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  • Annual Reviews
  • 2020-2022  (1,388)
  • 1
    Publication Date: 2020-05-30
    Description: Melanin and other pigments are now well known to be important in exceptional preservation of soft tissues in vertebrates and other animals. Because pigments confer coloration and even structural colors, they have opened a new field of paleocolor reconstruction. Since its inception about a decade ago, reconstruction of color patterns has been performed on several vertebrates, including feathered and scale-clad dinosaurs. Iridescence and other types of structural color can also be identified through melanosome shape and arrangement. How pigments and melanosomes fossilize and are altered has become an important research subject. Ancient color patterns that may range from crypsis to brilliant displays have revealed insights into the evolution and escalation of visual systems, the nature of ancient animal interactions, and how several unique characteristics of birds already arose among dinosaurs. ▪  Melanin and other pigments preserve in exceptional fossils; this opens paths for reconstructing coloration of extinct organisms, such as dinosaurs. ▪  The most abundant pigment is melanin, which can be identified chemically and through preserved melanosome microbodies. ▪  Melanosome shape reveals clues to original hue ranging from reddish brown and black to gray and structural coloration. ▪  Other pigments may preserve, such as porphyrin pigments in theropod dinosaur eggshells. ▪  Fossil color patterns contribute new insights into the evolution of visual systems, predator-prey interactions, and key innovations.
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 2
    Publication Date: 2020-05-30
    Description: The atmosphere is the synthesizer, transformer, and communicator of exchanges at its boundaries with the land and oceans. These exchanges depend on and, in turn, alter the states of the atmosphere, land, and oceans themselves. To a large extent, the interactions between the carbon cycle and climate have mapped, and will map, the trajectory of the Earth system. My quest to understand climate dynamics and the global carbon cycle has been propelled by new puzzles that emerge from each of the investigations and has led me to study subdisciplines of Earth science beyond my formal training. This article sketches my trek and the lessons I have learned. ▪  About half the CO2 emitted from combustion of fossil fuels and from cement production has remained airborne. Where are the contemporary carbon sinks? To what degree will these sinks evolve with, and in turn accelerate, climate change itself? ▪  The pursuit of these questions has been propelled by the integration of in situ and satellite observations of the atmosphere, land, and oceans, as well as by advances in theory and coupled climate–carbon cycle modeling. ▪  The urgency of climate change demands new approaches to cross-check national emission statistics.
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  • 3
    Publication Date: 2020-05-30
    Description: Carbonate sediments and rocks are valuable archives of Earth's past whose geochemical compositions inform our understanding of Earth's surface evolution. Yet carbonates are also reactive minerals and often undergo compositional alteration between the time of deposition and sampling and analysis. These changes may be mineralogical, structural, and/or chemical, and they are broadly referred to as diagenesis. Building on work over the past 40 years, we present an overview of key carbonate diagenesis terminology and a process-based framework for evaluating the geochemical impacts of carbonate diagenesis; we also highlight recent experimental and field observations that suggest metal isotopes as valuable diagenetic indicators. Our primary objectives are to demonstrate the value of coupling quantitative and analytical approaches, specifically with regard to metal isotopes and Mg/Ca, and to focus attention on key avenues for future work, including the role of authigenesis in impacting global geochemical cycles and the isotopic composition of the rock record. ▪  Quantitative frameworks utilizing well-understood diagenetic indicators and basic geochemical parameters allow us to assess the extent of diagenetic alteration in carbonate sediments. ▪  The reactivity, duration of reaction, and degree of isotopic or elemental/chemical disequilibrium determine the extent to which carbonates may be altered. ▪  Metal isotopic ratios (δ44Ca, δ26Mg, 87Sr/86Sr) can be used to constrain the extent and rate of carbonate recrystallization. ▪  Diagenetic signals may be globally synchronous, while diagenetic fluxes may impact global geochemical cycles.
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  • 4
    Publication Date: 2020-05-30
    Description: The strong ground motions, large crustal deformation, and tsunami generated by the 2011 Tohoku-oki earthquake ( Mw 9.1) reveal that a large coseismic slip likely propagated to shallow depth in the Japan Trench. Although data acquired by onshore networks cannot resolve the slip behavior of the updip fault rupture, marine geophysical and geological studies provide direct evidence of coseismic slip to the trench. Differential bathymetry data show ∼50 m of coseismic seafloor displacement extending to the central Japan Trench (38–39.2°N). Seismic data show that coseismic slip ruptured the seafloor within the trench. Pelagic clays may have promoted slip propagation to shallow depths, whereas disturbed/metamorphosed clays may have restricted slip to the main rupture zone. Those observations imply that a smooth, broadly distributed, weak, clay-rich sediment in a shallow part of a subduction zone is a characteristic factor that can foster a large coseismic slip to the trench and, consequently, the generation of a large tsunami. ▪  During the 2011 Tohoku-oki earthquake ( Mw 9.1), more than ∼50 m of slip occurred on a fault that ruptured the seafloor in the central Japan Trench. ▪  The fault rupture reaching the seafloor caused a large tsunami. ▪  Marine geophysical explorations revealed that a clay-rich sediment in the subduction zone was one factor fostering the large fault slip. ▪  Understanding of slip behavior in the shallow portion of a subduction zone will help us prepare for future large tsunamis along the Japan-Kuril Trench.
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  • 5
    Publication Date: 2020-05-30
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  • 6
    Publication Date: 2020-05-30
    Description: The Human System is within the Earth System. They should be modeled bidirectionally coupled, as they are in reality. The Human System is rapidly expanding, mostly due to consumption of fossil fuels (approximately one million times faster than Nature accumulated them) and fossil water. This threatens not only other planetary subsystems but also the Human System itself. Carrying Capacity is an important tool to measure sustainability, but there is a widespread view that Carrying Capacity is not applicable to humans. Carrying Capacity has generally been prescribed a priori, mostly using the logistic equation. However, the real dynamics of human population and consumption are not represented by this equation or its variants. We argue that Carrying Capacity should not be prescribed but should insteadbe dynamically derived a posteriori from the bidirectional coupling of Earth System submodels with the Human System model. We demonstrate this approach with a minimal model of Human–Nature interaction (HANDY). ▪  The Human System is a subsystem of the Earth System, with inputs (resources) from Earth System sources and outputs (waste, emissions) to Earth System sinks. ▪  The Human System is growing rapidly due to nonrenewable stocks of fossil fuels and water and threatens the sustainability of the Human System and to overwhelm the Earth System. ▪  Carrying Capacity has been prescribed a priori and using the logistic equation, which does not represent the dynamics of the Human System. ▪  Our new approach to human Carrying Capacity is derived from dynamically coupled Earth System–Human System models and can be used to estimate the sustainability of the Human System.
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  • 7
    Publication Date: 2020-05-30
    Description: The connection between the geological record and dynamic topography driven by mantle convective flow has been established over widely varying temporal and spatial scales. As observations of the process have increased and numerical modeling of thermochemical convection has improved, a burgeoning direction of research targeting outstanding issues in ice age paleoclimate has emerged. This review focuses on studies of the Plio-Pleistocene ice age, including investigations of the stability of ice sheets during ice age warm periods and the inception of Northern Hemisphere glaciation. However, studies that have revealed nuanced connections of dynamic topography to biodiversity, ecology, ocean chemistry, and circulation since the start of the current ice-house world are also considered. In some cases, a recognition of the importance of dynamic topography resolves enigmatic events and in others it confounds already complex, unanswered questions. All such studies highlight the role of solid Earth geophysics in paleoclimate research and undermine a common assumption, beyond the field of glacial isostatic adjustment, that the solid Earth remains a rigid, passive substrate during the evolution of the ice age climate system. ▪  Dynamic topography is the large-scale, vertical deflection of Earth's crust driven by mantle convective flow. ▪  This review highlights recent research exploring the implications of the process on key issues in ice age paleoclimate. ▪  This research includes studies of ice sheet stability and inception as well as inferences of peak sea levels during periods of relative ice age warmth. ▪  This review also includes studies on longer timescales, continental-scale ecology and biodiversity, the long-term carbon cycle, and water flux across oceanic gateways.
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  • 8
    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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  • 9
    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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  • 10
    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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  • 11
    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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  • 12
    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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  • 13
    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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  • 14
    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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  • 15
    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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  • 16
    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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  • 17
    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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  • 18
    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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  • 19
    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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  • 20
    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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  • 21
    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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  • 22
    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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  • 23
    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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  • 24
    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
    Topics: Biology
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  • 25
    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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  • 26
    Publication Date: 2020-06-12
    Description: Development and application of nanotechnology-enabled medical products, including drugs, devices, and in vitro diagnostics, are rapidly expanding in the global marketplace. In this review, the focus is on providing the reader with an introduction to the landscape of commercially available nanotechnology-enabled medical products as well as an overview of the international documentary standards and reference materials that support and facilitate efficient regulatory evaluation and reliable manufacturing of this diverse group of medical products. We describe the materials, test methods, and standards development needs for emerging medical products. Scientific and measurement challenges involved in the development and application of innovative nanoenabled medical products motivate discussion throughout this review.
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 27
    Publication Date: 2020-06-12
    Description: Acoustic microfluidic devices are powerful tools that use sound waves to manipulate micro- or nanoscale objects or fluids in analytical chemistry and biomedicine. Their simple device designs, biocompatible and contactless operation, and label-free nature are all characteristics that make acoustic microfluidic devices ideal platforms for fundamental research, diagnostics, and therapeutics. Herein, we summarize the physical principles underlying acoustic microfluidics and review their applications, with particular emphasis on the manipulation of macromolecules, cells, particles, model organisms, and fluidic flows. We also present future goals of this technology in analytical chemistry and biomedical research, as well as challenges and opportunities.
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  • 28
    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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  • 29
    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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    Topics: Biology , Ethnic Sciences
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  • 30
    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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  • 31
    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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  • 32
    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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  • 33
    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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  • 34
    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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  • 35
    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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  • 36
    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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  • 37
    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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  • 38
    Publication Date: 2020-06-12
    Description: High-resolution SIMS analysis can be used to explore a wide range of problems in material science and engineering materials, especially when chemical imaging with good spatial resolution (50–100 nm) can be combined with efficient detection of light elements and precise separation of isotopes and isobaric species. Here, applications of the NanoSIMS instrument in the analysis of inorganic materials are reviewed, focusing on areas of current interest in the development of new materials and degradation mechanisms under service conditions. We have chosen examples illustrating NanoSIMS analysis of grain boundary segregation, chemical processes in cracking, and corrosion of nuclear components. An area where NanoSIMS analysis shows potential is in the localization of light elements, in particular, hydrogen and deuterium. Hydrogen embrittlement is a serious problem for industries where safety is critical, including aerospace, nuclear, and oil/gas, so it is imperative to know where in the microstructure hydrogen is located. By charging the metal with deuterium, to avoid uncertainty in the origin of the hydrogen, the microstructural features that can trap hydrogenic species, such as precipitates and grain and phase boundaries, can be determined by NanoSIMS analysis on a microstructurally relevant scale.
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    Topics: Chemistry and Pharmacology
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  • 39
    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.
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  • 40
    Publication Date: 2020-06-12
    Description: Transporters are key to understanding how an individual will respond to a particular dose of a drug. Two patients with similar systemic concentrations may have quite different local concentrations of a drug at the required site. The transporter profile of any individual depends upon a variety of genetic and environmental factors, including genotype, age, and diet status. Robust models (virtual patients) are therefore required and these models are data hungry. Necessary data include quantitative transporter profiles at the relevant organ. Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is currently the most powerful method available for obtaining this information. Challenges include sourcing the tissue, isolating the hydrophobic membrane-embedded transporter proteins, preparing the samples for MS (including proteolytic digestion), choosing appropriate quantification methodology, and optimizing the LC-MS/MS conditions. Great progress has been made with all of these, especially within the last few years, and is discussed here.
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  • 41
    Publication Date: 2020-06-12
    Description: The electrochemical behavior of platinum single crystal surfaces can be taken as a model response for the interpretation of the activity of heterogeneous electrodes. The cyclic voltammogram of a given platinum electrode can be considered a fingerprint characteristic of the distribution of sites on its surface. We start this review by providing some simple mathematical descriptions of the voltammetric response in the presence of adsorption processes. We then describe the voltammogram of platinum basal planes, followed by the response of stepped surfaces. The voltammogram of polycrystalline materials can be understood as a composition of the response of the different basal contributions. Further resolution in the discrimination of different surface sites can be achieved with the aid of surface modification using adatoms such as bismuth or germanium. The application of these ideas is exemplified with the consideration of real catalysts composed of platinum nanoparticles with preferential shapes.
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  • 42
    Publication Date: 2020-06-12
    Description: Technological advances in mass spectrometry have enabled the extensive identification, characterization, and quantification of proteins in any biological system. In disease processes proteins are often altered in response to external stimuli; therefore, proteomics, the large-scale study of proteins and their functions, represents an invaluable tool for understanding the molecular basis of disease. This review highlights the use of mass spectrometry–based proteomics to study the pathogenesis, etiology, and pathology of several neglected tropical diseases (NTDs), a diverse group of disabling diseases primarily associated with poverty in tropical and subtropical regions of the world. While numerous NTDs have been the subject of proteomic studies, this review focuses on Buruli ulcer, dengue, leishmaniasis, and snakebite envenoming. The proteomic studies highlighted provide substantial information on the pathogenic mechanisms driving these diseases; they also identify molecular targets for drug discovery and development and uncover promising biomarkers that can assist in early diagnosis.
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  • 43
    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.
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    Topics: Biology , Geosciences
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  • 44
    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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  • 45
    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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  • 46
    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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  • 47
    Publication Date: 2020-02-15
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  • 48
    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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  • 49
    Publication Date: 2020-06-12
    Description: The detailed molecular characterization of petroleum-related samples by mass spectrometry, often referred to as petroleomics, continues to present significant analytical challenges. As a result, petroleomics continues to be a driving force for the development of new ultrahigh resolution instrumentation, experimental methods, and data analysis procedures. Recent advances in ionization, resolving power, mass accuracy, and the use of separation methods, have allowed for record levels of compositional detail to be obtained for petroleum-related samples. To address the growing size and complexity of the data generated, vital software tools for data processing, analysis, and visualization continue to be developed. The insights gained impact upon the fields of energy and environmental science and the petrochemical industry, among others. In addition to advancing the understanding of one of nature's most complex mixtures, advances in petroleomics methodologies are being adapted for the study of other sample types, resulting in direct benefits to other fields.
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  • 50
    Publication Date: 2020-06-12
    Description: Traditional microfabrication techniques suffer from several disadvantages, including the inability to create truly three-dimensional (3D) architectures, expensive and time-consuming processes when changing device designs, and difficulty in transitioning from prototyping fabrication to bulk manufacturing. 3D printing is an emerging technique that could overcome these disadvantages. While most 3D printed fluidic devices and features to date have been on the millifluidic size scale, some truly microfluidic devices have been shown. Currently, stereolithography is the most promising approach for routine creation of microfluidic structures, but several approaches under development also have potential. Microfluidic 3D printing is still in an early stage, similar to where polydimethylsiloxane was two decades ago. With additional work to advance printer hardware and software control, expand and improve resin and printing material selections, and realize additional applications for 3D printed devices, we foresee 3D printing becoming the dominant microfluidic fabrication method.
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  • 51
    Publication Date: 2020-06-12
    Description: Protein separations have gained increasing interest over the past two decades owing to the dramatic growth of proteins as therapeutics and the completion of the Human Genome Project. About every decade, the field of protein high-performance liquid chromatography (HPLC) seems to mature, having reached what appears to be a theoretical limit. But then scientists well versed in the basic principles of HPLC invented a way around the limit, generating another decade of exciting progress. There is still the need for higher resolution and better compatibility with mass spectrometry because it is an essential tool for identification of proteins and their modifications. To make advances, the fundamental principles need to be understood. This review covers recent advances and current needs in the context of the principles that underlie the many contributions to peak broadening.
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  • 52
    Publication Date: 2020-06-12
    Description: Avoiding the growth of SiOx has been an enduring task for the use of silicon as an electrode material in dynamic electrochemistry. This is because electrochemical assays become unstable when the SiOx levels change during measurements. Moreover, the silicon electrode can be completely passivated for electron transfer if a thick layer of insulating SiOx grows on the surface. As such, the field of silicon electrochemistry was mainly developed by electron-transfer studies in nonaqueous electrolytes and by applications employing SiOx-passivated silicon-electrodes where no DC currents are required to cross the electrode/electrolyte interface. A solution to this challenge began by functionalizing Si–H electrodes with monolayers based on Si–O–Si linkages. These monolayers have proven very efficient to avoid SiOx formation but are not stable for a long-term operation in aqueous electrolytes due to hydrolysis. It was only with the development of self-assembled monolayers based on Si–C linkages that a reliable protection against SiOx formation was achieved, particularly with monolayers based on α,ω-dialkynes. This review discusses in detail how this surface chemistry achieves such protection, the electron-transfer behavior of these monolayer-modified silicon surfaces, and the new opportunities for electrochemical applications in aqueous solution.
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  • 53
    Publication Date: 2020-06-12
    Description: The National Institute of Standards and Technology (NIST), formerly the National Bureau of Standards, was established by the US Congress in 1901 and charged with establishing a measurement foundation to facilitate US and international commerce. This broad language provides NIST with the ability to establish and implement its programs in response to changes in national needs and priorities. This review traces some of the changes in NIST's reference material programs over time and presents the NIST Material Measurement Laboratory's current approach to promoting accuracy and metrological traceability of chemical measurements and validation of chemical measurement processes.
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  • 54
    Publication Date: 2020-06-12
    Description: As the core component of cell metabolism, central carbon metabolism, consisting of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle converts nutrients into metabolic precursors for biomass and energy to sustain the life of virtually all extant species. The metabolite levels or distributions in central carbon metabolism often change dynamically with cell fates, development, and disease progression. However, traditional biochemical methods require cell lysis, making it challenging to obtain spatiotemporal information about metabolites in living cells and in vivo. Genetically encoded fluorescent sensors allow the rapid, sensitive, specific, and real-time readout of metabolite dynamics in living organisms, thereby offering the potential to fill the gap in current techniques. In this review, we introduce recent progress made in the development of genetically encoded fluorescent sensors for central carbon metabolism and discuss their advantages, disadvantages, and applications. Moreover, several future directions of metabolite sensors are also proposed.
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  • 55
    Publication Date: 2020-06-12
    Description: Neuronal transmission relies on electrical signals and the transfer of chemical signals from one neuron to another. Chemical messages are transmitted from presynaptic neurons to neighboring neurons through the triggered fusion of neurotransmitter-filled vesicles with the cell plasma membrane. This process, known as exocytosis, involves the rapid release of neurotransmitter solutions that are detected with high affinity by the postsynaptic neuron. The type and number of neurotransmitters released and the frequency of vesicular events govern brain functions such as cognition, decision making, learning, and memory. Therefore, to understand neurotransmitters and neuronal function, analytical tools capable of quantitative and chemically selective detection of neurotransmitters with high spatiotemporal resolution are needed. Electrochemistry offers powerful techniques that are sufficiently rapid to allow for the detection of exocytosis activity and provides quantitative measurements of vesicle neurotransmitter content and neurotransmitter release from individual vesicle events. In this review, we provide an overview of the most commonly used electrochemical methods for monitoring single-vesicle events, including recent developments and what is needed for future research.
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  • 56
    Publication Date: 2020-06-12
    Description: The current teaching and practice of analytical chemistry reflect the evolution of measurement science over time. Qualitative and quantitative measurements can be traced back to prebiblical times, have been important throughout human history, and today are key to the functioning of a modern society. This review is designed to provide a brief overview of the evolution of analytical science and a summary of the evolution, development, and growth of analytical chemistry in the United States, with emphasis on developments up to the mid-twentieth century. Some degree of emphasis is placed on early centers of analytical chemistry and contributions of pioneers of analytical chemistry within the United States. The evolution of journals, early textbooks, and reference books on analytical chemistry as well as developments in analytical chemistry curricula in the United States are traced.
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  • 57
    Publication Date: 2020-06-12
    Description: Single particle tracking (SPT) has proven to be a powerful technique in studying molecular dynamics in complicated systems. We review its recent development, including three-dimensional (3D) SPT and its applications in probing nanostructures and molecule-surface interactions that are important to analytical chemical processes. Several frequently used 3D SPT techniques are introduced. Especially of interest are those based on point spread function engineering, which are simple in instrumentation and can be easily adapted and used in analytical labs. Corresponding data analysis methods are briefly discussed. We present several important case studies, with a focus on probing mass transport and molecule-surface interactions in confined environments. The presented studies demonstrate the great potential of 3D SPT for understanding fundamental phenomena in confined space, which will enable us to predict basic principles involved in chemical recognition, separation, and analysis, and to optimize mass transport and responses by structural design and optimization.
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  • 58
    Publication Date: 2020-06-12
    Description: Organs-on-chips (OOC) are widely seen as being the next generation in vitro models able to accurately recreate the biochemical-physical cues of the cellular microenvironment found in vivo. In addition, they make it possible to examine tissue-scale functional properties of multicellular systems dynamically and in a highly controlled manner. Here we summarize some of the most remarkable examples of OOC technology's ability to extract clinically relevant tissue-level information. The review is organized around the types of OOC outputs that can be measured from the cultured tissues and transferred to clinically meaningful information. First, the creation of functional tissues-on-chip is discussed, followed by the presentation of tissue-level readouts specific to OOC, such as morphological changes, vessel formation and function, tissue properties, and metabolic functions. In each case, the clinical relevance of the extracted information is highlighted.
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  • 59
    Publication Date: 2020-06-12
    Description: Measurement of humoral factors secreted from cells has served as an indispensable method to monitor the states of a cell ensemble because humoral factors play crucial roles in cell–cell interaction and aptly reflect the states of individual cells. Although a cell ensemble consisting of a large number of cells has conventionally been the object of such measurements, recent advances in microfluidic technology together with highly sensitive immunoassays have enabled us to quantify secreted humoral factors even from individual cells in either a population or a temporal context. Many groups have reported various miniaturized platforms for immunoassays of proteins secreted from single cells. This review focuses on the current status of time-resolved assay platforms for protein secretion with single-cell resolution. We also discuss future perspectives of time-resolved immunoassays from the viewpoint of systems biology.
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    Topics: Chemistry and Pharmacology
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  • 60
    Publication Date: 2020-06-12
    Description: Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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  • 61
    Publication Date: 2020-06-12
    Description: Most of my research directions were opportunistic. Having worked with lasers in the early stages of laser applications in analytical chemistry, attending conferences, workshops, and administrative meetings that were not exactly aligned with our own research, locating to a building or in a department that housed scientists with different backgrounds, having certain specialized equipment at the right time, and having funding agencies that were broad-minded clearly contributed to my ventures into diverse fields. Most of all, it had to be the many eager minds that I have had the fortune to work with. I have always tried to suggest research topics that might be interesting to the individual coworker rather than something straight out of my own research proposals. Only then did each person actually own the project rather than consider it a chore. After all, we work in the field of analytical chemistry, in which almost anything we do can fit in.
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  • 62
    Publication Date: 2020-03-10
    Description: Due to its extremely rich phase diagram, the two-dimensional electron gas exposed to perpendicular magnetic fields has been the subject of intense and sustained study. One particularly interesting problem in this system is that of the half-filled Landau level, where the Fermi sea of composite fermions, a fractional quantum Hall state arising from a pairing instability of the composite fermions, and the quantum Hall nematic were observed in the half-filled N = 0, N = 1, and N ≥ 2 Landau levels, respectively. Thus, different ground states developed in different half-filled Landau levels. This situation has recently changed, when evidence for both the paired fractional quantum Hall state and the quantum Hall nematic was reported in the half-filled N = 1 Landau level. Furthermore, a direct quantum phase transition between these two ordered states was found. These results highlight an intimate connection between pairing and nematicity, which is a topic of current interest in several strongly correlated systems, in a well-understood and low-disorder environment.
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  • 63
    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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    Topics: Biology , Chemistry and Pharmacology
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  • 64
    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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  • 65
    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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  • 66
    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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  • 67
    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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  • 68
    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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  • 69
    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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  • 70
    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.
    Print ISSN: 1081-0706
    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 71
    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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  • 72
    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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  • 73
    Publication Date: 2020-03-10
    Description: Floquet systems are governed by periodic, time-dependent Hamiltonians. Prima facie they should absorb energy from the external drives involved in modulating their couplings and heat up to infinite temperature. However, this unhappy state of affairs can be avoided in many ways. Instead, as has become clear from much recent work, Floquet systems can exhibit a variety of nontrivial behavior—some of which is impossible in undriven systems. In this review, we describe the main ideas and themes of this work: novel Floquet drives that exhibit nontrivial topology in single-particle systems, the existence and classification of exotic Floquet drives in interacting systems, and the attendant notion of many-body Floquet phases and arguments for their stability to heating.
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  • 74
    Publication Date: 2020-03-10
    Description: Superconducting qubits are leading candidates in the race to build a quantum computer capable of realizing computations beyond the reach of modern supercomputers. The superconducting qubit modality has been used to demonstrate prototype algorithms in the noisy intermediate-scale quantum (NISQ) technology era, in which non-error-corrected qubits are used to implement quantum simulations and quantum algorithms. With the recent demonstrations of multiple high-fidelity, two-qubit gates as well as operations on logical qubits in extensible superconducting qubit systems, this modality also holds promise for the longer-term goal of building larger-scale error-corrected quantum computers. In this brief review, we discuss several of the recent experimental advances in qubit hardware, gate implementations, readout capabilities, early NISQ algorithm implementations, and quantum error correction using superconducting qubits. Although continued work on many aspects of this technology is certainly necessary, the pace of both conceptual and technical progress in recent years has been impressive, and here we hope to convey the excitement stemming from this progress.
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  • 75
    Publication Date: 2020-03-10
    Description: In this review, we summarize recent theoretical and computational developments in the field of smart responsive materials, together with complementary experimental data. A material is referred to as smart responsive when a slight change in external stimulus can drastically alter its structure, function, or stability. Because of this smart responsiveness, these systems are used for the design of advanced functional materials. The most characteristic properties of smart polymers are discussed, especially polymer properties in solvent mixtures. We show how multiscale simulation approaches can shed light on the intriguing experimental observations. Special emphasis is given to two symmetric phenomena: co-non-solvency and co-solvency. The first phenomenon is associated with the collapse of polymers in two miscible good solvents, whereas the latter is associated with the swelling of polymers in poor solvent mixtures. Furthermore, we discuss when the standard Flory–Huggins-type mean-field polymer theory can (or cannot) be applied to understand these complex solution properties. We also sketch a few examples to highlight possible future directions, that is, how smart polymer properties can be used for the design principles of advanced functional materials.
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  • 76
    Publication Date: 2020-03-10
    Description: We review the development of generative modeling techniques in machine learning for the purpose of reconstructing real, noisy, many-qubit quantum states. Motivated by its interpretability and utility, we discuss in detail the theory of the restricted Boltzmann machine. We demonstrate its practical use for state reconstruction, starting from a classical thermal distribution of Ising spins, then moving systematically through increasingly complex pure and mixed quantum states. We review recent techniques in reconstruction of a cold atom wavefunction, intended for use on experimental noisy intermediate-scale quantum (NISQ) devices. Finally, we discuss the outlook for future experimental state reconstruction using machine learning in the NISQ era and beyond.
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  • 77
    Publication Date: 2020-03-10
    Description: When the continuous symmetry of a physical system is spontaneously broken, two types of collective modes typically emerge: the amplitude and the phase modes of the order-parameter fluctuation. For superconductors, the amplitude mode is referred to most recently as the Higgs mode as it is a condensed-matter analog of a Higgs boson in particle physics. Higgs mode is a scalar excitation of the order parameter, distinct from charge or spin fluctuations, and thus does not couple to electromagnetic fields linearly. This is why the Higgs mode in superconductors has evaded experimental observations for over a half century after the initial theoretical prediction, except for a charge-density-wave coexisting system. With the advance of nonlinear and time-resolved terahertz spectroscopy techniques, however, it has become possible to study the Higgs mode through the nonlinear light–Higgs coupling. In this review, we overview recent progress in the study of the Higgs mode in superconductors.
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  • 78
    Publication Date: 2020-03-10
    Description: The measurement of superconductivity at above 200 K in compressed samples of hydrogen sulfide and in lanthanum hydride at 250 K is reinvigorating the search for conventional high temperature superconductors. At the same time, it exposes a fascinating interplay between theory, computation, and experiment. Conventional superconductivity is well understood, and theoretical tools are available for accurate predictions of the superconducting critical temperature. These predictions depend on knowing the microscopic structure of the material under consideration, which can now be provided by computational first-principles structure predictions. The experiments at the megabar pressures required are extremely challenging, but, for some groups at least, permit the experimental exploration of materials space. We discuss the prospects for the search for new superconductors, ideally at lower pressures.
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  • 79
    Publication Date: 2020-03-10
    Description: Active matter physics is about systems in which energy is dissipated at some local level to produce work. This is a generic situation, particularly in the living world but not only. What is at stake is the understanding of the fascinating, sometimes counterintuitive, emerging phenomena observed, from collective motion in animal groups to in vitro dynamical self-organization of motor proteins and biofilaments. Dry aligning dilute active matter (DADAM) is a corner of the multidimensional, fast-growing domain of active matter that has both historical and theoretical importance for the entire field. This restrictive setting only involves self-propulsion/activity, alignment, and noise, yet unexpected collective properties can emerge from it. This review provides a personal but synthetic and coherent overview of DADAM, focusing on the collective-level phenomenology of simple active particle models representing basic classes of systems and on the solutions of the continuous hydrodynamic theories that can be derived from them. The obvious fact that orientational order is advected by the aligning active particles at play is shown to be at the root of the most striking properties of DADAM systems: ( a) direct transitions to orientational order are not observed; ( b) instead generic phase separation occurs with a coexistence phase involving inhomogeneous nonlinear structures; ( c) orientational order, which can be long range even in two dimensions, is accompanied by long-range correlations and anomalous fluctuations; ( d) defects are not point-like, topologically bound objects.
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  • 80
    Publication Date: 2020-03-10
    Description: The recent striking success of deep neural networks in machine learning raises profound questions about the theoretical principles underlying their success. For example, what can such deep networks compute? How can we train them? How does information propagate through them? Why can they generalize? And how can we teach them to imagine? We review recent work in which methods of physical analysis rooted in statistical mechanics have begun to provide conceptual insights into these questions. These insights yield connections between deep learning and diverse physical and mathematical topics, including random landscapes, spin glasses, jamming, dynamical phase transitions, chaos, Riemannian geometry, random matrix theory, free probability, and nonequilibrium statistical mechanics. Indeed, the fields of statistical mechanics and machine learning have long enjoyed a rich history of strongly coupled interactions, and recent advances at the intersection of statistical mechanics and deep learning suggest these interactions will only deepen going forward.
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  • 81
    Publication Date: 2020-03-10
    Description: Fluid turbulence is commonly associated with stronger drag, greater heat transfer, and more efficient mixing than in laminar flows. In many natural and industrial settings, turbulent liquid flows contain suspensions of dispersed bubbles and light particles. Recently, much attention has been devoted to understanding the behavior and underlying physics of such flows by use of both experiments and high-resolution direct numerical simulations. This review summarizes our present understanding of various phenomenological aspects of bubbly and buoyant particle–laden turbulent flows. We begin by discussing different dynamical regimes, including those of crossing trajectories and wake-induced oscillations of rising particles, and regimes in which bubbles and particles preferentially accumulate near walls or within vortical structures. We then address how certain paradigmatic turbulent flows, such as homogeneous isotropic turbulence, channel flow, Taylor–Couette turbulence, and thermally driven turbulence, are modified by the presence of these dispersed bubbles and buoyant particles. We end with a list of summary points and future research questions.
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  • 82
    Publication Date: 2020-03-10
    Description: Turbulence is characterized by a large number of degrees of freedom, distributed over several length scales, that result in a disordered state of a fluid. The field of quantum turbulence deals with the manifestation of turbulence in quantum fluids, such as liquid helium and ultracold gases. We review, from both experimental and theoretical points of view, advances in quantum turbulence focusing on atomic Bose–Einstein condensates. We also explore the similarities and differences between quantum and classical turbulence. Last, we present challenges and possible directions for the field. We summarize questions that are being asked in recent works, which need to be answered in order to understand fundamental properties of quantum turbulence, and we provide some possible ways of investigating them.
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  • 83
    Publication Date: 2020-03-10
    Description: A wide range of experimental systems including gliding, swarming and swimming bacteria, in vitro motility assays, and shaken granular media are commonly described as self-propelled rods. Large ensembles of those entities display a large variety of self-organized, collective phenomena, including the formation of moving polar clusters, polar and nematic dynamic bands, mobility-induced phase separation, topological defects, and mesoscale turbulence, among others. Here, we give a brief survey of experimental observations and review the theoretical description of self-propelled rods. Our focus is on the emergent pattern formation of ensembles of dry self-propelled rods governed by short-ranged, contact mediated interactions and their wet counterparts that are also subject to long-ranged hydrodynamic flows. Altogether, self-propelled rods provide an overarching theme covering many aspects of active matter containing well-explored limiting cases. Their collective behavior not only bridges the well-studied regimes of polar self-propelled particles and active nematics, and includes active phase separation, but also reveals a rich variety of new patterns.
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  • 84
    Publication Date: 2020-03-10
    Description: Experimental advances have allowed for the exploration of nearly isolated quantum many-body systems whose coupling to an external bath is very weak. A particularly interesting class of such systems is those that do not thermalize under their own isolated quantum dynamics. In this review, we highlight the possibility for such systems to exhibit new nonequilibrium phases of matter. In particular, we focus on discrete time crystals, which are many-body phases of matter characterized by a spontaneously broken discrete time-translation symmetry. We give a definition of discrete time crystals from several points of view, emphasizing that they are a nonequilibrium phenomenon that is stabilized by many-body interactions, with no analog in noninteracting systems. We explain the theory behind several proposed models of discrete time crystals, and compare several recent realizations, in different experimental contexts.
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  • 85
    Publication Date: 2020-03-10
    Description: Liquid crystal elastomers and glasses suffer huge length changes on heating, illumination, exposure to humidity, etc. A challenge is to program these changes to give a complex mechanical response for micromachines and soft robotics. Also desirable can be strong response, where bend is avoided in favor of stretch and compression, even in the slender shells that are our subject. A new mechanics paradigm arises from such materials—spatially programmed anisotropy allows a spatially varying metric to develop upon stimulation, with evolving Gaussian curvature, topography changes, and superstrong actuation. We call this metric mechanics or topographical mechanics. Thus programmed, liquid crystalline solids meet the above aims. A frontier is the complete programming and control of topography, driving both Gaussian and mean curvature evolution. That, and smart shells, which sense and self-regulate, and exotic new realizations of anisotropic responsive structures, are our concluding themes.
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  • 86
    Publication Date: 2020-03-10
    Description: Recent experimental progress introduced devices that can combine topological superconductivity with Coulomb-blockade effects. Experiments with these devices have already provided additional evidence for Majorana zero modes in proximity-coupled semiconductor wires. They also stimulated numerous ideas for how to exploit interactions between Majorana zero modes generated by Coulomb charging effects in networks of Majorana wires. Coulomb effects promise to become a powerful tool in the quest for a topological quantum computer as well as for driving topological superconductors into topologically ordered insulating states. Here, we present a focused review of these recent developments, including discussions of recent experiments, designs of topological qubits, Majorana-based implementations of universal quantum computation, and topological quantum error correction. Motivated by the analogy between a qubit and a spin-1/2 degree of freedom, we also review how coupling between Cooper-pair boxes leads to emergent topologically ordered insulating phases.
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  • 87
    Publication Date: 2020-03-10
    Description: Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here, we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalog of the cell–cell and cell–substrate interactions that govern cell migration, which we classify into positional and orientational interactions. We then review the physical models that have been developed to explain how these interactions give rise to collective cellular movement. These models span the subcellular to the supracellular scales, and they include lattice models, phase-field models, active network models, particle models, and continuum models. For each type of model, we discuss its formulation, its limitations, and the main emergent phenomena that it has successfully explained. These phenomena include flocking and fluid–solid transitions, as well as wetting, fingering, and mechanical waves in spreading epithelial monolayers. We close by outlining remaining challenges and future directions in the physics of collective cell migration.
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  • 88
    Publication Date: 2020-03-10
    Description: Actin is the main protein used by biological cells to adapt their structure and mechanics to their needs. Cellular adaptation is made possible by molecular processes that strongly depend on mechanics. The actin cytoskeleton is also an active material that continuously consumes energy. This allows for dynamical processes that are possible only out of equilibrium and opens up the possibility for multiple layers of control that have evolved around this single protein. Here we discuss the actin cytoskeleton from the viewpoint of physics as an active adaptive material that can build structures superior to man-made soft matter systems. Not only can actin be used to build different network architectures on demand and in an adaptive manner, but it also exhibits the dynamical properties of feedback systems, like excitability, bistability, or oscillations. Therefore, it is a prime example of how biology couples physical structure and information flow and a role model for biology-inspired metamaterials.
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  • 89
    Publication Date: 2020-03-10
    Description: We review the physics of pair-density wave (PDW) superconductors. We begin with a macroscopic description that emphasizes order induced by PDW states, such as charge-density wave, and discuss related vestigial states that emerge as a consequence of partial melting of the PDW order. We review and critically discuss the mounting experimental evidence for such PDW order in the cuprate superconductors, the status of the theoretical microscopic description of such order, and the current debate on whether the PDW is a mother order or another competing order in the cuprates. In addition, we give an overview of the weak coupling version of PDW order, Fulde–Ferrell–Larkin–Ovchinnikov states, in the context of cold atom systems, unconventional superconductors, and noncentrosymmetric and Weyl materials.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
    Published by Annual Reviews
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  • 90
    Publication Date: 2020-03-10
    Description: When global continuous symmetries are spontaneously broken, there appear gapless collective excitations called Nambu–Goldstone modes (NGMs) that govern the low-energy property of the system. The application of this famous theorem ranges from high-energy particle physics to condensed matter and atomic physics. When a symmetry breaking occurs in systems that lack the Lorentz invariance to start with, as is usually the case in condensed matter systems, the number of resulting NGMs can be lower than that of broken symmetry generators, and the dispersion of NGMs is not necessarily linear. In this article, we review recently established formulae for NGMs associated with broken internal symmetries that work equally for relativistic and nonrelativistic systems. We also discuss complexities of NGMs originating from space-time symmetry breaking. Along the way we cover many illuminating examples from various context. We also present a complementary point of view from the Lieb–Schultz–Mattis theorem.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 91
    Publication Date: 2020-03-10
    Description: The physics of the pseudogap phase of high-temperature cuprate superconductors has been an enduring mystery over the past 30 years. The ubiquitous presence of the pseudogap phase in underdoped cuprates suggests that understanding it is key to unraveling the origin of high-temperature superconductivity. We review various theoretical approaches to this problem, emphasizing the concept of emergent symmetries in the underdoped region of those compounds. We differentiate these theories by considering a few fundamental questions related to the rich phenomenology of these materials. Lastly, we discuss a recent idea regarding two kinds of entangled preformed pairs that open a gap at the pseudogap onset temperature, T*, through a specific Higgs mechanism. We review the experimental consequences of this line of thought.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 92
    Publication Date: 2020-03-10
    Description: An understanding of the high-temperature copper oxide (cuprate) superconductors has eluded the physics community for over thirty years and represents one of the greatest unsolved problems in condensed matter physics. Particularly enigmatic is the normal state from which superconductivity emerges, so much so that this phase has been dubbed a “strange metal.” In this article, we review recent research into this strange metallic state as realized in the electron-doped cuprates with a focus on their transport properties. The electron-doped compounds differ in several ways from their more thoroughly studied hole-doped counterparts, and understanding these asymmetries of the phase diagram may prove crucial to developing a final theory of the cuprates. Most of the experimental results discussed in this review have yet to be explained and remain an outstanding challenge for theory.
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 93
    Publication Date: 2020-03-10
    Description: Driven by breakthroughs in experimental and theoretical techniques, the study of nonequilibrium quantum physics is a rapidly expanding field with many exciting new developments. Among the manifold ways the topic can be investigated, one-dimensional systems provide a particularly fine platform. The trifecta of strongly correlated physics, powerful theoretical techniques, and experimental viability have resulted in a flurry of research activity over the past decade or so. In this review, we explore the nonequilibrium aspects of one-dimensional systems that are integrable. Through a number of illustrative examples, we discuss nonequilibrium phenomena that arise in such models, the role played by integrability, and the consequences these have for more generic systems.
    Print ISSN: 1947-5454
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    Topics: Physics
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  • 94
    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.
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 95
    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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    Topics: Biology , Chemistry and Pharmacology
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  • 96
    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.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 97
    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.
    Print ISSN: 0066-4154
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    Topics: Biology , Chemistry and Pharmacology
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  • 98
    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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    Topics: Biology , Chemistry and Pharmacology
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  • 99
    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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    Topics: Biology , Chemistry and Pharmacology
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  • 100
    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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    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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