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  • Articles  (1,006)
  • American Institute of Physics (AIP)
  • American Meteorological Society
  • Annual Reviews
  • Molecular Diversity Preservation International (MDPI)
  • 2020-2022  (717)
  • 1935-1939  (289)
  • Biology  (1,006)
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  • Articles  (1,006)
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  • 1
    Publication Date: 2020-04-29
    Description: Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10–25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.
    Print ISSN: 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 2
    Publication Date: 2020-10-21
    Description: Aging occurs in all sexually reproducing organisms. That is, physical degradation over time occurs from conception until death. While the life span of a species is often viewed as a benchmark of aging, the pace and intensity of physical degradation over time varies owing to environmental influences, genetics, allocation of energetic investment, and phylogenetic history. Significant variation in aging within mammals, primates, and great apes, including humans, is therefore common across species. The evolution of aging in the hominin lineage is poorly known; however, clues can be derived from the fossil record. Ongoing advances continue to shed light on the interactions between life-history variables such as reproductive effort and aging. This review presents our current understanding of the evolution of aging in humans, drawing on population variation, comparative research, trade-offs, and sex differences, as well as tissue-specific patterns of physical degradation. Implications for contemporary health challenges and the future of human evolutionary anthropology research are also discussed.
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    Topics: Biology , Ethnic Sciences
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  • 3
    Publication Date: 2020-10-21
    Description: This article positions types at the center of anthropological knowledge production, considering them both from the abstract, analytical perspective of expert typologies and from the tacit, phenomenological perspective of everyday practices of typification. Proposing what an “anthropology of types,” broadly construed and across these two scales, might look like, I examine the histories and uses of types and typological thinking in anthropology, highlighting the empirical, analytical, methodological, ethical, and political questions they have raised. I then describe the phenomenological foundations of typification, how sociocultural and linguistic anthropologists have approached it, and the accompanying challenges related to translation and representation. Finally, I review ethnographies of expert practices of type production, tracing the circuit of typification–typology–type and back again to show how forms of expertise institutionalize lay knowledge in ways that further solidify the misrecognition of types as natural, and examine visual and arts-based interventions that draw attention to these processes.
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  • 4
    Publication Date: 2020-10-21
    Description: Fleeing violence, poverty, abuse, war, and climatic change, tens of millions of people have fled their homes in the Global South seeking refuge in adjacent nations and in the Global North. This modern migration entails a material, sensual experience in time. The craft of archaeology has traditionally engaged with the material, the sensual, and the temporal. Archaeologists who study the materiality of modern undocumented migration embrace activist-engaged research that applies the craft of archaeology to the contemporary world. They study the materiality of migration to reveal and comprehend the lived experience of displaced persons. They seek to understand the barriers erected to that journey, the things migrants acquire and leave on the trail, migrant placemaking, their stranded lives, how they build new lives, what the migrants have left behind in their home countries, and the heritage of forced migration. They approach this work in critical solidarity with displaced peoples.
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  • 5
    Publication Date: 2020-10-21
    Description: The prehistory of the Aegean, Balkans, and Carpathian Basin has changed dramatically in the last two decades. This review covers five aspects of these changes: ( a) the development of theoretical approaches, in which diversification from cultural archaeology has seen the spread of processual, postprocessual and later approaches; ( b) the acquisition of data, with the key major development being the proliferation of large-scale infrastructure projects; ( c) the synthesis of data, the most significant challenge being to make sense of the massive increase in paleo-environmental research, materials science, regional surveys, and site monographs; ( d) thematic questions, whose very diversity underscores the discipline's growth in these regions; and ( e) emergent trends, such as the creation of new forms of synthesis at the local, regional, and interregional scales, the theorizing and differentiation of new ways of relating people, places, plants, and animals and objects, and continuing diversification in the application of scientific techniques.
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  • 6
    Publication Date: 2020-10-21
    Description: While the proliferation of industrial toxic substances over the past century has had drastic environmental and bodily effects, conventional methods of measuring and mitigating those effects continue to produce uncertainty. The project of living in a toxic world entails ethical, technical, and aesthetic efforts to understand toxicity as a contingent encounter among beings, systems, and things, rather than as a fundamental characteristic of particular substances. Anthropologists do not just observe such encounters; they live and work within them. This review examines recent anthropological research on toxicity, proposing that responses to toxic disaster and occupational exposure, as well as acts of familial, state, or corporate care, are all modes of “toxic worlding.” The review concludes with a summary of recent research in collaborative and engaged anthropology, suggesting that such approaches are essential not so much for purifying or detoxifying the world as for making it otherwise.
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  • 7
    Publication Date: 2020-10-21
    Description: Unlike most mammals, human fathers cooperate with mothers to care for young to an extraordinary degree. Human paternal care likely evolved alongside our unique life history strategy of raising slow-developing, energetically costly children, often in rapid succession. Adaptive frameworks generally assume that paternal provisioning played a critical role in this pattern's emergence. We draw on nonhuman primate data to propose that nonprovisioning forms of low-cost hominin male care were potentially foundational and ratcheted up through evolutionary time, helping facilitate social contexts for later subsistence specialization and sharing. We then argue for expanding the breadth of anthropological research on paternal effects in families, particularly in three domains: direct care and teaching;social capital cultivation; and reduction of family conflict. Anthropologists can greatly contribute to conversations about the determinants of children's development across contexts, but we need to ask more expansive questions about the pathways through which caregivers (including fathers) affect child outcomes.
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  • 8
    Publication Date: 2020-10-21
    Description: Amenorrhea, anovulatory cycles, miscarriages, and other reproductive outcomes are often seen as pathological. Life history theory, in contrast, treats those outcomes as adaptations that helped women optimize the timing of reproductive ventures across our evolutionary history. Women's bodies adjust their reproductive strategies in response to socio-ecological conditions, a process mediated by the hypothalamic-pituitary-adrenal axis (HPAA). Here, we review the links between socio-ecological conditions, HPAA activity, and the pace of women's reproductive transitions such as puberty, age at first birth, interbirth interval, and perimenopause. We also discuss the HPAA's role as a modulator of reproductive function: It not only suppresses it but may also prime women's bodies for future reproductive ventures. We conclude by reviewing challenges and opportunities within our subfield, including the need for transdisciplinary teams to develop longitudinal studies to improve our understanding of women's reproductive trajectories and outcomes from the moment they are conceived.
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  • 9
    Publication Date: 2020-10-21
    Description: The Anthropocene, a proposed name for a geological epoch marked by human impacts on global ecosystems, has inspired anthropologists to critique, to engage in theoretical and methodological experimentation, and to develop new forms of collaboration. Critics are concerned that the term Anthropocene overemphasizes human mastery or erases differential human responsibilities, including imperialism, capitalism, and racism, and new forms of technocratic governance. Others find the term helpful in drawing attention to disastrous environmental change, inspiring a reinvigorated attention to the ontological unruliness of the world, to multiple temporal scales, and to intertwined social and natural histories. New forms of noticing can be linked to systems analytics, including capitalist world systems, structural comparisons of patchy landscapes, infrastructures and ecological models, emerging sociotechnical assemblages, and spirits. Rather than a historical epoch defined by geologists, the Anthropocene is a problem that is pulling anthropologists into new forms of noticing and analysis, and into experiments and collaborations beyond anthropology.
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  • 10
    Publication Date: 2020-10-21
    Description: Alloparental or extramaternal care is an integral aspect of human childrearing. This behavior has been explored both as an extension of the primary mother–infant dyad that evolved to meet the demands of altricial offspring and as an economic exchange of energy and resources. Much of this research centers on foraging or small-scale communities and positions the household as the central unit through which to explore negotiations of care. In this review, I use evidence from Black Caribbean communities living in industrialized countries to challenge the broad applicability of the analytical model of the bounded household and to question whether our current articulations of theory and empirical assessments of extramaternal care are well suited to investigations of these behaviors in the vast majority of contemporary human populations. Alloparental practices in the Caribbean reflect dynamic responses to maternal migration and the local influence of global labor markets. The children who remain at home experience variability in the care received from their surrogate parents. The dynamic aspect of the care practices enacted by these transnational families reveals the behavioral flexibility that has been integral to human survival.
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  • 11
    Publication Date: 2020-10-21
    Description: This review demonstrates that recent contributions by archaeologists to the study of cuisine and cooking present a new addition to the field of anthropology. Archaeologists situate their work historically and contextually by examining cuisines that are culturally constructed. Studying cooking and food preparation helps elucidate relationships among material practices, understandings of taste, identity, power, and meaning in a society. Archaeologists can not only discover specific ingredients in food, but also reconstruct recipes, decipher regional cuisines, ascertain sensory experiences, recover the tools in spatial context, recreate techniques used to prepare food in the past, and overall learn more about the social and cultural contexts of the human experience. This type of investigation is possible because archaeological work uses complementary data to explain social practices and because advances in archaeological methods make accessible previously undetectable data. Experimental archaeology focused on cooking in the past has not only revealed important social information but also captured the imagination of the public. Archaeological research on cooking and cuisine reveals social, political, religious, and economic practices in the past, and it has a unique ability to engage the present with the past through public outreach and solutions to food-related problems.
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  • 12
    Publication Date: 2020-10-21
    Description: Everyday life is critical in the constitution of selves and societies alike. Archaeology, with its attention to material and spatial remains, is in a unique position to further studies of everyday life, as ordinary materials and spaces formalize how people learn about themselves and their world. This review defines an archaeology of everyday life, examines its historical roots, synthesizes new literature on the topic, and outlines future directions. Although there is no established subfield called “everyday archaeology,” a rich and ever-growing body of recent research illustrates the impact of everyday life studies on archaeological interpretations and practice. Research on everyday life peoples the past in a way that few other paradigms do.
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  • 13
    Publication Date: 2020-10-21
    Description: The adaptive origins of primates and anthropoid primates are topics of enduring interest to biological anthropologists. A convention in these discussions is to treat the light environment as binary—night is dark, day is light—and to impute corresponding selective pressure on the visual systems and behaviors of primates. In consequence, debate has tended to focus on whether a given trait can be interpreted as evidence of nocturnal or diurnal behavior in the primate fossil record. Such classification elides the variability in light, or the ways that primates internalize light in their environments. Here, we explore the liminality of light by focusing on what it is, its many sources, and its flux under natural conditions. We conclude by focusing on the intensity and spectral properties of twilight, and we review the mounting evidence of its importance as a cue that determines the onset or offset of primate activities as well as the entrainment of circadian rhythms.
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  • 14
    Publication Date: 2020-10-21
    Description: On November 16, 1990, US President George H.W. Bush signed into law the Native American Graves Protection and Repatriation Act (NAGPRA). This federal legislation marked the culmination of decades of debate among scientists, curators, and Native American leaders and activists over the control of ancestral human remains and sacred, funerary, and communally owned objects. Anthropologists have now investigated myriad aspects of NAGPRA, from its underlying philosophical arguments; to its legislative history, its legal ramifications and political effects, and the methods of its implementation; to how it has remade American museums, archaeologists, tribes, and federally funded repositories; and to how it has ushered in a new (even if imperfect) period of collaboration and partnership. This article reviews the last 50 years of scholarship on repatriation, with a particular focus on NAGPRA's last 30 years.
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  • 15
    Publication Date: 2020-10-21
    Description: Previous research on language and emotion in anthropology has demonstrated that rather than being a private, subjective, and prediscursive experience belonging to individuals, emotion is an intersubjective, emergent process that is not only everywhere in language but also everywhere language is. In this review, I discuss how recent research in linguistic anthropology and related fields has continued to build on such insights in investigations of the flow of affect across bodies, the ways in which politically situated ideologies of language and emotion function at various institutional scales, and the role of language and emotion in the enactment of agency. Overall, my discussion is framed in a consideration of how this body of work contributes both theoretically and methodologically to understanding the role that language and emotion play in mediating the dynamic relationship between vulnerability and political agency.
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  • 16
    Publication Date: 2020-10-21
    Description: As complex institutions extend into and govern greater spheres of social life, ethnographers contend with policy in an ever-widening range of fieldsites. This review examines anthropology of policy as an emerging subfield of political anthropology, focusing on policy making as central to contemporary governance in English-language ethnographies. Broadening the analytical field in the study of policy to include the targets of policy and their allies is one of the central contributions of an anthropological approach to policy making. Anthropological studies of policy production, implementation, and effects face significant methodological and ethical challenges. Scholarly debates in the United States and Europe continue to erupt over the production of scholarship intended to inform policy making, including the co-option of ethnography. While turning the anthropological gaze on powerful political actors could contribute to decolonization efforts within the discipline, ethically adopting ethnographic research into policy making requires complex alliances with communities targeted by policy.
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  • 17
    Publication Date: 2020-02-15
    Description: Immunoglobulins (Igs), as one of the hallmarks of adaptive immunity, first arose approximately 500 million years ago with the emergence of jawed vertebrates. Two events stand out in the evolutionary history of Igs from cartilaginous fish to mammals: ( a) the diversification of Ig heavy chain (IgH) genes, resulting in Ig isotypes or subclasses associated with novel functions, and ( b) the diversification of genetic and structural strategies, leading to the creation of the antibody repertoire we know today. This review first gives an overview of the IgH isotypes identified in jawed vertebrates to date and then highlights the implications or applications of five new recent discoveries arising from comparative studies of Igs derived from different vertebrate species.
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
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  • 18
    Publication Date: 2020-02-15
    Description: Evidence for global bee population declines has catalyzed a rapidly evolving area of research that aims to identify the causal factors and to effectively assess the status of pollinator populations. The term pollinator health emerged through efforts to understand causes of bee decline and colony losses, but it lacks a formal definition. In this review, we propose a definition for pollinator health and synthesize the available literature on the application of standardized biomarkers to assess health at the individual, colony, and population levels. We focus on biomarkers in honey bees, a model species, but extrapolate the potential application of these approaches to monitor the health status of wild bee populations. Biomarker-guided health measures can inform beekeeper management decisions, wild bee conservation efforts, and environmental policies. We conclude by addressing challenges to pollinator health from a One Health perspective that emphasizes the interplay between environmental quality and human, animal, and bee health.
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  • 19
    Publication Date: 2020-10-21
    Description: Climate anthropology has broadened over the past decade from predominately locally focused studies on climate impacts to encompass new approaches to climate science, mitigation, sustainability transformations, risks, and resilience. We examine how theoretical positionings, including from actor–network theory, new materialisms, ontologies, and cosmopolitics, have helped expand anthropological climate research, particularly in three key interrelated areas. First, we investigate ethnographic approaches to climate science knowledge production, particularly around epistemic authority, visioning of futures, and engagements with the material world. Second, we consider climate adaptation studies that critically examine discourses and activities surrounding concepts of vulnerability, subjectivities, and resilience. Third, we analyze climate mitigation, including energy transitions, technological optimism, market-based solutions, and other ways of living in a carbon-constrained world. We conclude that anthropological approaches provide novel perspectives, made possible through engagements with our uniquely situated research partners, as well as opportunities for opening up diverse solutions and possible transformative futures.
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  • 20
    Publication Date: 2020-10-21
    Description: Archaeological investigations of late prehistoric Iberia between the Neolithic and Bronze Age (6000–1500 BCE) have long been a battleground between indigenist and exogenous models, and understandings of mobility and alterity have played an important role in these debates. Prior to the development of radiocarbon dating, key cultural transformations, such as megaliths, copper metallurgy, fortified hilltop settlements, and Beakers, were generally associated with nonlocal peoples, migrants, or colonizers. With the incorporation of radiocarbon dating to Iberian archaeological contexts in the 1980s and the determination of the antiquity of many of these cultural changes, the pendulum swung in the other direction, with a marked shift toward viewing autochthonous origins for these watershed transitions. In recent years, developments in strontium isotope analyses, genetics, and raw material characterization studies have provided new evidence for the mobility of peoples and things, and diffusionist models, sometimes without critical theorization, have once again reemerged.
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  • 21
    Publication Date: 2020-02-15
    Description: African swine fever is a devastating disease that can result in death in almost all infected pigs. The continuing spread of African swine fever from Africa to Europe and recently to the high–pig production countries of China and others in Southeast Asia threatens global pork production and food security. The African swine fever virus is an unusual complex DNA virus and is not related to other viruses. This has presented challenges for vaccine development, and currently none is available. The virus is extremely well adapted to replicate in its hosts in the sylvatic cycle in East and South Africa. Its spread to other regions, with different wildlife hosts, climatic conditions, and pig production systems, has revealed unexpected epidemiological scenarios and different challenges for control. Here we review the epidemiology of African swine fever in these different scenarios and methods used for control. We also discuss progress toward vaccine development and research priorities to better understand this complex disease and improve control.
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  • 22
    Publication Date: 2020-02-15
    Description: In pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complexspans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models.
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  • 23
    Publication Date: 2020-02-15
    Description: Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: ( a) Large increases in the numbers of genetic markers (from dozens to 104–106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and ( b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.
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  • 24
    Publication Date: 2020-02-15
    Description: Development of assisted reproductive technologies has been driven by the goals of reducing the incidence of infertility, increasing the number of offspring from genetically elite animals, facilitating genetic manipulation, aiding preservation and long-distance movement of germplasm, and generating research material. Superovulation is associated with reduced fertilization rate and alterations in endometrial function. In vitro production of embryos can have a variety of consequences. Most embryos produced in vitro are capable of establishing pregnancy and developing into healthy neonatal animals. However, in vitro production is associated with reduced ability to develop to the blastocyst stage, increased incidence of failure to establish pregnancy, placental dysfunction, and altered fetal development. Changes in the developmental program mean that some consequences of being produced in vitro can extend into adult life. Reduced competence of the embryo produced in vitro to develop to the blastocyst stage is caused largely by disruption of events during oocyte maturation and fertilization. Conditions during embryo culture can affect embryo freezability and competence to establish pregnancy after transfer. Culture conditions, including actions of embryokines, can also affect the postnatal phenotype of the resultant progeny.
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  • 25
    Publication Date: 2020-02-15
    Description: Pigs are increasingly important animals for modeling human pediatric nutrition and gastroenterology and complementing mechanistic studies in rodents. The comparative advantages in size and physiology of the neonatal pig have led to new translational and clinically relevant models of important diseases of the gastrointestinal tract and liver in premature infants. Studies in pigs have established the essential roles of prematurity, microbial colonization, and enteral nutrition in the pathogenesis of necrotizing enterocolitis. Studies in neonatal pigs have demonstrated the intestinal trophic effects of akey gut hormone, glucagon-like peptide 2 (GLP-2), and its role in the intestinal adaptation process and efficacy in the treatment of short bowel syndrome. Further, pigs have been instrumental in elucidating the physiology of parenteral nutrition–associated liver disease and the means by which phytosterols, fibroblast growth factor 19, and a new generation of lipid emulsions may modify disease. The premature pig will continue to be a valuable model in the development of optimal infant diets (donor human milk, colostrum), specific milk bioactives (arginine, growth factors), gut microbiota modifiers (pre-, pro-, and antibiotics), pharmaceutical drugs (GLP-2 analogs, FXR agonists), and novel diagnostic tools (near-infrared spectroscopy) to prevent and treat these pediatric diseases.
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  • 26
    Publication Date: 2020-02-15
    Description: To feed people in the coming decades, an increase in sustainable animal food production is required. The efficiency of the global food production system is dependent on the knowledge and improvement of its submodels, such as food animal production. Scientists use statistical models to interpret their data, but models are also used to understand systems and to integrate their components. However, empirical models cannot explain systems. Mechanistic models yield insight into the mechanism and provide guidance regarding the exploration of the system. This review offers an overview of models, from simple empirical to more mechanistic models. We demonstrate their applications to amino acid transport, mass balance, whole-tissue metabolism, digestion and absorption, growth curves, lactation, and nutrient excretion. These mechanistic models need to be integrated into a full model using big data from sensors, which represents a new challenge. Soon, training in quantitative and computer science skills will be required to develop, test, and maintain advanced food system models.
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  • 27
    Publication Date: 2020-02-15
    Description: Fish show extraordinary sexual plasticity, changing sex naturally as part of their life cycle or reversing sex because of environmental stressors. This plasticity shows that sexual fate is not an irreversible process but the result of an ongoing tug-of-war for supremacy between male and female signaling networks. The behavioral, gonadal, and morphological changes involved in this process are well described, yet the molecular events that underpin those changes remain poorly understood. Epigenetic modifications emerge as a critical link between environmental stimuli, the onset of sex change, and subsequent maintenance of sexual phenotype. Here we synthesize current knowledge of sex change, focusing on the genetic and epigenetic processes that are likely involved in the initiation and regulation of sex change. We anticipate that better understanding of sex change in fish will shed new light on sex determination and development in vertebrates and on how environmental perturbations affect sexual fate.
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  • 28
    Publication Date: 2020-02-15
    Description: This narrative is a personal view of adventures in genetic science and society that have blessed my life and career across five decades. The advances I enjoyed and the lessons I learned derive from educational training, substantial collaboration, and growing up in the genomics age. I parse the stories into six research disciplines my students, fellows, and colleagues have entered and, in some cases, made an important difference. The first is comparative genetics, where evolutionary inference is applied to genome organization, from building gene maps in the 1970s to building whole genome sequences today. The second area tracks the progression of molecular evolutionary advances and applications to resolve the hierarchical relationship among living species in the silence of prehistory. The third endeavor outlines the birth and maturation of genetic studies and application to species conservation. The fourth theme discusses how emerging viruses studied in a genomic sense opened our eyes to host–pathogen interaction and interdependence. The fifth research emphasis outlines the population genetic–based search and discovery of human restriction genes that influence the epidemiological outcome of abrupt outbreaks, notably HIV–AIDS and several cancers. Finally, the last arena explored illustrates how genetic individualization in human and animals has improved forensic evidence in capital crimes. Each discipline has intuitive and technological overlaps, and each has benefitted from the contribution of genetic and genomic principles I learned so long ago from Drosophila. The journey continues.
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  • 29
    Publication Date: 2020-02-15
    Description: Ruminant production systems face significant challenges currently, driven by heightened awareness of their negative environmental impact and the rapidly rising global population. Recent findings have underscored how the composition and function of the rumen microbiome are associated with economically valuable traits, including feed efficiency and methane emission. Although omics-based technological advances in the last decade have revolutionized our understanding of host-associated microbial communities, there remains incongruence over the correct approach for analysis of large omic data sets. A global approach that examines host/microbiome interactions in both the rumen and the lower digestive tract is required to harness the full potential of the gastrointestinal microbiome for sustainable ruminant production. This review highlights how the ruminant animal production community may identify and exploit the causal relationships between the gut microbiome and host traits of interest for a practical application of omic data to animal health and production.
    Print ISSN: 2165-8102
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  • 30
    Publication Date: 2020-09-25
    Description: Ocean temperature variability is a fundamental component of the Earth's climate system, and extremes in this variability affect the health of marine ecosystems around the world. The study of marine heatwaves has emerged as a rapidly growing field of research, given notable extreme warm-water events that have occurred against a background trend of global ocean warming. This review summarizes the latest physical and statistical understanding of marine heatwaves based on how they are identified, defined, characterized, and monitored through remotely sensed and in situ data sets. We describe the physical mechanisms that cause marine heatwaves, along with their global distribution, variability, and trends. Finally, we discuss current issues in this developing research area, including considerations related to the choice of climatological baseline periods in defining extremes and how to communicate findings in the context of societal needs. Expected final online publication date for the Annual Review of Marine Science, Volume 13 is January 4, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 31
    Publication Date: 2020-09-28
    Description: Over the last few decades, an increasing number of vertebrate taxa have been identified that undergo programmed genome rearrangement, or programmed DNA loss, during development. In these organisms, the genome of germ cells is often reproducibly different from the genome of all other cells within the body. Although we clearly have not identified all vertebrate taxa that undergo programmed genome loss, the list of species known to undergo loss now represents ∼10% of vertebrate species, including several basally diverging lineages. Recent studies have shed new light on the targets and mechanisms of DNA loss and their association with canonical modes of DNA silencing. Ultimately, expansion of these studies into a larger collection of taxa will aid in reconstructing patterns of shared/independent ancestry of programmed DNA loss in the vertebrate lineage, as well as more recent evolutionary events that have shaped the structure and content of eliminated DNA. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 32
    Publication Date: 2020-10-21
    Description: The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.
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    Topics: Biology , Ethnic Sciences
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  • 33
    Publication Date: 2020-02-15
    Description: Marsupial genomes, which are packaged into large chromosomes, provide a powerful resource for studying the mechanisms of genome evolution. The extensive and valuable body of work on marsupial cytogenetics, combined more recently with genome sequence data, has enabled prediction of the 2 n = 14 karyotype ancestral to all marsupial families. The application of both chromosome biology and genome sequencing, or chromosomics, has been a necessary approach for various aspects of mammalian genome evolution, such as understanding sex chromosome evolution and the origin and evolution of transmissible tumors in Tasmanian devils. The next phase of marsupial genome evolution research will employ chromosomics approaches to begin addressing fundamental questions in marsupial genome evolution and chromosome evolution more generally. The answers to these complex questions will impact our understanding across a broad range of fields, including the genetics of speciation, genome adaptation to environmental stressors, and species management.
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  • 34
    Publication Date: 2020-02-15
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  • 35
    Publication Date: 2020-02-15
    Description: The concept of influenza A virus (IAV) subpopulations emerged approximately 75 years ago, when Preben von Magnus described “incomplete” virus particles that interfere with the replication of infectious virus. It is now widely accepted that infectious particles constitute only a minor portion of biologically active IAV subpopulations. The IAV quasispecies is an extremely diverse swarm of biologically and genetically heterogeneous particle subpopulations that collectively influence the evolutionary fitness of the virus. This review summarizes the current knowledge of IAV subpopulations, focusing on their biologic and genomic diversity. It also discusses the potential roles IAV subpopulations play in virus pathogenesis and live attenuated influenza vaccine development.
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  • 36
    Publication Date: 2020-06-20
    Description: The investigation of water oxidation in photosynthesis has remained a central topic in biochemical research for the last few decades due to the importance of this catalytic process for technological applications. Significant progress has been made following the 2011 report of a high-resolution X-ray crystallographic structure resolving the site of catalysis, a protein-bound Mn4CaOx complex, which passes through ≥5 intermediate states in the water-splitting cycle. Spectroscopic techniques complemented by quantum chemical calculations aided in understanding the electronic structure of the cofactor in all (detectable) states of the enzymatic process. Together with isotope labeling, these techniques also revealed the binding of the two substrate water molecules to the cluster. These results are described in the context of recent progress using X-ray crystallography with free-electron lasers on these intermediates. The data are instrumental for developing a model for the biological water oxidation cycle.
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  • 37
    Publication Date: 2020-06-20
    Description: DNA methylation at the 5-position of cytosine (5mC) plays vital roles in mammalian development. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), and the two DNMT families, DNMT3 and DNMT1, are responsible for methylation establishment and maintenance, respectively. Since their discovery, biochemical and structural studies have revealed the key mechanisms underlying how DNMTs catalyze de novo and maintenance DNA methylation. In particular, recent development of low-input genomic and epigenomic technologies has deepened our understanding of DNA methylation regulation in germ lines and early stage embryos. In this review, we first describe the methylation machinery including the DNMTs and their essential cofactors. We then discuss how DNMTs are recruited to or excluded from certain genomic elements. Lastly, we summarize recent understanding of the regulation of DNA methylation dynamics in mammalian germ lines and early embryos with a focus on both mice and humans.
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  • 38
    Publication Date: 2020-06-20
    Description: Clustered regularly interspaced short palindromic repeats (CRISPR) together with their accompanying cas (CRISPR-associated) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA, such as viral genomes. CRISPR-Cas systems provide a uniquely powerful defense because they can adapt to newly encountered genomes. The adaptive ability of these systems has been exploited, leading to their development as highly effective tools for genome editing. The widespread use of CRISPR-Cas systems has driven a need for methods to control their activity. This review focuses on anti-CRISPRs (Acrs), proteins produced by viruses and other mobile genetic elements that can potently inhibit CRISPR-Cas systems. Discovered in 2013, there are now 54 distinct families of these proteins described, and the functional mechanisms of more than a dozen have been characterized in molecular detail. The investigation of Acrs is leading to a variety of practical applications and is providing exciting new insight into the biology of CRISPR-Cas systems.
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  • 39
    Publication Date: 1937-06-01
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  • 40
    Publication Date: 2020-06-20
    Description: ATP-binding cassette (ABC) transporters constitute one of the largest and most ancient protein superfamilies found in all living organisms. They function as molecular machines by coupling ATP binding, hydrolysis, and phosphate release to translocation of diverse substrates across membranes. The substrates range from vitamins, steroids, lipids, and ions to peptides, proteins, polysaccharides, and xenobiotics. ABC transporters undergo substantial conformational changes during substrate translocation. A comprehensive understanding of their inner workings thus requires linking these structural rearrangements to the different functional state transitions. Recent advances in single-particle cryogenic electron microscopy have not only delivered crucial information on the architecture of several medically relevant ABC transporters and their supramolecular assemblies, including the ATP-sensitive potassium channel and the peptide-loading complex, but also made it possible to explore the entire conformational space of these nanomachines under turnover conditions and thereby gain detailed mechanistic insights into their mode of action.
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  • 41
    Publication Date: 2020-06-20
    Description: The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1–4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2–ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.
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  • 42
    Publication Date: 2020-06-20
    Description: It is impossible to do justice in one review article to a researcher of the stature of Christopher Dobson. His career spanned almost five decades, resulting in more than 870 publications and a legacy that will continue to influence the lives of many for decades to come. In this review, I have attempted to capture Chris's major contributions: his early work, dedicated to understanding protein-folding mechanisms; his collaborative work with physicists to understand the process of protein aggregation; and finally, his later career in which he developed strategies to prevent misfolding. However, it is not only this body of work but also the man himself who inspired an entire generation of scientists through his patience, ability to mentor, and innate generosity. These qualities remain a hallmark of the way in which he conducted his research—research that will leave a lasting imprint on science.
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  • 43
    Publication Date: 1935-06-01
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  • 44
    Publication Date: 2020-06-20
    Description: Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs’ central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and Escherichia coli class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.
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  • 45
    Publication Date: 2020-10-06
    Description: Thriving in times of resource scarcity requires an incredible flexibility of behavioral, physiological, cellular, and molecular functions that must change within a relatively short time. Hibernation is a collection of physiological strategies that allows animals to inhabit inhospitable environments, where they experience extreme thermal challenges and scarcity of food and water. Many different kinds of animals employ hibernation, and there is a spectrum of hibernation phenotypes. Here, we focus on obligatory mammalian hibernators to identify the unique challenges they face and the adaptations that allow hibernators to overcome them. This includes the cellular and molecular strategies used to combat low environmental and body temperatures and lack of food and water. We discuss metabolic, neuronal, and hormonal cues that regulate hibernation and how they are thought to be coordinated by internal clocks. Last, we touch on questions that are left to be addressed in the field of hibernation research. Studies from the last century and more recent work reveal that hibernation is not simply a passive reduction in body temperature and vital parameters but rather an active process seasonally regulated at the molecular, cellular, and organismal levels.
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    Topics: Biology , Medicine
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  • 46
    Publication Date: 2020-10-06
    Description: Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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  • 47
    Publication Date: 2020-10-06
    Description: Development encapsulates the morphogenesis of an organism from a single fertilized cell to a functional adult. A critical part of development is the specification of organ forms. Beyond the molecular control of morphogenesis, shape in essence entails structural constraints and thus mechanics. Revisiting recent results in biophysics and development, and comparing animal and plant model systems, we derive key overarching principles behind the formation of organs across kingdoms. In particular, we highlight how growing organs are active rather than passive systems and how such behavior plays a role in shaping the organ. We discuss the importance of considering different scales in understanding how organs form. Such an integrative view of organ development generates new questions while calling for more cross-fertilization between scientific fields and model system communities.
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  • 48
    Publication Date: 2020-06-20
    Description: Mitochondria are essential metabolic hubs that dynamically adapt to physiological demands. More than 40 proteases residing in different compartments of mitochondria, termed mitoproteases, preserve mitochondrial proteostasis and are emerging as central regulators of mitochondrial plasticity. These multifaceted enzymes limit the accumulation of short-lived, regulatory proteins within mitochondria, modulate the activity of mitochondrial proteins by protein processing, and mediate the degradation of damaged proteins. Various signaling cascades coordinate the activity of mitoproteases to preserve mitochondrial homeostasis and ensure cell survival. Loss of mitoproteases severely impairs the functional integrity of mitochondria, is associated with aging, and causes pleiotropic diseases. Understanding the dual function of mitoproteases as regulatory and quality control enzymes will help unravel the role of mitochondrial plasticity in aging and disease.
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  • 49
    Publication Date: 2020-06-20
    Description: DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.
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  • 50
    Publication Date: 2020-06-20
    Description: Transcription in several organisms from certain bacteria to humans has been observed to be stochastic in nature: toggling between active and inactive states. Periods of active nascent RNA synthesis known as bursts represent individual gene activation events in which multiple polymerases are initiated. Therefore, bursting is the single locus illustration of both gene activation and repression. Although transcriptional bursting was originally observed decades ago, only recently have technological advances enabled the field to begin elucidating gene regulation at the single-locus level. In this review, we focus on how biochemical, genomic, and single-cell data describe the regulatory steps of transcriptional bursts.
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  • 51
    Publication Date: 2020-06-20
    Description: This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.
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  • 52
    Publication Date: 2020-06-20
    Description: Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type–specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type–specific transcriptional programming with exquisite fidelity is essential for normal development.
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  • 53
    Publication Date: 2020-06-20
    Description: The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5′ splice site (5′SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5′SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5′SS, producing a free 5′ exon. Removal of the BP adenosine from the active site allows the 3′SS to bind, so that the 5′ exon attacks the 3′SS to produce mature mRNA and an excised lariat intron.
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  • 54
    Publication Date: 2020-06-20
    Description: Mitochondria are essential in most eukaryotes and are involved in numerous biological functions including ATP production, cofactor biosyntheses, apoptosis, lipid synthesis, and steroid metabolism. Work over the past two decades has uncovered the biogenesis of cellular iron-sulfur (Fe/S) proteins as the essential and minimal function of mitochondria. This process is catalyzed by the bacteria-derived iron-sulfur cluster assembly (ISC) machinery and has been dissected into three major steps: de novo synthesis of a [2Fe-2S] cluster on a scaffold protein; Hsp70 chaperone–mediated trafficking of the cluster and insertion into [2Fe-2S] target apoproteins; and catalytic conversion of the [2Fe-2S] into a [4Fe-4S] cluster and subsequent insertion into recipient apoproteins. ISC components of the first two steps are also required for biogenesis of numerous essential cytosolic and nuclear Fe/S proteins, explaining the essentiality of mitochondria. This review summarizes the molecular mechanisms underlying the ISC protein–mediated maturation of mitochondrial Fe/S proteins and the importance for human disease.
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  • 55
    Publication Date: 2020-06-20
    Description: Natural rubber (NR), principally comprising cis-1,4-polyisoprene, is an industrially important natural hydrocarbon polymer because of its unique physical properties, which render it suitable for manufacturing items such as tires. Presently, industrial NR production depends solely on latex obtained from the Pará rubber tree, Hevea brasiliensis. In latex, NR is enclosed in rubber particles, which are specialized organelles comprising a hydrophobic NR core surrounded by a lipid monolayer and membrane-bound proteins. The similarity of the basic carbon skeleton structure between NR and dolichols and polyprenols, which are found in most organisms, suggests that the NR biosynthetic pathway is related to the polyisoprenoid biosynthetic pathway and that rubber transferase, which is the key enzyme in NR biosynthesis, belongs to the cis-prenyltransferase family. Here, we review recent progress in the elucidation of molecular mechanisms underlying NR biosynthesis through the identification of the enzymes that are responsible for the formation of the NR backbone structure.
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  • 56
    Publication Date: 2020-06-20
    Description: Protein folding in the cell is mediated by an extensive network of 〉1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology–informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.
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  • 57
    Publication Date: 1937-06-01
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  • 58
    Publication Date: 2020-06-20
    Description: My coworkers and I have used animal viruses and their interaction with host cells to investigate cellular processes difficult to study by other means. This approach has allowed us to branch out in many directions, including membrane protein characterization, endocytosis, secretion, protein folding, quality control, and glycobiology. At the same time, our aim has been to employ cell biological approaches to expand the fundamental understanding of animal viruses and their pathogenic lifestyles. We have studied mechanisms of host cell entry and the uncoating of incoming viruses as well as the synthesis, folding, maturation, and intracellular movement of viral proteins and molecular assemblies. I have had the privilege to work in institutions in four different countries. The early years in Finland (the University of Helsinki) were followed by 6 years in Germany (European Molecular Biology Laboratory), 16 years in the United States (Yale School of Medicine), and 16 years in Switzerland (ETH Zurich).
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  • 59
    Publication Date: 2020-10-06
    Description: Plants constantly perceive internal and external cues, many of which they need to address to safeguard their proper development and survival. They respond to these cues by selective activation of specific metabolic pathways involving a plethora of molecular players that act and interact in complex networks. In this review, we illustrate and discuss the complexity in the combinatorial control of plant specialized metabolism. We hereby go beyond the intuitive concept of combinatorial control as exerted by modular-acting complexes of transcription factors that govern expression of specialized metabolism genes. To extend this discussion, we also consider all known hierarchical levels of regulation of plant specialized metabolism and their interfaces by referring to reported regulatory concepts from the plant field. Finally, we speculate on possible yet-to-be-discovered regulatory principles of plant specialized metabolism that are inspired by knowledge from other kingdoms of life and areas of biological research.
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  • 60
    Publication Date: 2020-10-21
    Description: Recent anthropological works on the aftermath of mass violence can be studied as having generated a negative methodology. New work has addressed the gaps, voids, and hollows of knowledge production in and about sites of mass atrocity and is developing novel research practices within these schisms. While considering the (im)possibility of research as the condition of possibility (as well as the question) for anthropological (and historical) work on the long durée of mass violence, this review highlights some adverse ethnographic methods that have emerged (and have been conceptualized) in the interstices. A critical positionality vis-à-vis anthropology's positive outlook for evidentiary presences in the field has moved scholars of mass atrocity and its aftermath toward methods that would tarry in and through the negative.
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    Topics: Biology , Ethnic Sciences
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  • 61
    Publication Date: 2020-10-21
    Description: Deaf anthropology is a field that exists in conversation with but is not reducible to the interdisciplinary field of deaf studies. Deaf anthropology is predicated upon a commitment to understanding deafnesses across time and space while holding on to “deaf” as a category that does something socially, politically, morally, and methodologically. In doing so, deaf anthropology moves beyond compartmentalizing the body, the senses, and disciplinary boundaries. We analyze the close relationship between anthropology writ large and deaf studies: Deaf studies scholars have found analytics and categories from anthropology, such as the concept of culture, to be productive in analyzing deaf peoples’ experiences and the sociocultural meanings of deafness. As we note, however, scholarship on deaf peoples’ experiences is increasingly variegated. This review is arranged into four overlapping sections titled Socialities and Similitudes; Mobilities, Spaces, and Networks; Modalities and the Sensorium; and Technologies and Futures.
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  • 62
    Publication Date: 2020-10-21
    Description: This article summarizes my perspective on vital lessons that I have learned over my 45 years as a practicing anthropologist. To avoid repeating previously published biographical details of my life, I have only briefly described the facts and stages of my career here. Instead I have focused on a personal account of what I have learned from the events and experiences of my career and have attempted to distill them into underlying premises that have guided my academic vocation. I call them “nine truths I live by.”
    Print ISSN: 0084-6570
    Electronic ISSN: 1545-4290
    Topics: Biology , Ethnic Sciences
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  • 63
    Publication Date: 2020-02-15
    Description: Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
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  • 64
    Publication Date: 2020-02-15
    Description: Recent research has convincingly demonstrated a bidirectional communication axis between the gut and liver that enables the gut microbiota to strongly affect animals’ feeding behavior and energy metabolism. As such, the gut–liver axis enables the host to control and shape the gut microbiota and to protect the intestinal barrier. Gut microbiota–host communication is based on several gut-derived compounds, such as short-chain fatty acids, bile acids, methylamines, amino acid–derived metabolites, and microbial-associated molecular patterns, which act as communication signals, and multiple host receptors, which sense the signals, thereby stimulating signaling and metabolic pathways in all key tissues of energy metabolism and food intake regulation. Disturbance in the microbial ecosystem balance, or microbial dysbiosis, causes profound derangements in the regulation of appetite and satiety in the hypothalamic centers of the brain and in key metabolic pathways in peripheral tissues owing to intestinal barrier disruption and subsequent induction of hepatic and hypothalamic inflammation.
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  • 65
    Publication Date: 2020-02-15
    Description: Snake venoms are primarily composed of proteins and peptides, and these toxins have developed high selectivity to their biological targets. This makes venoms interesting for exploration into protein evolution and structure–function relationships. A single venom protein superfamily can exhibit a variety of pharmacological effects; these variations in activity originate from differences in functional sites, domains, posttranslational modifications, and the formations of toxin complexes. In this review, we discuss examples of how the major venom protein superfamilies have diversified, as well as how newer technologies in the omics fields, such as genomics, transcriptomics, and proteomics, can be used to characterize both known and unknown toxins.Because toxins are bioactive molecules with a rich diversity of activities, they can be useful as therapeutic and diagnostic agents, and successful examples of toxin applications in these areas are also reviewed. With the current rapid pace of technology, snake venom research and its applications will only continue to expand.
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  • 66
    Publication Date: 2020-02-15
    Description: Early embryogenesis is characterized by the segregation of cell lineages that fulfill critical roles in the establishment of pregnancy and development of the fetus. The formation of the blastocyst marks the emergence of extraembryonic precursors, needed for implantation, and of pluripotent cells, which differentiate toward the major lineages of the adult organism. The coordinated emergence of these cell types shows that these processes are broadly conserved in mammals. However, developmental heterochrony and changes in gene regulatory networks highlight unique evolutionary adaptations that may explain the diversity in placentation and in the mechanisms controlling pluripotency in mammals. The incorporation of new technologies, including single-cell omics, imaging, and gene editing, is instrumental for comparative embryology. Broadening the knowledge of mammalian embryology will provide new insights into the mechanisms driving evolution and development. This knowledge can be readily translated into biomedical and biotechnological applications in humans and livestock, respectively.
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  • 67
    Publication Date: 2020-06-20
    Description: In all human cells, human leukocyte antigen (HLA) class I glycoproteins assemble with a peptide and take it to the cell surface for surveillance by lymphocytes. These include natural killer (NK) cells and γδ T cells of innate immunity and αβ T cells of adaptive immunity. In healthy cells, the presented peptides derive from human proteins, to which lymphocytes are tolerant. In pathogen-infected cells, HLA class I expression is perturbed. Reduced HLA class I expression is detected by KIR and CD94:NKG2A receptors of NK cells. Almost any change in peptide presentation can be detected by αβ CD8+ T cells. In responding to extracellular pathogens, HLA class II glycoproteins, expressed by specialized antigen-presenting cells, present peptides to αβ CD4+ T cells. In comparison to the families of major histocompatibility complex (MHC) class I, MHC class II and αβ T cell receptors, the antigenic specificity of the γδ T cell receptors is incompletely understood.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 68
    Publication Date: 2020-06-20
    Description: Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.
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    Topics: Biology , Chemistry and Pharmacology
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  • 69
    Publication Date: 2020-06-20
    Description: Complex carbohydrates are essential for many biological processes, from protein quality control to cell recognition, energy storage, and cell wall formation. Many of these processes are performed in topologically extracellular compartments or on the cell surface; hence, diverse secretion systems evolved to transport the hydrophilic molecules to their sites of action. Polyprenyl lipids serve as ubiquitous anchors and facilitators of these transport processes. Here, we summarize and compare bacterial biosynthesis pathways relying on the recognition and transport of lipid-linked complex carbohydrates. In particular, we compare transporters implicated in O antigen and capsular polysaccharide biosyntheses with those facilitating teichoic acid and N-linked glycan transport. Further, we discuss recent insights into the generation, recognition, and recycling of polyprenyl lipids.
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    Topics: Biology , Chemistry and Pharmacology
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  • 70
    Publication Date: 1937-06-01
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    Topics: Biology , Chemistry and Pharmacology
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  • 71
    Publication Date: 2020-06-20
    Description: The evolution of eukaryotic genomes has been propelled by a series of gene duplication events, leading to an expansion in new functions and pathways. While duplicate genes may retain some functional redundancy, it is clear that to survive selection they cannot simply serve as a backup but rather must acquire distinct functions required for cellular processes to work accurately and efficiently. Understanding these differences and characterizing gene-specific functions is complex. Here we explore different gene pairs and families within the context of the endoplasmic reticulum (ER), the main cellular hub of lipid biosynthesis and the entry site for the secretory pathway. Focusing on each of the ER functions, we highlight specificities of related proteins and the capabilities conferred to cells through their conservation. More generally, these examples suggest why related genes have been maintained by evolutionary forces and provide a conceptual framework to experimentally determine why they have survived selection.
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    Topics: Biology , Chemistry and Pharmacology
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  • 72
    Publication Date: 2020-06-20
    Description: Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox ( Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription ( Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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    Topics: Biology , Chemistry and Pharmacology
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  • 73
    Publication Date: 2020-06-20
    Description: Splicing of the precursor messenger RNA, involving intron removal and exon ligation, is mediated by the spliceosome. Together with biochemical and genetic investigations of the past four decades, structural studies of the intact spliceosome at atomic resolution since 2015 have led to mechanistic delineation of RNA splicing with remarkable insights. The spliceosome is proven to be a protein-orchestrated metalloribozyme. Conserved elements of small nuclear RNA (snRNA) constitute the splicing active site with two catalytic metal ions and recognize three conserved intron elements through duplex formation, which are delivered into the splicing active site for branching and exon ligation. The protein components of the spliceosome stabilize the conformation of the snRNA, drive spliceosome remodeling, orchestrate the movement of the RNA elements, and facilitate the splicing reaction. The overall organization of the spliceosome and the configuration of the splicing active site are strictly conserved between human and yeast.
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    Topics: Biology , Chemistry and Pharmacology
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  • 74
    Publication Date: 2020-10-06
    Description: Neutrophils are critical to innate immunity, including host defense against bacterial and fungal infections. They achieve their host defense role by phagocytosing pathogens, secreting their granules full of cytotoxic enzymes, or expelling neutrophil extracellular traps (NETs) during the process of NETosis. NETs are weblike DNA structures decorated with histones and antimicrobial proteins released by activated neutrophils. Initially described as a means for neutrophils to neutralize pathogens, NET release also occurs in sterile inflammation, promotes thrombosis, and can mediate tissue damage. To effectively manipulate this double-edged sword to fight a particular disease, researchers must work toward understanding the mechanisms driving NETosis. Such understanding would allow the generation of new drugs to promote or prevent NETosis as needed. While knowledge regarding the (patho)physiological roles of NETosis is accumulating, little is known about the cellular and biophysical bases of this process. In this review, we describe and discuss our current knowledge of the molecular, cellular, and biophysical mechanisms mediating NET release as well as open questions in the field.
    Print ISSN: 1081-0706
    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 75
    Publication Date: 2020-10-06
    Description: The brain is our most complex organ. During development, neurons extend axons, which may grow over long distances along well-defined pathways to connect to distant targets. Our current understanding of axon pathfinding is largely based on chemical signaling by attractive and repulsive guidance cues. These cues instruct motile growth cones, the leading tips of growing axons, where to turn and where to stop. However, it is not chemical signals that cause motion—motion is driven by forces. Yet our current understanding of the mechanical regulation of axon growth is very limited. In this review, I discuss the origin of the cellular forces controlling axon growth and pathfinding, and how mechanical signals encountered by growing axons may be integrated with chemical signals. This mechanochemical cross talk is an important but often overlooked aspect of cell motility that has major implications for many physiological and pathological processes involving neuronal growth.
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    Topics: Biology , Medicine
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  • 76
    Publication Date: 2020-08-17
    Description: All species within ecosystems contribute to regulating carbon cycling because of their functional integration into food webs. Yet carbon modeling and accounting still assumes that only plants, microbes, and invertebrate decomposer species are relevant to the carbon cycle. Our multifaceted review develops a case for considering a wider range of species, especially herbivorous and carnivorous wild animals. Animal control over carbon cycling is shaped by the animals’ stoichiometric needs and functional traits in relation to the stoichiometry and functional traits of their resources. Quantitative synthesis reveals that failing to consider these mechanisms can lead to serious inaccuracies in the carbon budget. Newer carbon-cycle models that consider food-web structure based on organismal functional traits and stoichiometry can offer mechanistically informed predictions about the magnitudes of animal effects that will help guide new empirical research aimed at developing a coherent understanding of the interactions and importance of all species within food webs. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 77
    Publication Date: 2020-08-17
    Description: Flower evolution is characterized by widespread repetition, with adaptations to pollinator environment evolving in parallel. Recent studies have expanded our understanding of the developmental basis of adaptive floral novelties—petal fusion, bilateral symmetry, heterostyly, and floral dimensions. In this article, we describe patterns of trait evolution and review developmental genetic mechanisms underlying floral novelties. We discuss the diversity of mechanisms for parallel adaptation, the evidence for constraints on these mechanisms, and how constraints help explain observed macroevolutionary patterns. We describe parallel evolution resulting from similarities at multiple hierarchical levels—genetic, developmental, morphological, functional—which indicate general principles in floral evolution, including the central role of hormone signaling. An emerging pattern is mutational bias that may contribute to rapid patterns of parallel evolution, especially if the derived trait can result from simple degenerative mutations. We argue that such mutational bias may be less likely to govern the evolution of novelties patterned by complex developmental pathways. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 78
    Publication Date: 2020-07-31
    Description: The origin of turtles and their uniquely shelled body plan is one of the longest standing problems in vertebrate biology. The unfulfilled need for a hypothesis that both explains the derived nature of turtle anatomy and resolves their unclear phylogenetic position among reptiles largely reflects the absence of a transitional fossil record. Recent discoveries have dramatically improved this situation, providing an integrated, time-calibrated model of the morphological, developmental, and ecological transformations responsible for the modern turtle body plan. This evolutionary trajectory was initiated in the Permian (〉260 million years ago) when a turtle ancestor with a diapsid skull evolved a novel mechanism for lung ventilation. This key innovation permitted the torso to become apomorphically stiff, most likely as an adaption for digging and a fossorial ecology. The construction of the modern turtle body plan then proceeded over the next 100 million years following a largely stepwise model of osteological innovation. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 79
    Publication Date: 2020-09-04
    Description: Interactions between plants and microbes have important influences on evolutionary processes, population dynamics, community structure, and ecosystem function. We review the literature to document how climate change may disrupt these ecological interactions and develop a conceptual framework to integrate the pathways of plant-microbe responses to climate over different scales in space and time. We then create a blueprint to aid generalization that categorizes climate effects into changes in the context dependency of plant-microbe pairs, temporal mismatches and altered feedbacks over time, or spatial mismatches that accompany species range shifts. We pair a new graphical model of how plant-microbe interactions influence resistance to climate change with a statistical approach to predict the consequences of increasing variability in climate. Finally, we suggest pathways through which plant-microbe interactions can affect resilience during recovery from climate disruption. Throughout, we take a forward-looking perspective, highlighting knowledge gaps and directions for future research. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 80
    Publication Date: 2020-08-31
    Description: Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 81
    Publication Date: 2020-08-17
    Description: While the importance of mutualisms across the tree of life is recognized, it is not understood why some organisms evolve high levels of dependence on mutualistic partnerships, while other species remain autonomous or retain or regain minimal dependence on partners. We identify four main pathways leading to the evolution of mutualistic dependence. Then, we evaluate current evidence for three predictions: ( a) Mutualisms with different levels of dependence have distinct stabilizing mechanisms against exploitation and cheating, ( b) less dependent mutualists will return to autonomy more often than those that are highly dependent, and ( c) obligate mutualisms should be less context dependent than facultative ones. Although we find evidence supporting all three predictions, we stress that mutualistic partners follow diverse paths toward—and away from—dependence. We also highlight the need to better examine asymmetry in partner dependence. Recognizing how variation in dependence influences the stability, breakdown, and context dependence of mutualisms generates new hypotheses regarding how and why the benefits of mutualistic partnerships differ over time and space. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 82
    Publication Date: 2020-08-17
    Description: Flowers at times host abundant and specialized communities of bacteria and fungi that influence floral phenotypes and interactions with pollinators. Ecological processes drive variation in microbial abundance and composition at multiple scales, including among plant species, among flower tissues, and among flowers on the same plant. Variation in microbial effects on floral phenotype suggests that microbial metabolites could cue the presence or quality of rewards for pollinators, but most plants are unlikely to rely on microbes for pollinator attraction or reproduction. From a microbial perspective, flowers offer opportunities to disperse between flowers, but microbial species differ in requirements for and benefits received from such dispersal. The extent to which floral microbes shape the evolution of floral traits, influence fitness of floral visitors, and respond to anthropogenic change is unclear. A deeper understanding of these phenomena could illuminate the ecological and evolutionary importance of floral microbiomes and their role in the conservation of plant–pollinator interactions. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 83
    Publication Date: 2020-08-14
    Description: Plants are the foundation of the food web and therefore interact directly and indirectly with myriad organisms at higher trophic levels. They directly provide nourishment to mutualistic and antagonistic primary consumers (e.g., pollinators and herbivores), which in turn are consumed by predators. These interactions produce cascading indirect effects on plants (either trait-mediated or density-mediated). We review how predators affect plant-pollinator interactions and thus how predators indirectly affect plant reproduction, fitness, mating systems, and trait evolution. Predators can influence pollinator abundance and foraging behavior. In many cases, predators cause pollinators to visit plants less frequently and for shorter durations. This decline in visitation can lead to pollen limitation and decreased seed set. However, alternative outcomes can result due to differences in predator, pollinator, and plant functional traits as well as due to altered interaction networks with plant enemies. Furthermore, predators may indirectly affect the evolution of plant traits and mating systems. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 84
    Publication Date: 2020-07-31
    Description: Plant defense theory explores how plants invest in defenses against natural enemies but has focused primarily on the traits expressed by juvenile and mature plants. Here we describe the diverse ways in which seeds are chemically and physically defended. We suggest that through associations with other traits, seeds are likely to exhibit defense syndromes that reflect constraints or trade-offs imposed by selection to attract dispersers, enable effective dispersal, ensure appropriate timing of seed germination, and enhance seedling performance. We draw attention to seed and reproductive traits that are analogous to defense traits in mature plants and describe how the effectiveness of defenses is likely to differ at pre- and postdispersal stages. We also highlight recent insights into the mutualistic and antagonistic interactions between seeds and microbial communities, including fungi and endohyphal bacteria, that can influence seed survival in the soil and subsequent seedling vigor. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 85
    Publication Date: 2020-07-31
    Description: Hedge density, structure, and function vary with primary production and slope gradient and are subject to other diverse factors. Hedgerows are emerging ecosystems with both above- and belowground components. Functions of hedges can be categorized as provisioning, regulating, cultural, and supporting ecosystem services; these functions include food production, noncrop food and wood production, firewood production, pollination, pest control, soil conservation and quality improvement, mitigation of water flux and availability, carbon sequestration, landscape connectivity and character maintenance, and contributions to biodiversity. Urban hedges provide a relatively equitable microclimate and critical connections between green spaces and enhance human health and well-being through contact with biodiversity. Soil and water conservation are well researched in tropical hedges but less is known about their contribution to pollination, pest control, and biodiversity. Establishing a minimum hedge width and longer intervals between cutting of temperate hedges would enhance biosecurity and promote carbon sequestration and biodiversity. Hedges have a global role in mitigating biodiversity loss and climate change, which restoration should maximize, notwithstanding regional character. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 86
    Publication Date: 2020-08-28
    Description: Flowering plants exhibit two principal life-history strategies: annuality (living and reproducing in one year) and perenniality (living more than one year). The advantages of either strategy depend on the relative benefits of immediate reproduction balanced against survivorship and future reproduction. This trade-off means that life-history strategies are associated with particular environments, with annuals being found more often in unpredictable habitats. Annuality and perenniality are the outcome of developmental genetic programs responding to their environment, with perennials being distinguished by their delayed competence to flower and reversion to growth after flowering. Evolutionary transitions between these strategies are frequent and have consequences for mating systems and genome evolution, with perennials being more likely to outcross with higher inbreeding depression and lower rates of molecular evolution. Integrating expectations from life-history theory with knowledge of the developmental genetics of flowering and seasonality is required to understand the mechanisms involved in the evolution of annual and perennial life histories. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 87
    Publication Date: 2020-08-28
    Description: The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 88
    Publication Date: 2020-08-10
    Description: Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity in the distribution of adaptive genetic variation throughout species ranges. In the coming decades, global climate change is expected to induce shifts in the selective pressures that shape this adaptive variation. These changes in selective pressures will likely result in varying degrees of local climate maladaptation and spatial reshuffling of the underlying distributions of adaptive alleles. There is a growing interest in using population genomic data to help predict future disruptions to locally adaptive gene-environment associations. One motivation behind such work is to better understand how the effects of changing climate on populations’ short-term fitness could vary spatially across species ranges. Here we review the current use of genomic data to predict the disruption of local adaptation across current and future climates. After assessing goals and motivations underlying the approach, we review the main steps and associated statistical methods currently in use and explore our current understanding of the limits and future potential of using genomics to predict climate change (mal)adaptation. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 89
    Publication Date: 2020-07-31
    Description: Commensalisms, interactions between two species in which one species benefits and the other experiences no net effect, are frequently mentioned in the ecological literature but are surprisingly little studied. Here we review and synthesize our limited understanding of commensalism. We then argue that commensalism is not a single type of interaction; rather, it is a suite of phenomena associated with distinct ecological processes and evolutionary consequences. For each form of commensalism we define, we present evidence for how, where, and why it occurs, including when it is evolutionarily persistent and when it is an occasional outcome of interactions that are usually mutualistic or antagonistic. We argue that commensalism should be of great interest in the study of species interactions due to its location at the center of the continuum between positive and negative outcomes. Finally, we offer a roadmap for future research. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 90
    Publication Date: 2020-08-10
    Description: Parthenogenesis is asexual reproduction without any required participation from males and, as such, is a null model for sexual reproduction. In a comparative context, we can expand our understanding of the evolution and ecology of sex by investigating the consequences of parthenogenesis. In this review, we examine the theoretical predictions of and empirical results on the evolution of asexual reproduction in vertebrates, focusing on recent studies addressing the origins and geographic spread of parthenogenetic lineages and the genomic consequences of an asexual life history. With advances in computational methods and genome technologies, researchers are poised to make rapid and significant progress in studying the origin and evolution of parthenogenesis in vertebrates, thus providing an important perspective on understanding biodiversity patterns of both asexual and sexual populations. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 91
    Publication Date: 2020-08-28
    Description: The spread of synthetic gene drives is often discussed in the context of panmictic populations connected by gene flow and described with simple deterministic models. Under such assumptions, an entire species could be altered by releasing a single individual carrying an invasive gene drive, such as a standard homing drive. While this remains a theoretical possibility, gene drive spread in natural populations is more complex and merits a more realistic assessment. The fate of any gene drive released in a population would be inextricably linked to the population's ecology. Given the uncertainty often involved in ecological assessment of natural populations, understanding the sensitivity of gene drive spread to important ecological factors is critical. Here we review how different forms of density dependence, spatial heterogeneity, and mating behaviors can impact the spread of self-sustaining gene drives. We highlight specific aspects of gene drive dynamics and the target populations that need further research. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
    Published by Annual Reviews
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  • 92
    Publication Date: 2020-07-31
    Description: Half a million species of herbivorous insects have been described. Most of them are diet specialists, using only a few plant species as hosts. Biologists suspect that their specificity is key to their diversity. But why do herbivorous insects tend to be diet specialists? In this review, we catalog a broad range of explanations. We review the evidence for each and suggest lines of research to obtain the evidence we lack. We then draw attention to a second major question, namely how changes in diet breadth affect the rest of a species’ biology. In particular, we know little about how changes in diet breadth feed back on genetic architecture, the population genetic environment, and other aspects of a species’ ecology. Knowing more about how generalists and specialists differ should go a long way toward sorting out potential explanations of specificity, and yield a deeper understanding of herbivorous insect diversity. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 93
    Publication Date: 2020-09-04
    Description: Evolution has been viewed as occurring primarily through selection among individuals. We present a framework based on multilevel selection for evaluating evolutionary change from individuals to communities, with supporting empirical evidence. Essential to this evaluation is the role that interspecific indirect genetic effects play in shaping community organization, in generating variation among community phenotypes, and in creating community heritability. If communities vary in phenotype, and those phenotypes are heritable and subject to selection at multiple levels, then a community view of evolution must be merged with mainstream evolutionary theory. Rapid environmental change during the Anthropocene will require a better understanding of these evolutionary processes, especially selection acting at the community level, which has the potential to eliminate whole communities while favoring others. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 94
    Publication Date: 2020-08-21
    Description: Integrating knowledge and principles of animal behavior into wildlife conservation and management has led to some concrete successes but has failed to improve conservation outcomes in other cases. Many conservation interventions involve attempts to either attract or repel animals, which we refer to as approach/avoidance issues. These attempts can be reframed as issues of manipulating the decisions animals make, which are driven by their perceptual abilities and attentional biases, as well as the value animals attribute to current stimuli and past learned experiences. These processes all fall under the umbrella of animal cognition. Here, we highlight rules that emerge when considering approach/avoidance conservation issues through the lens of cognitive-based management. For each rule, we review relevant conservation successes and failures to better predict the conditions in which behavior can be manipulated, and we suggest how to avoid future failures. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 95
    Publication Date: 2020-07-31
    Description: Phylogenomics underpins a stable and mostly well-resolved hypothesis for the interrelationships of extant arthropods. Exceptionally preserved fossils are integrated into this framework by coding their morphological characters, as exemplified by total-evidence dating approaches that treat fossils as dated tips in analyses numerically dominated by molecular data. Cambrian fossils inform on the sequence of character acquisition in the arthropod stem group and in the stems of its main extant clades. The arthropod head problem incorporates unique appendage combinations and remains of the nervous system in fossils into a scheme mostly based on neuroanatomy and Hox expression domains for extant forms. Molecular estimates of arthropod origins in the Cryogenian or Ediacaran predate a coherent picture from the arthropod fossil record, which commences as trace fossils in the earliest Cambrian. Probabilistic morphological clock analysis of trilobites, which exemplify the earliest arthropod body fossils, supports a Cambrian origin, without the need to posit an unfossilized Ediacaran history. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 51 is November 2, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 96
    Publication Date: 2020-05-06
    Description: Advances in sequencing techniques and statistical methods have made it possible not only to predict sequences of ancestral proteins but also to identify thousands of mutations in the human exome, some of which are disease associated. These developments have motivated numerous theories and raised many questions regarding the fundamental principles behind protein evolution, which have been traditionally investigated horizontally using the tip of the phylogenetic tree through comparative studies of extant proteins within a family. In this article, we review a vertical comparison of the modern and resurrected ancestral proteins. We focus mainly on the dynamical properties responsible for a protein's ability to adapt new functions in response to environmental changes. Using the Dynamic Flexibility Index and the Dynamic Coupling Index to quantify the relative flexibility and dynamic coupling at a site-specific, single-amino-acid level, we provide evidence that the migration of hinges, which are often functionally critical rigid sites, is a mechanism through which proteins can rapidly evolve. Additionally, we show that disease-associated mutations in proteins often result in flexibility changes even at positions distal from mutational sites, particularly in the modulation of active site dynamics.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 97
    Publication Date: 2020-05-06
    Description: Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 98
    Publication Date: 2020-05-06
    Description: Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, lead to a novel view of enzymes as active matter. Enzyme chemotaxis and EED may be important in biology and could have practical applications in biotechnology and nanotechnology. They are also of considerable biophysical interest; indeed, their physical mechanisms are still quite uncertain. This review provides an analytic summary of experimental studies of these phenomena and of the mechanisms that have been proposed to explain them and offers a perspective on future directions for the field.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 99
    Publication Date: 2020-05-06
    Description: Mitochondria are essential for eukaryotic life. These double-membrane organelles often form highly dynamic tubular networks interacting with many cellular structures. Their highly convoluted contiguous inner membrane compartmentalizes the organelle, which is crucial for mitochondrial function. Since the diameter of the mitochondrial tubules is generally close to the diffraction limit of light microscopy, it is often challenging, if not impossible, to visualize submitochondrial structures or protein distributions using conventional light microscopy. This renders super-resolution microscopy particularly valuable, and attractive, for studying mitochondria. Super-resolution microscopy encompasses a diverse set of approaches that extend resolution, as well as nanoscopy techniques that can even overcome the diffraction limit. In this review, we provide an overview of recent studies using super-resolution microscopy to investigate mitochondria, discuss the strengths and opportunities of the various methods in addressing specific questions in mitochondrial biology, and highlight potential future developments.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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  • 100
    Publication Date: 2020-05-06
    Description: Liquid–liquid phase separation is emerging as the universal mechanism by which membraneless cellular granules form. Despite many previous studies on condensation of intrinsically disordered proteins and low complexity domains, we lack understanding about the role of RNA, which is the essential component of all ribonucleoprotein (RNP) granules. RNA, as an anionic polymer, is inherently an excellent platform for achieving multivalency and can accommodate many RNA binding proteins. Recent findings have highlighted the diverse function of RNA in tuning phase-separation propensity up or down, altering viscoelastic properties and thereby driving immiscibility between different condensates. In addition to contributing to the biophysical properties of droplets, RNA is a functionally critical constituent that defines the identity of cellular condensates and controls the temporal and spatial distribution of specific RNP granules. In this review, we summarize what we have learned so far about such roles of RNA in the context of in vitro and in vivo studies.
    Print ISSN: 1936-122X
    Electronic ISSN: 1936-1238
    Topics: Biology , Physics
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