is satisfactorily modeled with a Mars-sized impactor on proto-Earth (proto-Earth to impactor ratio of 9:1) to form the Moon at Đ♯30 Myr.
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    Annual Review of Earth and Planetary Sciences 33 (2005), S. 645-671 
    ISSN: 0084-6597
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Geosciences , Physics
    Notes: The influence of surface orography on patterns of precipitation gives rise to some of the most pronounced climate gradients on Earth, and plays a fundamental role in the interaction between the atmosphere and the rest of the Earth System on a wide variety of time scales. The physical mechanisms involved comprise a rich set of interactions encompassing fluid dynamics, thermodynamics, and micron-scale cloud processes, as well as being dependent on the larger-scale patterns of the atmospheric general circulation. Investigations into orographic precipitation have pursued three parallel tracks of inquiry: observations, theory, and modeling. Significant advances have been made in each over the last few decades, and these are summarized and synthesized here. While many aspects of the basic mechanisms responsible for orographic precipitation have been understood, important issues remain unresolved. The sheer number of contributing processes, together with their convoluted interactions, make the quantitative prediction of precipitation in complex terrain a very hard task. However, while prediction of precipitation amounts for any given event may be difficult, various lines of evidence suggest that the patterns of orgraphic precipitation, even on scales of a few kilometers, are much more robust.
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    Annual Review of Neuroscience 28 (2005), S. 109-126 
    ISSN: 0147-006X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Although the neurobiological understanding of autism has been increasing exponentially, the diagnosis of autism spectrum conditions still rests entirely on behavioral criteria. Autism is therefore most productively approached using a combination of biological and psychological theory. The triad of behavioral abnormalities in social function, communication, and restricted and repetitive behaviors and interests can be explained psychologically by an impaired capacity for empathizing, or modeling the mental states governing the behavior of people, along with a superior capacity for systemizing, or inferring the rules governing the behavior of objects. This empathizing-systemizing theory explains other psychological models such as impairments of executive function or central coherence, and may have a neurobiological basis in abnormally low activity of brain regions subserving social cognition, along with abnormally high activity of regions subserving lower-level, perceptual processingĐ??a pattern that may result from a skewed balance of local versus long-range functional connectivity.
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    Annual Review of Neuroscience 28 (2005), S. 223-250 
    ISSN: 0147-006X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Forty years since the initial discovery of neurogenesis in the postnatal rat hippocampus, investigators have now firmly established that active neurogenesis from neural progenitors continues throughout life in discrete regions of the central nervous systems (CNS) of all mammals, including humans. Significant progress has been made over the past few years in understanding the developmental process and regulation of adult neurogenesis, including proliferation, fate specification, neuronal maturation, targeting, and synaptic integration of the newborn neurons. The function of this evolutionarily conserved phenomenon, however, remains elusive in mammals. Adult neurogenesis represents a striking example of structural Plasticity in the mature CNS environment. Advances in our understanding of adult neurogenesis will not only shed light on the basic principles of adult Plasticity, but also may lead to strategies for cell replacement therapy after injury or degenerative neurological diseases.
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    Annual Review of Neuroscience 28 (2005), S. 533-563 
    ISSN: 0147-006X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Proteins with engineered sensitivities to light are infiltrating the biological mechanisms by which neurons generate and detect electrochemical signals. Encoded in DNA and active only in genetically specified target cells, these proteins provide selective optical interfaces for observing and controlling signaling by defined groups of neurons in functioning circuits, in vitro and in vivo. Light-emitting sensors of neuronal activity (reporting calcium increase, neurotransmitter release, or membrane depolarization) have begun to reveal how information is represented by neuronal assemblies, and how these representations are transformed during the computations that inform behavior. Light-driven actuators control the electrical activities of central neurons in freely moving animals and establish causal connections between the activation of specific neurons and the expression of particular behaviors. Anchored within mathematical systems and control theory, the combination of finely resolved optical field sensing and finely resolved optical field actuation will open new dimensions for the analysis of the connectivity, dynamics, and plasticity of neuronal circuits, and perhaps even for replacing lostĐ??or designing novelĐ??functionalities.
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    Annual Review of Neuroscience 28 (2005), S. 327-355 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Gradients of axon guidance molecules have long been postulated to control the development of the organization of neural connections into topographic maps. We review progress in identifying molecules required for mapping and the mechanisms by which they act, focusing on the visual system, the predominant model for map development. The Eph family of receptor tyrosine kinases and their ligands, the ephrins, remain the only molecules that meet all criteria for graded topographic guidance molecules, although others fulfill some criteria. Recent reports further define their modes of action and new roles for them, including EphB/ephrin-B control of dorsal-ventral mapping, bidirectional signaling of EphAs/ephrin-As, bifunctional action of ephrins as attractants or repellents in a context-dependent manner, and complex interactions between multiple guidance molecules. In addition, spontaneous patterned neural activity has recently been shown to be required for map refinement during a brief critical period. We speculate on additional activities required for map development and suggest a synthesis of molecular and cellular mechanisms within the context of the complexities of map development.
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    Annual Review of Immunology 23 (2005), S. 1-21 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: This essay summarizes my 40 years of research in immunology. As a young physician, I encountered a patient with Waldenstro?m's macroglobulinemia, and this inspired me to study the structure of IgM. I began to ask how antibody responses are regulated. In the late 1960s, the essential role of T cells in antibody production had been reported. In search of molecules mediating T cell helper function, I discovered activities in the culture supernatant of T cells that induced proliferation and differentiation of B cells. This led to my life's work: studying one of those factors, interleukin-6 (IL-6). To my surprise, IL-6 turned out to play additional roles, including myeloma growth factor and hepatocyte-stimulating factor activities. More importantly, it was involved in a number of diseases, such as rheumatoid arthritis and Castleman's disease. I feel exceptionally fortunate that my work not only revealed the framework of cytokine signaling, including identification of the IL-6 receptor, gp130, NF-IL6, STAT3, and SOCS-1, but also led to the development of a new therapy for chronic inflammatory diseases.
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    Annual Review of Immunology 23 (2005), S. 945-974 
    ISSN: 0732-0582
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The Notch pathway is gaining increasing recognition as a key regulator of developmental choices, differentiation, and function throughout the hematolymphoid system. Notch controls the generation of hematopoietic stem cells during embryonic development and may affect their subsequent homeostasis. Commitment to the T??cell lineage and subsequent stages of early thymopoiesis is critically regulated by Notch. Recent data indicate that Notch can also direct the differentiation and activity of peripheral T and B cells. Thus, the full spectrum of Notch effects is just beginning to be understood. In this review, we discuss this explosion of knowledge as well as current controversies and challenges in the field.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 93-122 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Psoriasis is an inflammatory/autoimmune disease and, as with many autoimmune diseases, is associated with alleles from the major histocompatibility complex (MHC). With psoriasis and autoimmune disease, the penetrance of the MHC-associated alleles is never 100%, even for monozygotic twins. This may be because development requires additional environmental and/or genetic modifiers or requires specific T-cell receptor arrangements. Families segregating single or multilocus susceptibility alleles other than the MHC have also been reported. Overlapping genetic locations of loci for different autoimmune diseases have been known for several years and are starting to reveal common genes or genetic variants. These include genes normally involved in preventing spontaneous T-cell activation or proliferation, immune synapse formation, or cytokine production via pathways such as those mediated by NF?”B and those involved in thymic selection. Autoimmunity may also involve dysregulation of genes or pathways regulated by the RUNX family of transcription factors. RUNX is involved in hematopoietic cell development, development of T cells in the thymus, chromatin remodeling, and gene silencing. Hence, its effect on cells of the immune system may be due to variable changes in gene expression and could account for variable body surface involvement and waxing and waning of disease.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 381-406 
    ISSN: 1527-8204
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The availability of complete genome sequences and the wealth of large-scale biological data sets now provide an unprecedented opportunity to elucidate the genetic basis of rare and common human diseases. Here we review some of the emerging genomics technologies and data resources that can be used to infer gene function to prioritize candidate genes. We then describe some computational strategies for integrating these large-scale data sets to provide more faithful descriptions of gene function, and how such approaches have recently been applied to discover genes underlying Mendelian disorders. Finally, we discuss future prospects and challenges for using integrative genomics to systematically discover not only single genes but also entire gene networks that underlie and modify human disease.
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    Annual Review of Genomics and Human Genetics 6 (2005), S. 69-92 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mammalian X chromosome inactivation is one of the most striking examples of epigenetic gene regulation. Early in development one of the pair of Đ♯160-Mb X chromosomes is chosen to be silenced, and this silencing is then stably inherited through subsequent somatic cell divisions. Recent advances have revealed many of the chromatin changes that underlie this stable silencing of an entire chromosome. The key initiator of these changes is a functional RNA, XIST, which is transcribed from, and associates with, the inactive X chromosome, although the mechanism of association with the inactive X and recruitment of facultative heterochromatin remain to be elucidated. This review describes the unique evolutionary history and resulting genomic structure of the X chromosome as well as the current understanding of the factors and events involved in silencing an X chromosome in mammals.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 499-518 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Cooperation is common across nonhuman animal taxa, from the hunting of large game in lions to the harvesting of building materials in ants. Theorists have proposed a number of models to explain the evolution of cooperative behavior. These ultimate explanations, however, rarely consider the proximate constraints on the implementation of cooperative behavior. Here we review several types of cooperation and propose a suite of cognitive abilities required for each type to evolve. We propose that several types of cooperation, though theoretically possible and functionally adaptive, have not evolved in some animal species because of cognitive constraints. We argue, therefore, that future modeling efforts and experimental investigations into the adaptive function of cooperation in animals must be grounded in a realistic assessment of the psychological ingredients required for cooperation. Such an approach can account for the puzzling distribution of cooperative behaviors across taxa, especially the seemingly unique occurrence of cooperation observed in our own species.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 643-689 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 23-46 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Two consequences of terrestrial ectothermy (low energy needs and behavioral control of body temperatures) have had major consequences for the evolution of reptile life-history traits. For example, reproducing females can manipulate incubation temperatures and thus phenotypic traits of their offspring by retaining developing eggs in utero. This ability has resulted in multiple evolutionary transitions from oviparity to viviparity in cool-climate reptile populations. The spatial and temporal heterogeneity of operative temperatures in terrestrial habitats also has favored careful nest-site selection and a matching of embryonic reaction norms to thermal regimes during incubation (e.g., via temperature-dependent sex determination). Many of the life-history features in which reptiles differ from endothermic vertebratesĐ??such as their small offspring sizes, large litter sizes, and infrequent reproductionĐ??are direct consequences of ectothermy, reflecting freedom from heat-conserving constraints on body size and energy storage. Ectothermy confers immense flexibility, enabling a dynamic matching of life-history traits to local circumstances. This flexibility has generated massive spatial and temporal variation in life-history traits via phenotypic plasticity as well as adaptation. The diversity of life histories in reptiles can best be interpreted within a conceptual framework that views reptiles as low-energy, variable-temperature systems.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 541-562 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 147-168 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 319-346 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Bacteria communicate with one another using chemical signal molecules. As in higher organisms, the information supplied by these molecules is critical for synchronizing the activities of large groups of cells. In bacteria, chemical communication involves producing, releasing, detecting, and responding to small hormone-like molecules termed autoinducers . This process, termed quorum sensing, allows bacteria to monitor the environment for other bacteria and to alter behavior on a population-wide scale in response to changes in the number and/or species present in a community. Most quorum-sensing-controlled processes are unproductive when undertaken by an individual bacterium acting alone but become beneficial when carried out simultaneously by a large number of cells. Thus, quorum sensing confuses the distinction between prokaryotes and eukaryotes because it enables bacteria to act as multicellular organisms. This review focuses on the architectures of bacterial chemical communication networks; how chemical information is integrated, processed, and transduced to control gene expression; how intra- and interspecies cell-cell communication is accomplished; and the intriguing possibility of prokaryote-eukaryote cross-communication.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 177-201 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Brassinosteroids (BRs), the polyhydroxylated steroid hormones of plants, regulate the growth and differentiation of plants throughout their life cycle. Over the past several years, genetic and biochemical approaches have yielded great progress in understanding BR signaling. Unlike their animal counterparts, BRs are perceived at the plasma membrane by direct binding to the extracellular domain of the BRI1 receptor S/T kinase. BR perception initiates a signaling cascade, acting through a GSK3 kinase, BIN2, and the BSU1 phosphatase, which in turn modulates the phosphorylation state and stability of the nuclear transcription factors BES1 and BZR1. Microarray technology has been used extensively to provide a global view of BR genomic effects, as well as a specific set of target genes for BES1 and BZR1. These gene products thus provide a framework for how BRs regulate the growth of plants.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 381-410 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: ʼ̛?‚ heterodimeric integrins mediate dynamic adhesive cell-cell and cell-extracellular matrix (ECM) interactions in metazoa that are critical in growth and development, hemostasis, and host defense. A central feature of these receptors is their capacity to change rapidly and reversibly their adhesive functions by modulating their ligand-binding affinity. This is normally achieved through interactions of the short cytoplasmic integrin tails with intracellular proteins, which trigger restructuring of the ligand-binding site through long-range conformational changes in the ectodomain. Ligand binding in turn elicits conformational changes that are transmitted back to the cell to regulate diverse responses. The publication of the integrin ʼ̛V?‚3 crystal structure has provided the context for interpreting decades-old biochemical studies. Newer NMR, crystallographic, and EM data, reviewed here, are providing a better picture of the dynamic integrin structure and the allosteric changes that guide its diverse functions.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 581-603 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Over the past decades, intravital microscopy (IVM), the imaging of cells in living organisms, has become a valuable tool for studying the molecular determinants of lymphocyte trafficking. Recent advances in microscopy now make it possible to image cell migration and cell-cell interactions in vivo deep within intact tissues. Here, we summarize the principal techniques that are currently used in IVM, discuss options and tools for fluorescence-based visualization of lymphocytes in microvessels and tissues, and describe IVM models used to explore lymphoid and non-lymphoid organs. The latter will be introduced according to the physiologic itinerary of developing and differentiating T and B lymphocytes as they traffic through the body, beginning with their development in bone marrow and thymus and continuing with their migration to secondary lymphoid organs and peripheral tissues.
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    Annual Review of Biochemistry 39 (1970), S. 1-25 
    ISSN: 0066-4154
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    Annual Review of Biochemistry 39 (1970), S. 131-150 
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    Annual Review of Biochemistry 39 (1970), S. 291-322 
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    Annual Review of Biochemistry 39 (1970), S. 429-472 
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    Annual Review of Biochemistry 39 (1970), S. 841-866 
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    Annual Review of Biochemistry 39 (1970), S. 867-888 
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    Annual Review of Biochemistry 39 (1970), S. 777-820 
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    Annual Review of Biochemistry 40 (1971), S. 345-374 
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    Annual Review of Biochemistry 40 (1971), S. 449-464 
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    Annual Review of Biochemistry 40 (1971), S. 465-500 
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    Annual Review of Biochemistry 40 (1971), S. 573-604 
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    Annual Review of Biochemistry 40 (1971), S. 775-810 
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    Annual Review of Biochemistry 41 (1972), S. 179-202 
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    Annual Review of Biochemistry 41 (1972), S. 377-408 
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    Annual Review of Biochemistry 41 (1972), S. 467-502 
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    Annual Review of Biochemistry 41 (1972), S. 731-752 
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    Annual Review of Biochemistry 40 (1971), S. 827-854 
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    Annual Review of Biochemistry 40 (1971), S. 969-1012 
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    Annual Review of Biochemistry 42 (1973), S. 235-258 
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    Annual Review of Biochemistry 42 (1973), S. 303-328 
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    Annual Review of Biochemistry 41 (1972), S. 129-160 
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    Annual Review of Biochemistry 43 (1974), S. 1-14 
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    Annual Review of Biochemistry 41 (1972), S. 231-300 
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    Annual Review of Biochemistry 43 (1974), S. 215-241 
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    Annual Review of Biochemistry 42 (1973), S. 507-540 
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    Annual Review of Biochemistry 43 (1974), S. 401-417 
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    Annual Review of Biochemistry 74 (2005), S. 649-679 
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    Notes: Antibiotics target ribosomes at distinct locations within functionally relevant sites. They exert their inhibitory action by diverse modes, including competing with substrate binding, interfering with ribosomal dynamics, minimizing ribosomal mobility, facilitating miscoding, hampering the progression of the mRNA chain, and blocking the nascent protein exit tunnel. Although the ribosomes are highly conserved organelles, they possess subtle sequence and/or conformational variations. These enable drug selectivity, thus facilitating clinical usage. The structural implications of these differences were deciphered by comparisons of high-resolution structures of complexes of antibiotics with ribosomal particles from eubacteria resembling pathogens and from an archaeon that shares properties with eukaryotes. The various antibiotic-binding modes detected in these structures demonstrate that members of antibiotic families possessing common chemical elements with minute differences might bind to ribosomal pockets in significantly different modes, governed by their chemical properties. Similarly, the nature of seemingly identical mechanisms of drug resistance is dominated, directly or via cellular effects, by the antibiotics' chemical properties. The observed variability in antibiotic binding and inhibitory modes justifies expectations for structurally based improved properties of existing compounds as well as for the discovery of novel drug classes.
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    Annual Review of Biochemistry 74 (2005), S. 595-648 
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    Notes: Protein complexes consisting of structural maintenance of chromosomes (SMC) and kleisin subunits are crucial for the faithful segregation of chromosomes during cell proliferation in prokaryotes and eukaryotes. Two of the best-studied SMC complexes are cohesin and condensin. Cohesin is required to hold sister chromatids together, which allows their biorientation on the mitotic spindle. Cleavage of cohesin's kleisin subunit by the separase protease then triggers the movement of sister chromatids into opposite halves of the cell during anaphase. Condensin is required to organize mitotic chromosomes into coherent structures that prevent them from getting tangled up during segregation. Here we describe the discovery of SMC complexes and discuss recent advances in determining how members of this ancient protein family may function at a mechanistic level.
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    Annual Review of Biochemistry 74 (2005), S. 115-128 
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    Notes: Hypoxia-inducible factor (HIF) is a master transcriptional regulator of hypoxia-inducible genes and consists of a labile ʼ̛ subunit (such as HIF1ʼ̛) and a stable subunit (such as HIF1?‚ or ARNT). In the presence of oxygen, HIFʼ̛ family members are hydroxylated on one of two conserved prolyl residues by members of the egg-laying-defective nine (EGLN) family. Prolyl hydroxylation generates a binding site for a ubiquitin ligase complex containing the von Hippel-Lindau (VHL) tumor suppressor protein, which results in HIFʼ̛ destruction. In addition, the HIFʼ̛ transcriptional activation function is modulated further by asparagine hydroxylation by FIH (factor-inhibiting HIF), which affects recruitment of the coactivators p300 and CBP. These findings provide new mechanistic insights into oxygen sensing by metazoans and are the first examples of protein hydroxylation being used in intracellular signaling. The existence of three human EGLN family members, as well as other putative hydroxylases, raises the possibility that this signal is used in other contexts by other proteins.
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    Annual Review of Biochemistry 74 (2005), S. 129-177 
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    Notes: The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75??A?? away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, amongf other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.
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    Annual Review of Biochemistry 74 (2005), S. 739-789 
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    Notes: In the endoplasmic reticulum (ER), secretory and transmembrane proteins fold into their native conformation and undergo posttranslational modifications important for their activity and structure. When protein folding in the ER is inhibited, signal transduction pathways, which increase the biosynthetic capacity and decrease the biosynthetic burden of the ER to maintain the homeostasis of this organelle, are activated. These pathways are called the unfolded protein response (UPR). In this review, we briefly summarize principles of protein folding and molecular chaperone function important for a mechanistic understanding of UPR-signaling events. We then discuss mechanisms of signal transduction employed by the UPR in mammals and our current understanding of the remodeling of cellular processes by the UPR. Finally, we summarize data that demonstrate that UPR signaling feeds into decision making in other processes previously thought to be unrelated to ER function, e.g., eukaryotic starvation responses and differentiation programs.
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    Annual Review of Biochemistry 74 (2005), S. 179-198 
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    Notes: There is very significant evidence that cognate codons and/or anticodons are unexpectedly frequent in RNA-binding sites for seven of eight biological amino acids that have been tested. This suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acidĐ??binding sites to become modern codons and anticodons. We explicitly show that this stereochemical basis is consistent with subsequent optimization of the code to minimize the effect of coding mistakes on protein structure. These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself.
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    Annual Review of Biochemistry 74 (2005), S. 481-514 
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    Notes: Large-genome eukaryotes use heritable cytosine methylation to silence promoters, especially those associated with transposons and imprinted genes. Cytosine methylation does not reinforce or replace ancestral gene regulation pathways but instead endows methylated genomes with the ability to repress specific promoters in a manner that is buffered against changes in the internal and external environment. Recent studies have shown that the targeting of de novo methylation depends on multiple inputs; these include the interaction of repeated sequences, local states of histone lysine methylation, small RNAs and components of the RNAi pathway, and divergent and catalytically inert cytosine methyltransferase homologues that have acquired regulatory roles. There are multiple families of DNA (cytosine-5) methyltransferases in eukaryotes, and each family appears to be controlled by different regulatory inputs. Sequence-specific DNA-binding proteins, which regulate most aspects of gene expression, do not appear to be involved in the establishment or maintenance of genomic methylation patterns.
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    Annual Review of Biochemistry 74 (2005), S. 199-217 
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    Notes: The importance of small, noncoding RNAs that act as regulators of transcription, of RNA modification or stability, and of mRNA translation is becoming increasingly apparent. Here we discuss current knowledge of regulatory RNA function and review how the RNAs have been identified in a variety of organisms. Many of the regulatory RNAs act through base-pairing interactions with target RNAs. The base-pairing RNAs can be grouped into two general classes: those that are encoded on the opposite strand of their target RNAs such that they contain perfect complementarity with their targets, and those that are encoded at separate locations on the chromosome and have imperfect base-pairing potential with their targets. Other regulatory RNAs act by modifying protein activity, in some cases by mimicking the structures of other RNA or DNA molecules.
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    Annual Review of Biochemistry 74 (2005), S. 711-738 
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    Topics: Chemistry and Pharmacology , Biology
    Notes: Broadly defined, the concept of gene therapy involves the transfer of genetic material into a cell, tissue, or whole organ, with the goal of curing a disease or at least improving the clinical status of a patient. A key factor in the success of gene therapy is the development of delivery systems that are capable of efficient gene transfer in a variety of tissues, without causing any associated pathogenic effects. Vectors based upon many different viral systems, including retroviruses, lentiviruses, adenoviruses, and adeno-associated viruses, currently offer the best choice for efficient gene delivery. Their performance and pathogenicity has been evaluated in animal models, and encouraging results form the basis for clinical trials to treat genetic disorders and acquired diseases. Despite some initial success in these trials, vector development remains a seminal concern for improved gene therapy technologies.
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    Annual Review of Biochemistry 74 (2005), S. 867-900 
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    Notes: We can now assign about two thirds of the sequences from completed genomes to as few as 1400 domain families for which structures are known and thus more ancient evolutionary relationships established. About 200 of these domain families are common to all kingdoms of life and account for nearly 50% of domain structure annotations in the genomes. Some of these domain families have been very extensively duplicated within a genome and combined with different domain partners giving rise to different multidomain proteins. The ways in which these domain combinations evolve tend to be specific to the organism so that less than 15% of the protein families found within a genome appear to be common to all kingdoms of life. Recent analyses of completed genomes, exploiting the structural data, have revealed the extent to which duplication of these domains and modifications of their functions can expand the functional repertoire of the organism, contributing to increasing complexity.
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