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  • Annual Reviews  (20,900)
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  • 1
    Publication Date: 2021-09-21
    Description: The repeated evolution of multicellularity across the tree of life has profoundly affected the ecology and evolution of nearly all life on Earth. Many of these origins were in different groups of photosynthetic eukaryotes, or algae. Here, we review the evolution and genetics of multicellularity in several groups of green algae, which include the closest relatives of land plants. These include millimeter-scale, motile spheroids of up to 50,000 cells in the volvocine algae; decimeter-scale seaweeds in the genus Ulva (sea lettuce); and very plantlike, meter-scale freshwater algae in the genus Chara (stoneworts). We also describe algae in the genus Caulerpa, which are giant, multinucleate, morphologically complex single cells. In each case, we review the life cycle, phylogeny, and genetics of traits relevant to the evolution of multicellularity, and genetic and genomic resources available for the group in question. Finally, we suggest routes toward developing these groups as model organisms for the evolution of multicellularity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 2
    Publication Date: 2021-09-23
    Description: Since the spread of tobacco from the Americas hundreds of years ago, tobacco cigarettes and, more recently, alternative tobacco products have become global products of nicotine addiction. Within the evolving alternative tobacco product space, electronic cigarette (e-cigarette) vaping has surpassed conventional cigarette smoking among adolescents and young adults in the United States and beyond. This review describes the experimental and clinical evidence of e-cigarette toxicity and deleterious health effects. Adverse health effects related to e-cigarette aerosols are influenced by several factors, including e-liquid components, physical device factors, chemical changes related to heating, and health of the e-cigarette user (e.g., asthmatic). Federal, state, and local regulations have attempted to govern e-cigarette flavors, manufacturing, distribution, and availability, particularly to underaged youths. However, the evolving e-cigarette landscape continues to impede timely toxicological studies and hinder progress made toward our understanding of the long-term health consequence of e-cigarettes. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 3
    Publication Date: 2021-09-23
    Description: The field of endoscopic bariatric and metabolic therapy has rapidly evolved from offering endoscopic treatment of weight regain following bariatric surgery to providing primary weight loss options as alternatives to pharmacologic and surgical interventions. Gastric devices and remodeling procedures were initially designed to work through a mechanism of volume restriction, leading to earlier satiety and reduced caloric intake. As the field continues to grow, small bowel interventions are evolving that may have some effect on weight loss but focus on the treatment of obesity-related comorbidities. Future implementation of combination therapy that utilizes both gastric and small bowel interventions offers an exciting option to further augment weight loss and alleviate metabolic disease. This review considers gastric devices and techniques including space-occupying intragastric balloons, aspiration therapy, endoscopic tissue suturing, and plication interventions, followed by a review of small bowel interventions including endoluminal bypass liners, duodenal mucosal resurfacing, and endoscopically delivered devices to create incisionless anastomoses. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4219
    Electronic ISSN: 1545-326X
    Topics: Medicine
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  • 4
    Publication Date: 2021-09-15
    Description: Most animals have at least some binocular overlap, i.e., a region of space that is viewed by both eyes. This reduces the overall visual field and raises the problem of combining two views of the world, seen from different vantage points, into a coherent whole. However, binocular vision also offers many potential advantages, including increased ability to see around obstacles and increased contrast sensitivity. One particularly interesting use for binocular vision is comparing information from both eyes to derive information about depth. There are many different ways in which this might be done, but in this review, I refer to them all under the general heading of stereopsis. This review examines the different possible uses of binocular vision and stereopsis and compares what is currently known about the neural basis of stereopsis in different taxa. Studying different animals helps us break free of preconceptions stemming from the way that stereopsis operates in human vision and provides new insights into the different possible forms of stereopsis.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 5
    Publication Date: 2021-09-15
    Description: The simultaneous six-pack photo lineup is a standard eyewitness identification procedure, consisting of one police suspect plus five physically similar fillers. The photo lineup is either a target-present array (the suspect is guilty) or a target-absent array (the suspect is innocent). The eyewitness is asked to search the six photos in the array with respect to a target template stored in memory (namely, the memory of the perpetrator's face). If the witness determines that the perpetrator is in fact in the lineup (detection), then the next step is to specify the position of the perpetrator's face in the lineup (localization). The witness may also determine that the perpetrator is not present and reject the lineup. In other words, a police lineup is a detection-plus-localization visual search task. Signal detection concepts that have long guided thinking about visual search have recently had a significant impact on our understanding of police lineups.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 6
    Publication Date: 2021-09-15
    Description: Visual processing is dynamically controlled by multiple neuromodulatory molecules that modify the responsiveness of neurons and the strength of the connections between them. In particular, modulatory control of processing in the lateral geniculate nucleus of the thalamus, V1, and V2 will alter the outcome of all subsequent processing of visual information, including the extent to and manner in which individual inputs contribute to perception and decision making and are stored in memory. This review addresses five small-molecule neuromodulators—acetylcholine, dopamine, serotonin, noradrenaline, and histamine—considering the structural basis for their action, and the effects of their release, in the early visual pathway of the macaque monkey. Traditionally, neuromodulators are studied in isolation and in discrete circuits; this review makes a case for considering the joint action of modulatory molecules and differences in modulatory effects across brain areas as a better means of understanding the diverse roles that these molecules serve.
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    Topics: Medicine
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  • 7
    Publication Date: 2021-09-15
    Description: Eye movements are indispensable for visual image stabilization during self-generated and passive head and body motion and for visual orientation. Eye muscles and neuronal control elements are evolutionarily conserved, with novel behavioral repertoires emerging during the evolution of frontal eyes and foveae. The precise execution of eye movements with different dynamics is ensured by morphologically diverse yet complementary sets of extraocular muscle fibers and associated motoneurons. Singly and multiply innervated muscle fibers are controlled by motoneuronal subpopulations with largely selective premotor inputs from task-specific ocular motor control centers. The morphological duality of the neuromuscular interface is matched by complementary biochemical and molecular features that collectively assign different physiological properties to the motor entities. In contrast, the functionality represents a continuum where most motor elements contribute to any type of eye movement, although within preferential dynamic ranges, suggesting that signal transmission and muscle contractions occur within bands of frequency-selective pathways.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 8
    Publication Date: 2021-09-15
    Description: The eye sends information about the visual world to the brain on over 20 parallel signal pathways, each specialized to signal features such as spectral reflection (color), edges, and motion of objects in the environment. Each pathway is formed by the axons of a separate type of retinal output neuron (retinal ganglion cell). In this review, we summarize what is known about the excitatory retinal inputs, brain targets, and gene expression patterns of ganglion cells in humans and nonhuman primates. We describe how most ganglion cell types receive their input from only one or two of the 11 types of cone bipolar cell and project selectively to only one or two target regions in the brain. We also highlight how genetic methods are providing tools to characterize ganglion cells and establish cross-species homologies.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 9
    Publication Date: 2021-09-13
    Description: Metabotropic glutamate receptor 5 (mGluR5) is ubiquitously expressed in brain regions responsible for memory and learning. It plays a key role in modulating rapid changes in synaptic transmission and plasticity. mGluR5 supports long-term changes in synaptic strength by regulating the transcription and translation of essential synaptic proteins. β-Amyloid 42 (Aβ42) oligomers interact with a mGluR5/cellular prion protein (PrPC) complex to disrupt physiological mGluR5 signal transduction. Aberrant mGluR5 signaling and associated synaptic failure are considered an emerging pathophysiological mechanism of Alzheimer's disease (AD). Therefore, mGluR5 represents an attractive therapeutic target for AD, and recent studies continue to validate the efficacy of various mGluR5 allosteric modulators in improving memory deficits and mitigating disease pathology. However, sex-specific differences in the pharmacology of mGluR5 and activation of noncanonical signaling downstream of the receptor suggest that its utility as a therapeutic target in female AD patients needs to be reconsidered. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 10
    Publication Date: 2021-09-15
    Description: Color is a continuous variable, and humans can distinguish more than a million colors, yet world color lexicons contain no more than a dozen basic color terms. It has been understood for 160 years that the number of color terms in a lexicon varies greatly across languages, yet the lexical color categories defined by these terms are similar worldwide. Starting with the seminal study by Berlin and Kay, this review considers how and why this is so. Evidence from psychological, linguistic, and computational studies has advanced our understanding of how color categories came into being, how they contribute to our shared understanding of color, and how the resultant categories influence color perception and cognition. A key insight from the last 50 years of research is how human perception and the need for communication within a society worked together to create color lexicons that are somewhat diverse, yet show striking regularities worldwide.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 11
    Publication Date: 2021-09-15
    Description: It has been known for over a century that the basic organization of the retina is conserved across vertebrates. It has been equally clear that retinal cells can be classified into numerous types, but only recently have methods been devised to explore this diversity in unbiased, scalable, and comprehensive ways. Advances in high-throughput single-cell RNA sequencing (scRNA-seq) have played a pivotal role in this effort. In this article, we outline the experimental and computational components of scRNA-seq and review studies that have used them to generate retinal atlases of cell types in several vertebrate species. These atlases have enabled studies of retinal development, responses of retinal cells to injury, expression patterns of genes implicated in retinal disease, and the evolution of cell types. Recently, the inquiry has expanded to include the entire eye and visual centers in the brain. These studies have enhanced our understanding of retinal function and dysfunction and provided tools and insights for exploring neural diversity throughout the brain.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 12
    Publication Date: 2021-09-15
    Description: Advances in retinal imaging are enabling researchers and clinicians to make precise noninvasive measurements of the retinal vasculature in vivo. This includes measurements of capillary blood flow, the regulation of blood flow, and the delivery of oxygen, as well as mapping of perfused blood vessels. These advances promise to revolutionize our understanding of vascular regulation, as well as the management of retinal vascular diseases. This review provides an overview of imaging and optical measurements of the function and structure of the ocular vasculature. We include general characteristics of vascular systems with an emphasis on the eye and its unique status. The functions of vascular systems are discussed, along with physical principles governing flow and its regulation. Vascular measurement techniques based on reflectance and absorption are briefly introduced, emphasizing ways of generating contrast. One of the prime ways to enhance contrast within vessels is to use techniques sensitive to the motion of cells, allowing precise measurements of perfusion and blood velocity. Finally, we provide a brief introduction to retinal vascular diseases.
    Print ISSN: 2374-4642
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    Topics: Medicine
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  • 13
    Publication Date: 2021-09-13
    Description: Since prehistory, human species have depended on plants for both food and medicine. Even in countries with ready access to modern medicines, alternative treatments are still highly regarded and commonly used. Unlike modern pharmaceuticals, many botanical medicines are in widespread use despite a lack of safety and efficacy data derived from controlled clinical trials and often unclear mechanisms of action. Contributing to this are the complex and undefined composition and likely multifactorial mechanisms of action and multiple targets of many botanical medicines. Here, we review the newfound importance of the ubiquitous KCNQ subfamily of voltage-gated potassium channels as targets for botanical medicines, including basil, capers, cilantro, lavender, fennel, chamomile, ginger, and Camellia, Sophora, and Mallotus species. We discuss the implications for the traditional use of these plants for disorders such as seizures, hypertension, and diabetes and the molecular mechanisms of plant secondary metabolite effects on KCNQ channels. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 14
    Publication Date: 2021-09-13
    Description: Human leukocyte antigen (HLA) is a hallmark genetic marker for the prediction of certain immune-mediated adverse drug reactions (ADRs). Numerous basic and clinical research studies have provided the evidence base to push forward the clinical implementation of HLA testing for the prevention of such ADRs in susceptible patients. This review explores current translational progress in using HLA as a key susceptibility factor for immune ADRs and highlights gaps in our knowledge. Furthermore, relevant findings of HLA-mediated drug-specific T cell activation are covered, focusing on cellular approaches to link genetic associations to drug-HLA binding as a complementary approach to understand disease pathogenesis. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 15
    Publication Date: 2021-09-15
    Description: Selectivity for many basic properties of visual stimuli, such as orientation, is thought to be organized at the scale of cortical columns, making it difficult or impossible to measure directly with noninvasive human neuroscience measurement. However, computational analyses of neuroimaging data have shown that selectivity for orientation can be recovered by considering the pattern of response across a region of cortex. This suggests that computational analyses can reveal representation encoded at a finer spatial scale than is implied by the spatial resolution limits of measurement techniques. This potentially opens up the possibility to study a much wider range of neural phenomena that are otherwise inaccessible through noninvasive measurement. However, as we review in this article, a large body of evidence suggests an alternative hypothesis to this superresolution account: that orientation information is available at the spatial scale of cortical maps and thus easily measurable at the spatial resolution of standard techniques. In fact, a population model shows that this orientation information need not even come from single-unit selectivity for orientation tuning, but instead can result from population selectivity for spatial frequency. Thus, a categorical error of interpretation can result whereby orientation selectivity can be confused with spatial frequency selectivity. This is similarly problematic for the interpretation of results from numerous studies of more complex representations and cognitive functions that have built upon the computational techniques used to reveal stimulus orientation. We suggest in this review that these interpretational ambiguities can be avoided by treating computational analyses as models of the neural processes that give rise to measurement. Building upon the modeling tradition in vision science using considerations of whether population models meet a set of core criteria is important for creating the foundation for a cumulative and replicable approach to making valid inferences from human neuroscience measurements.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 16
    Publication Date: 2021-09-15
    Description: The first mobile camera phone was sold only 20 years ago, when taking pictures with one's phone was an oddity, and sharing pictures online was unheard of. Today, the smartphone is more camera than phone. How did this happen? This transformation was enabled by advances in computational photography—the science and engineering of making great images from small-form-factor, mobile cameras. Modern algorithmic and computing advances, including machine learning, have changed the rules of photography, bringing to it new modes of capture, postprocessing, storage, and sharing. In this review, we give a brief history of mobile computational photography and describe some of the key technological components, including burst photography, noise reduction, and super-resolution. At each step, we can draw naive parallels to the human visual system.
    Print ISSN: 2374-4642
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    Topics: Medicine
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  • 17
    Publication Date: 2021-09-15
    Description: Some images evoke bistable percepts: two different visual experiences seen in alternation while continuously viewing an unchanged stimulus. The Necker Cube and Rubin's Vase are classic examples, each of which gives alternating percepts of different shapes. Other bistable percepts are alternating colors or directions of motion. Although stimuli that result in salient bistability are rare and sometimes cleverly constructed to emphasize ambiguity, they have been influential for over 150 years, since the work of von Helmholtz, who considered them to be evidence for perceptual visual processes that interpret retinal stimuli. While bistability in natural viewing is uncommon, the main point of this review is that implicit ambiguity in visual neural representations is pervasive. Resolving ambiguity, therefore, is a fundamental and ubiquitous process of vision that routinely affects what we see, not an oddity arising from cleverly crafted images. This review focuses on the causes of widespread ambiguity, historical perspectives on it, and modern knowledge and theory about resolving it.
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  • 18
    Publication Date: 2021-09-10
    Description: We review current data on clinically suspected [European Society of Cardiology (ESC) 2013 criteria] and biopsy-proven [ESC and World Health Organization (WHO) criteria] myocarditis that is temporally associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. ESC/WHO etiological diagnosis of viral myocarditis is based on histological, and immunohistological evidence of nonischemic myocyte necrosis and monolymphocytic infiltration, i.e., myocarditis, plus the identification of a specific cardiotropic virus by molecular techniques, in particular polymerase chain reaction (PCR)/in-situ hybridization, on endomyocardial biopsy (EMB)/autopsy tissue. There is not yet definitive EMB/autopsy proof that SARS-CoV-2 causes direct cardiomyocyte damage in association with histological myocarditis. Clinical epidemiology data suggest that myocarditis is uncommon for both SARS-CoV-2-positive and -negative PCR cases. We hypothesize that the rare virus-negative biopsy-proven cases may represent new-onset immune-mediated or latent pre-existing autoimmune forms, triggered or fostered by the hyperinflammatory state of severe COVID-19. We recommend the application of the ESC/WHO definitions and diagnostic criteria in future reports to avoid low-quality scientific information leading to an inaccurate estimate of myocarditis incidence based on misdiagnosis. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4219
    Electronic ISSN: 1545-326X
    Topics: Medicine
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  • 19
    Publication Date: 2021-09-15
    Description: The beginning of the twenty-first century was marked by the innovative use of pharmacochemical interventions, which have since expanded to include gene-based molecular therapies. For years, treatment has focused on tackling the pathophysiology of monogenic orphan diseases, and one of the first applications of these novel genome editing technologies was the treatment of rare inherited retinal dystrophies. In this review, we present recent, ongoing, and future gene therapy–based treatment trials for choroideremia, X-linked retinitis pigmentosa, Stargardt disease, and age-related macular degeneration. As these trials pave the way toward halting the progression of such devastating diseases, we will begin to see the exciting development of newer, cutting-edge strategies including base editing and prime editing, ushering in a new era of precision medicine.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 20
    Publication Date: 2021-08-25
    Description: Fire blight, caused by the bacterial phytopathogen Erwinia amylovora, is an economically important and mechanistically complex disease that affects apple and pear production in most geographic production hubs worldwide. We compile, assess, and present a genetic outlook on the progression of an E. amylovora infection in the host. We discuss the key aspects of type III secretion–mediated infection and systemic movement, biofilm formation in xylem, and pathogen dispersal via ooze droplets, a concentrated suspension of bacteria and exopolysaccharide components. We present an overall outlook on the genetic elements contributing to E. amylovora pathogenesis, including an exploration of the impact of floral microbiomes on E. amylovora colonization, and summarize the current knowledge of host responses to an incursion and how this response stimulates further infection and systemic spread. We hope to facilitate the identification of new, unexplored areas of research in this pathosystem that can help identify evolutionarily susceptible genetic targets to ultimately aid in the design of sustainable strategies for fire blight disease mitigation.
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 21
    Publication Date: 2021-08-25
    Description: The genomics era has ushered in exciting possibilities to examine the genetic bases that undergird the characteristic features of Verticillium dahliae and other plant pathogens. In this review, we provide historical perspectives on some of the salient biological characteristics of V. dahliae, including its morphology, microsclerotia formation, host range, disease symptoms, vascular niche, reproduction, and population structure. The kaleidoscopic population structure of this pathogen is summarized, including different races of the pathogen, defoliating and nondefoliating phenotypes, vegetative compatibility groupings, and clonal populations. Where possible, we place the characteristic differences in the context of comparative and functional genomics analyses that have offered insights into population divergence within V. dahliae and the related species.Current challenges are highlighted along with some suggested future population genomics studies that will contribute to advancing our understanding of the population divergence in V. dahliae.
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 22
    Publication Date: 2021-08-25
    Description: Plant diagnostic laboratories (PDLs) are at the heart of land-grant universities (LGUs) and their extension mission to connect citizens with research-based information. Although research and technological advances have led to many modern methods and technologies in plant pathology diagnostics, the pace of adopting those methods into services at PDLs has many complexities we aim to explore in this review. We seek to identify current challenges in plant disease diagnostics, as well as diagnosticians' and administrators'perceptions of PDLs' many roles. Surveys of diagnosticians and administrators were conducted to understand the current climate on these topics. We hope this article reaches researchers developing diagnostic methods with modern and new technologies to foster a better understanding of PDL diagnosticians’ perspective on method implementation. Ultimately, increasing researchers’ awareness of the factors influencing method adoption by PDLs encourages support, collaboration, and partnerships to advance plant diagnostics.
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 23
    Publication Date: 2021-08-23
    Description: Environmental pharmaceuticals represent a threat of emerging concern for marine ecosystems. Widely distributed and bioaccumulated, these contaminants could provoke adverse effects on aquatic organisms through modes of action like those reported for target species. In contrast to pharmacological uses, organisms in field conditions are exposed to complex mixtures of compounds with similar, different, or even opposing therapeutic effects. This review summarizes current knowledge of the main cellular pathways modulated by the most common classes of environmental pharmaceuticals occurring in marine ecosystems and accumulated by nontarget species—including nonsteroidal anti-inflammatory drugs, psychiatric drugs, cardiovascular and lipid regulator agents, steroidal hormones, and antibiotics—and describes an intricate network of possible interactions with both synergistic and antagonistic effects on the same cellular targets and metabolic pathways. This complexity reveals the intrinsic limits of the single-chemical approach to predict the long-term consequences and future impact of pharmaceuticals at organismal, population, and community levels. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 24
    Publication Date: 2021-08-23
    Description: Desmosomal cadherins are a recent evolutionary innovation that make up the adhesive core of highly specialized intercellular junctions called desmosomes. Desmosomal cadherins, which are grouped into desmogleins and desmocollins, are related to the classical cadherins, but their cytoplasmic domains are tailored for anchoring intermediate filaments instead of actin to sites of cell–cell adhesion. The resulting junctions are critical for resisting mechanical stress in tissues such as the skin and heart. Desmosomal cadherins also act as signaling hubs that promote differentiation and facilitate morphogenesis, creating more complex and effective tissue barriers in vertebrate tissues. Interference with desmosomal cadherin adhesive and supra-adhesive functions leads to a variety of autoimmune, hereditary, toxin-mediated, and malignant diseases. We review our current understanding of how desmosomal cadherins contribute to human health and disease, highlight gaps in our knowledge about their regulation and function, and introduce promising new directions toward combatting desmosome-related diseases. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1553-4006
    Electronic ISSN: 1553-4014
    Topics: Medicine
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  • 25
    Publication Date: 2021-08-24
    Description: The cytosolic selenoprotein thioredoxin reductase 1 (TrxR1, TXNRD1), and to some extent mitochondrial TrxR2 (TXNRD2), can be inhibited by a wide range of electrophilic compounds. Many such compounds also yield cytotoxicity toward cancer cells in culture or in mouse models, and most compounds are likely to irreversibly modify the easily accessible selenocysteine residue in TrxR1, thereby inhibiting its normal activity to reduce cytosolic thioredoxin (Trx1, TXN) and other substrates of the enzyme. This leads to an oxidative challenge. In some cases, the inhibited forms of TrxR1 are not catalytically inert and are instead converted to prooxidant NADPH oxidases, named SecTRAPs, thus further aggravating the oxidative stress, particularly in cells expressing higher levels of the enzyme. In this review, the possible molecular and cellular consequences of these effects are discussed in relation to cancer therapy, with a focus on outstanding questions that should be addressed if targeted TrxR1 inhibition is to be further developed for therapeutic use. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 26
    Publication Date: 2021-08-25
    Description: Hybrid necrosis in plants refers to a genetic autoimmunity syndrome in the progeny of interspecific or intraspecific crosses. Although the phenomenon was first documented in 1920, it has been unequivocally linked to autoimmunity only recently, with the discovery of the underlying genetic and biochemical mechanisms. The most common causal loci encode immune receptors, which are known to differ within and between species. One mechanism can be explained by the guard hypothesis, in which a guard protein, often a nucleotide-binding site–leucine-rich repeat protein, is activated by interaction with a plant protein that mimics standard guardees modified by pathogen effector proteins. Another surprising mechanism is the formation of inappropriately active immune receptor complexes. In this review, we summarize our current knowledge of hybrid necrosis and discuss how its study is not only informing the understanding of immune gene evolution but also revealing new aspects of plant immune signaling.
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 27
    Publication Date: 2021-08-23
    Description: During the past 541 million years, marine animals underwent three intervals of diversification (early Cambrian, Ordovician, Cretaceous–Cenozoic) separated by nondirectional fluctuation, suggesting diversity-dependent dynamics with the equilibrium diversity shifting through time. Changes in factors such as shallow-marine habitat area and climate appear to have modulated the nondirectional fluctuations. Directional increases in diversity are best explained by evolutionary innovations in marine animals and primary producers coupled with stepwise increases in the availability of food and oxygen. Increasing intensity of biotic interactions such as predation and disturbance may have led to positive feedbacks on diversification as ecosystems became more complex. Important areas for further research include improving the geographic coverage and temporal resolution of paleontological data sets, as well as deepening our understanding of Earth system evolution and the physiological and ecological traits that modulated organismal responses to environmental change. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 28
    Publication Date: 2021-09-17
    Description: Meta-analyses contribute critically to cumulative science, but they can produce misleading conclusions if their constituent primary studies are biased, for example by unmeasured confounding in nonrandomized studies. We provide practical guidance on how meta-analysts can address confounding and other biases that affect studies’ internal validity, focusing primarily on sensitivity analyses that help quantify how biased the meta-analysis estimates might be. We review a number of sensitivity analysis methods to do so, especially recent developments that are straightforward to implement and interpret and that use somewhat less stringent statistical assumptions than do earlier methods. We give recommendations for how these newer methods could be applied in practice and illustrate using a previously published meta-analysis. Sensitivity analyses can provide informative quantitative summaries of evidence strength, and we suggest reporting them routinely in meta-analyses of potentially biased studies. This recommendation in no way diminishes the importance of defining study eligibility criteria that reduce bias and of characterizing studies’ risks of bias qualitatively. Expected final online publication date for the Annual Review of Public Health, Volume 43 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0163-7525
    Electronic ISSN: 1545-2093
    Topics: Medicine
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  • 29
    Publication Date: 2021-08-25
    Description: Potyviruses (viruses in the genus Potyvirus, family Potyviridae) constitute the largest group of known plant-infecting RNA viruses and include many agriculturally important viruses that cause devastating epidemics and significant yield losses in many crops worldwide. Several potyviruses are recognized as the most economically important viral pathogens. Therefore, potyviruses are more studied than other groups of plant viruses. In the past decade, a large amount of knowledge has been generated to better understand potyviruses and their infection process. In this review, we list the top 10 economically important potyviruses and present a brief profile of each. We highlight recent exciting findings on the novel genome expression strategy and the biological functions of potyviral proteins and discuss recent advances in molecular plant–potyvirus interactions, particularly regarding the coevolutionary arms race. Finally, we summarize current disease control strategies, with a focus on biotechnology-based genetic resistance, and point out future research directions.
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 30
    Publication Date: 2021-08-25
    Description: Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 31
    Publication Date: 2021-08-31
    Description: Mutually beneficial interspecific interactions are abundant throughout the natural world, including between microbes. Mutualisms between microbes are critical for everything from human health to global nutrient cycling. Studying model microbial mutualisms in the laboratory enables highly controlled experiments for developing and testing evolutionary and ecological hypotheses. In this review, we begin by describing the tools available for studying model microbial mutualisms. We then outline recent insights that laboratory systems have shed on the evolutionary origins, evolutionary dynamics, and ecological features of microbial mutualism. We touch on gaps in our current understanding of microbial mutualisms, note connections to mutualism in nonmicrobial systems, and call attention to open questions ripe for future study. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 32
    Publication Date: 2021-09-28
    Description: Human activity has facilitated the introduction of many exotic species via global trade. Asia-Pacific countries comprise one of the most economically and trade-active regions in the world, which makes it one of the most vulnerable regions to invasive species, including ants. There are currently over 60 exotic ant species in the Asia-Pacific, with the red imported fire ant, Solenopsis invicta, among the most destructive. Exotic ants pose many economic and ecological problems for the region. Countries in the Asia-Pacific have dealt with the problem of exotic ants in very different ways, and there has been an overall lack of preparedness. To improve the management of risks associated with invasive ants, we recommend that countries take action across the biosecurity spectrum, spanning prevention, containment, and quarantine. The creation of an Asia-Pacific network for management of invasive ants should help prevent their introduction and mitigate their impacts. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4170
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  • 33
    Publication Date: 2021-09-29
    Description: Gammaherpesviruses are an important class of oncogenic pathogens that are exquisitely evolved to their respective hosts. As such, the human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi sarcoma herpesvirus (KSHV) do not naturally infect nonhuman primates or rodents. There is a clear need to fully explore mechanisms of gammaherpesvirus pathogenesis, host control, and immune evasion in the host. A gammaherpesvirus pathogen isolated from murid rodents was first reported in 1980; 40 years later, murine gammaherpesvirus 68 (MHV68, MuHV-4, γHV68) infection of laboratory mice is a well-established pathogenesis system recognized for its utility in applying state-of-the-art approaches to investigate virus-host interactions ranging from the whole host to the individual cell. Here, we highlight recent advancements in our understanding of the processes by which MHV68 colonizes the host and drives disease. Lessons that inform KSHV and EBV pathogenesis and provide future avenues for novel interventions against infection and virus-associated cancers are emphasized.
    Print ISSN: 2327-056X
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  • 34
    Publication Date: 2021-10-06
    Description: T cell activation is a critical event in the adaptive immune response, indispensable for cell-mediated and humoral immunity as well as for immune regulation. Recent years have witnessed an emerging trend emphasizing the essential role that physical force and mechanical properties play at the T cell interface. In this review, we integrate current knowledge of T cell antigen recognition and the different models of T cell activation from the perspective of mechanobiology, focusing on the interaction between the T cell receptor (TCR) and the peptide–major histocompatibility complex (pMHC) antigen. We address the shortcomings of TCR affinity alone in explaining T cell functional outcomes and the rising status of force-regulated TCR bond lifetimes, most notably the TCR catch bond. Ultimately, T cell activation and the ensuing physiological responses result from mechanical interaction between TCRs and the pMHC.
    Print ISSN: 1081-0706
    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 35
    Publication Date: 2021-10-06
    Description: Viral egress and transmission have long been described to take place through single free virus particles. However, viruses can also shed into the environment and transmit as populations clustered inside extracellular vesicles (EVs), a process we had first called vesicle-mediated en bloc transmission. These membrane-cloaked virus clusters can originate from a variety of cellular organelles including autophagosomes, plasma membrane, and multivesicular bodies. Their viral cargo can be multiples of nonenveloped or enveloped virus particles or even naked infectious genomes, but egress is always nonlytic, with the cell remaining intact. Here we put forth the thesis that EV-cloaked viral clusters are a distinct form of infectious unit as compared to free single viruses (nonenveloped or enveloped) or even free virus aggregates. We discuss how efficient and prevalent these infectious EVs are in the context of virus-associated diseases and highlight the importance of their proper detection and disinfection for public health.
    Print ISSN: 1081-0706
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  • 36
    Publication Date: 2021-10-06
    Description: The purpose of this review is to explore self-organizing mechanisms that pattern microtubules (MTs) and spatially organize animal cell cytoplasm, inspired by recent experiments in frog egg extract. We start by reviewing conceptual distinctions between self-organizing and templating mechanisms for subcellular organization. We then discuss self-organizing mechanisms that generate radial MT arrays and cell centers in the absence of centrosomes. These include autocatalytic MT nucleation, transport of minus ends, and nucleation from organelles such as melanosomes and Golgi vesicles that are also dynein cargoes. We then discuss mechanisms that partition the cytoplasm in syncytia, in which multiple nuclei share a common cytoplasm, starting with cytokinesis, when all metazoan cells are transiently syncytial. The cytoplasm of frog eggs is partitioned prior to cytokinesis by two self-organizing modules, protein regulator of cytokinesis 1 (PRC1)-kinesin family member 4A (KIF4A) and chromosome passenger complex (CPC)-KIF20A. Similar modules may partition longer-lasting syncytia, such as early Drosophila embryos. We end by discussing shared mechanisms and principles for the MT-based self-organization of cellular units.
    Print ISSN: 1081-0706
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  • 37
    Publication Date: 2021-10-06
    Description: One of the most common bacterial shapes is a rod, yet we have a limited understanding of how this simple shape is constructed. While only six proteins are required for rod shape, we are just beginning to understand how they self-organize to build the micron-sized enveloping structures that define bacterial shape out of nanometer-sized glycan strains. Here, we detail and summarize the insights gained over the last 20 years into this complex problem that have been achieved with a wide variety of different approaches. We also explain and compare both current and past models of rod shape formation and maintenance and then highlight recent insights into how the Rod complex might be regulated.
    Print ISSN: 1081-0706
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  • 38
    Publication Date: 2021-10-06
    Description: Tribolium castaneum has a long history as a model species in many distinct subject areas, but improved connections among the genetics, genomics, behavioral, ecological, and pest management fields are needed to fully realize this species’ potential as a model. Tribolium castaneum was the first beetle whose genome was sequenced, and a new genome assembly and enhanced annotation, combined with readily available genomic research tools, have facilitated its increased use in a wide range of functional genomics research. Research into T. castaneum’s sensory systems, response to pheromones and kairomones, and patterns of movement and landscape utilization has improved our understanding of behavioral and ecological processes. Tribolium castaneum has also been a model in the development of pest monitoring and management tactics, including evaluation of insecticide resistance mechanisms. Application of functional genomics approaches to behavioral, ecological, and pest management research is in its infancy but offers a powerful tool that can link mechanism with function and facilitate exploitation of these relationships to better manage this important food pest. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4170
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  • 39
    Publication Date: 2021-10-06
    Description: The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells provides examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine.
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  • 40
    Publication Date: 2021-10-06
    Description: Nuclei are central hubs for information processing in eukaryotic cells. The need to fit large genomes into small nuclei imposes severe restrictions on genome organization and the mechanisms that drive genome-wide regulatory processes. How a disordered polymer such as chromatin, which has vast heterogeneity in its DNA and histone modification profiles, folds into discernibly consistent patterns is a fundamental question in biology. Outstanding questions include how genomes are spatially and temporally organized to regulate cellular processes with high precision and whether genome organization is causally linked to transcription regulation. The advent of next-generation sequencing, super-resolution imaging, multiplexed fluorescent in situ hybridization, and single-molecule imaging in individual living cells has caused a resurgence in efforts to understand the spatiotemporal organization of the genome. In this review, we discuss structural and mechanistic properties of genome organization at different length scales and examine changes in higher-order chromatin organization during important developmental transitions.
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  • 41
    Publication Date: 2021-07-13
    Description: Cells of the vascular wall are exquisitely sensitive to changes in their mechanical environment. In healthy vessels, mechanical forces regulate signaling and gene expression to direct the remodeling needed for the vessel wall to maintain optimal function. Major diseases of arteries involve maladaptive remodeling with compromised or lost homeostatic mechanisms. Whereas homeostasis invokes negative feedback loops at multiple scales to mediate mechanobiological stability, disease progression often occurs via positive feedback that generates mechanobiological instabilities. In this review, we focus on the cell biology, wall mechanics, and regulatory pathways associated with arterial health and how changes in these processes lead to disease. We discuss how positive feedback loops arise via biomechanical and biochemical means. We conclude that inflammation plays a central role in overriding homeostatic pathways and suggest future directions for addressing therapeutic needs.
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 42
    Publication Date: 2021-10-04
    Description: Inward rectifier K+ (Kir) channels have been studied extensively in mammals, where they play critical roles in health and disease. In insects, Kir channels have recently been found to be key regulators of diverse physiological processes in several tissues. The importance of Kir channels in insects has positioned them to serve as emerging targets for the development of insecticides with novel modes of action. In this article, we provide the first comprehensive review of insect Kir channels, highlighting the rapid progress made in understanding their molecular biology, physiological roles, pharmacology, and toxicology. In addition, we highlight key gaps in our knowledge and suggest directions for future research to advance our understanding of Kir channels and their roles in insect physiology. Further knowledge of their functional roles will also facilitate their exploitation as targets for controlling arthropod pests and vectors of economic, medical, and/or veterinary relevance. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4170
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  • 43
    Publication Date: 2021-10-06
    Description: Male and female brains display anatomical and functional differences. Such differences are observed in species across the animal kingdom, including humans, but have been particularly well-studied in two classic animal model systems, the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Here we summarize recent advances in understanding how the worm and fly brain acquire sexually dimorphic features during development. We highlight the advantages of each system, illustrating how the precise anatomical delineation of sexual dimorphisms in worms has enabled recent analysis into how these dimorphisms become specified during development, and how focusing on sexually dimorphic neurons in the fly has enabled an increasingly detailed understanding of sex-specific behaviors.
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    Topics: Biology , Medicine
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  • 44
    Publication Date: 2021-10-06
    Print ISSN: 1081-0706
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    Topics: Biology , Medicine
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  • 45
    Publication Date: 2021-10-05
    Description: Every facet of human culture is in some way affected by our abundant, diverse insect neighbors. Our relationship with insects has been on display throughout the history of art, sometimes explicitly but frequently in inconspicuous ways. This is because artists can depict insects overtly, but they can also allude to insects conceptually or use insect products in a purely utilitarian manner. Insects themselves can serve as art media, and artists have explored or exploited insects for their products (silk, wax, honey, propolis, carmine, shellac, nest material), body parts (e.g., wings), and whole bodies (dead, alive, individually, or as collectives). This review surveys insects and their products used as media in the visual arts and considers the untapped potential for artistic exploration of media derived from insects. The history, value, and ethics of insect media art are relevant topics at a time when the natural world is at unprecedented risk. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 46
    Publication Date: 2021-10-08
    Description: Most bacteria are protected from environmental offenses by a cell wall consisting of strong yet elastic peptidoglycan. The cell wall is essential for preserving bacterial morphology and viability, and thus the enzymes involved in the production and turnover of peptidoglycan have become preferred targets for many of our most successful antibiotics. In the past decades, Vibrio cholerae, the gram-negative pathogen causing the diarrheal disease cholera, has become a major model for understanding cell wall genetics, biochemistry, and physiology. More than 100 articles have shed light on novel cell wall genetic determinants, regulatory links, and adaptive mechanisms. Here we provide the first comprehensive review of V. cholerae’s cell wall biology and genetics. Special emphasis is placed on the similarities and differences with Escherichia coli, the paradigm for understanding cell wall metabolism and chemical structure in gram-negative bacteria.
    Print ISSN: 0066-4227
    Electronic ISSN: 1545-3251
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  • 47
    Publication Date: 2021-10-08
    Description: Quorum sensing (QS) is one of the most studied cell-cell communication mechanisms in fungi. Research in the last 20 years has explored various fungal QS systems that are involved in a wide range of biological processes, especially eukaryote- or fungus-specific behaviors, mirroring the significant contribution of QS regulation to fungal biology and evolution. Based on recent progress, we summarize in this review fungal QS regulation, with an emphasis on its functional role in behaviors unique to fungi or eukaryotes. We suggest that using fungi as genetically amenable eukaryotic model systems to address why and how QS regulation is integrated into eukaryotic reproductive strategies and molecular or cellular processes could be an important direction for QS research.
    Print ISSN: 0066-4227
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  • 48
    Publication Date: 2021-10-08
    Description: African trypanosomes are responsible for important diseases of humans and animals in sub-Saharan Africa. The best-studied species is Trypanosoma brucei, which is characterized by development in the mammalian host between morphologically slender and stumpy forms. The latter are adapted for transmission by the parasite's vector, the tsetse fly. The development of stumpy forms is driven by density-dependent quorum sensing (QS), the molecular basis for which is now coming to light. In this review, I discuss the historical context and biological features of trypanosome QS and how it contributes to the parasite's infection dynamics within its mammalian host. Also, I discuss how QS can be lost in different trypanosome species, such as T. brucei evansi and T. brucei equiperdum, or modulated when parasites find themselves competing with others of different genotypes or of different trypanosome species in the same host. Finally, I consider the potential to exploit trypanosome QS therapeutically.
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  • 49
    Publication Date: 2021-10-08
    Description: Chitin is a structural polymer in many eukaryotes. Many organisms can degrade chitin to defend against chitinous pathogens or use chitin oligomers as food. Beneficial microorganisms like nitrogen-fixing symbiotic rhizobia and mycorrhizal fungi produce chitin-based signal molecules called lipo-chitooligosaccharides (LCOs) and short chitin oligomers to initiate a symbiotic relationship with their compatible hosts and exchange nutrients. A recent study revealed that a broad range of fungi produce LCOs and chitooligosaccharides (COs), suggesting that these signaling molecules are not limited to beneficial microbes. The fungal LCOs also affect fungal growth and development, indicating that the roles of LCOs beyond symbiosis and LCO production may predate mycorrhizal symbiosis. This review describes the diverse structures of chitin; their perception by eukaryotes and prokaryotes; and their roles in symbiotic interactions, defense, and microbe-microbe interactions. We also discuss potential strategies of fungi to synthesize LCOs and their roles in fungi with different lifestyles.
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  • 50
    Publication Date: 2021-09-28
    Description: Thomas Seeley's research has focused on analyzing the collective intelligence and natural lives of honey bees. This account describes how the author encountered honey bees as a boy and became a beekeeper; how he switched his career path from medicine to biology to study the behavior and social life of honey bees; and how he focuses on understanding how a honey bee colony functions when it lives in the wild, rather than in a beekeeper's hive. He has shown how a honey bee colony works as a single decision-making unit to adaptively allocate its foragers among flower patches and to choose its nesting site in a hollow tree. These findings buttress the view that, in some social insect species, the colony is a group-level vehicle of gene survival. Beyond his research, he has written three books to synthesize these findings for biologists and share these discoveries with beekeepers. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 51
    Publication Date: 2021-09-29
    Print ISSN: 2327-056X
    Electronic ISSN: 2327-0578
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  • 52
    Publication Date: 2021-09-29
    Description: Combinatory antiretroviral therapy (cART) reduces human immunodeficiency virus type 1 (HIV-1) replication but is not curative because cART interruption almost invariably leads to a rapid rebound of viremia due to the persistence of stable HIV-1-infected cellular reservoirs. These reservoirs are mainly composed of CD4+ T cells harboring replication-competent latent proviruses. A broadly explored approach to reduce the HIV-1 reservoir size, the shock and kill strategy, consists of reactivating HIV-1 gene expression from the latently infected cellular reservoirs (the shock), followed by killing of the virus-producing infected cells (the kill). Based on improved understanding of the multiple molecular mechanisms controlling HIV-1 latency, distinct classes of latency reversing agents (LRAs) have been studied for their efficiency to reactivate viral gene expression in in vitro and ex vivo cell models. Here, we provide an up-to-date review of these different mechanistic classes of LRAs and discuss optimizations of the shock strategy by combining several LRAs simultaneously or sequentially.
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  • 53
    Publication Date: 2021-09-29
    Description: Bacteriophages and bacterial biofilms are widely present in natural environments, a fact that has accelerated the evolution of phages and their bacterial hosts in these particular niches. Phage-host interactions in biofilm communities are rather complex, where phages are not always merely predators but also can establish symbiotic relationships that induce and strengthen biofilms. In this review we provide an overview of the main features affecting phage-biofilm interactions as well as the currently available methods of studying these interactions. In addition, we address the applications of phages for biofilm control in different contexts.
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  • 54
    Publication Date: 2021-09-27
    Description: Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
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  • 55
    Publication Date: 2021-09-29
    Description: Techniques for atomic-resolution structural biology have evolved during the past several decades. Breakthroughs in instrumentation, sample preparation, and data analysis that occurred in the past decade have enabled characterization of viruses with an unprecedented level of detail. Here we review the recent advances in magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for structural analysis of viruses and viral assemblies. MAS NMR is a powerful method that yields information on 3D structures and dynamics in a broad range of experimental conditions. After a brief introduction, we discuss recent structural and functional studies of several viruses investigated with atomic resolution at various levels of structural organization, from individual domains of a membrane protein reconstituted into lipid bilayers to virus-like particles and intact viruses. We present examples of the unique information revealed by MAS NMR about drug binding, conduction mechanisms, interactions with cellular host factors, and DNA packaging in biologically relevant environments that are inaccessible by other methods.
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  • 56
    Publication Date: 2021-09-29
    Description: Despite their simplicity, viruses exhibit certain types of social interactions. Situations in which a given virus achieves higher fitness in combination with other members of the viral population have been described at the level of transmission, replication, suppression of host immune responses, and host killing, enabling the evolution of viral cooperation. Although cellular coinfection with multiple viral particles is the typical playground for these interactions, cooperation between viruses infecting different cells is also established through cellular and viral-encoded communication systems. In general, the stability of cooperation is compromised by cheater genotypes, as best exemplified by defective interfering particles. As predicted by social evolution theory, cheater invasion can be avoided when cooperators interact preferentially with other cooperators, a situation that is promoted in spatially structured populations. Processes such as transmission bottlenecks, organ compartmentalization, localized spread of infection foci, superinfection exclusion, and even discrete intracellular replication centers promote multilevel spatial structuring in viruses.
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  • 57
    Publication Date: 2021-09-29
    Description: The longlegged ant ( Anoplolepis gracilipes) is one of the most damaging invasive tramp ants globally. It is generally found between latitudes 27°N and 27°S in Asia, although it has been introduced to other continents. Its native range remains debatable, but it is believed to be in Southeast Asia. Anoplolepis gracilipes invasion has many serious ecological consequences, especially for native invertebrate, vertebrate, and plant communities, altering ecosystem dynamics and functions. We examine and synthesize the literature about this species’ origin and distribution, impacts on biodiversity and ecosystems, biology and ecology, chemical control, and potential biocontrol agents. We highlight emerging research needs on the origin and invasion history of this species, its reproductive mode, its relationship with myrmecophiles, and its host–microbial interactions, and we discuss future research directions. Expected final online publication date for the Annual Review of Entomology, Volume 67 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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  • 58
    Publication Date: 2021-09-29
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  • 59
    Publication Date: 2021-09-29
    Description: The zinc finger antiviral protein (ZAP) restricts the replication of a broad range of RNA and DNA viruses. ZAP directly binds viral RNA, targeting it for degradation and inhibiting its translation. While the full scope of RNA determinants involved in mediating selective ZAP activity is unclear, ZAP binds CpG dinucleotides, dictating at least part of its target specificity. ZAP interacts with many cellular proteins, although only a few have been demonstrated to be essential for its antiviral activity, including the 3′–5′ exoribonuclease exosome complex, TRIM25, and KHNYN. In addition to inhibiting viral gene expression, ZAP also directly and indirectly targets a subset of cellular messenger RNAs to regulate the innate immune response. Overall, ZAP protects a cell from viral infection by restricting viral replication and regulating cellular gene expression. Further understanding of the ZAP antiviral system may allow for novel viral vaccine and anticancer therapy development.
    Print ISSN: 2327-056X
    Electronic ISSN: 2327-0578
    Topics: Medicine
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  • 60
    Publication Date: 2021-09-27
    Description: Systems biology can be defined as the study of a biological process in which all of the relevant components are investigated together in parallel to discover the mechanism. Although the approach is not new, it has come to the forefront as a result of genome sequencing projects completed in the first few years of the current century. It has elements of large-scale data acquisition (chiefly next-generation sequencing–based methods and protein mass spectrometry) and large-scale data analysis (big data integration and Bayesian modeling). Here we discuss these methodologies and show how they can be applied to understand the downstream effects of GPCR signaling, specifically looking at how the neurohypophyseal peptide hormone vasopressin, working through the V2 receptor and PKA activation, regulates the water channel aquaporin-2. The emerging picture provides a detailed framework for understanding the molecular mechanisms involved in water balance disorders, pointing the way to improved treatment of both polyuric disorders and water-retention disorders causing dilutional hyponatremia. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 61
    Publication Date: 2021-09-27
    Description: Epilepsy is an etiologically heterogeneous condition; however, genetic factors are thought to play a role in most patients. For those with infantile-onset developmental and epileptic encephalopathy (DEE), a genetic diagnosis is now obtained in more than 50% of patients. There is considerable motivation to utilize these molecular diagnostic data to help guide treatment, as children with DEEs often have drug-resistant seizures as well as developmental impairment related to cerebral epileptiform activity. Precision medicine approaches have the potential to dramatically improve the quality of life for these children and their families. At present, treatment can be targeted for patients with diagnoses in many genetic causes of infantile-onset DEE, including genes encoding sodium or potassium channel subunits, tuberous sclerosis, and congenital metabolic diseases. Precision medicine may refer to more intelligent choices of conventional antiseizure medications, repurposed agents previously used for other indications, novel compounds, enzyme replacement, or gene therapy approaches. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 62
    Publication Date: 2021-09-29
    Description: Aquatic eddy covariance (AEC) is increasingly being used to study benthic oxygen (O2) flux dynamics, organic carbon cycling, and ecosystem health in marine and freshwater environments. Because it is a noninvasive technique, has a high temporal resolution (∼15 min), and integrates over a large area of the seafloor (typically 10–100 m2), it has provided new insights on the functioning of aquatic ecosystems under naturally varying in situ conditions and has given us more accurate assessments of their metabolism. In this review, we summarize biogeochemical, ecological, and biological insights gained from AEC studies of marine ecosystems. A general finding for all substrates is that benthic O2 exchange is far more dynamic than earlier recognized, and thus accurate mean values can only be obtained from measurements that integrate over all timescales that affect the local O2 exchange. Finally, we highlight new developments of the technique, including measurements of air–water gas exchange and long-term deployments. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 63
    Publication Date: 2021-09-23
    Description: Inflammatory bowel diseases (IBD) arise from a convergence of genetic risk, environmental factors, and gut microbiota, where each is necessary but not sufficient to cause disease. Emerging evidence supports a bidirectional relationship between disease progression and changes in microbiota membership and function. Thus, the study of the gut microbiome and host–microbe interactions should provide critical insights into disease pathogenesis as well as leads for developing microbiome-based diagnostics and interventions for IBD. In this article, we review the most recent advances in understanding the relationship between the gut microbiota and IBD and highlight the importance of going beyond establishing description and association to gain mechanistic insights into causes and consequences of IBD. The review aims to contextualize recent findings to form conceptional frameworks for understanding the etiopathogenesis of IBD and for the future development of microbiome-based diagnostics and interventions. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4219
    Electronic ISSN: 1545-326X
    Topics: Medicine
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  • 64
    Publication Date: 2021-09-23
    Description: Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics—genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations—has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 65
    Publication Date: 2021-09-15
    Description: Measuring when exactly perceptual decisions are made is crucial for defining how the activation of specific neurons contributes to behavior. However, in traditional, nonurgent visuomotor tasks, the uncertainty of this temporal measurement is very large. This is a problem not only for delimiting the capacity of perception, but also for correctly interpreting the functional roles ascribed to choice-related neuronal responses. In this article, we review psychophysical, neurophysiological, and modeling work based on urgent visuomotor tasks in which this temporal uncertainty can be effectively overcome. The cornerstone of this work is a novel behavioral metric that describes the evolution of the subject's perceptual judgment moment by moment, allowing us to resolve numerous perceptual events that unfold within a few tens of milliseconds. In this framework, the neural distinction between perceptual evaluation and motor selection processes becomes particularly clear, as the conclusion of one is not contingent on that of the other.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 66
    Publication Date: 2021-09-15
    Description: Our sense of sight relies on photoreceptors, which transduce photons into the nervous system's electrochemical interpretation of the visual world. These precious photoreceptors can be disrupted by disease, injury, and aging. Once photoreceptors start to die, but before blindness occurs, the remaining retinal circuitry can withstand, mask, or exacerbate the photoreceptor deficit and potentially be receptive to newfound therapies for vision restoration. To maximize the retina's receptivity to therapy, one must understand the conditions that influence the state of the remaining retina. In this review, we provide an overview of the retina's structure and function in health and disease. We analyze a collection of observations on photoreceptor disruption and generate a predictive model to identify parameters that influence the retina's response. Finally, we speculate on whether the retina, with its remarkable capacity to function over light levels spanning nine orders of magnitude, uses these same adaptational mechanisms to withstand and perhaps mask photoreceptor loss.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 67
    Publication Date: 2021-09-15
    Description: In addition to the role that our visual system plays in determining what we are seeing right now, visual computations contribute in important ways to predicting what we will see next. While the role of memory in creating future predictions is often overlooked, efficient predictive computation requires the use of information about the past to estimate future events. In this article, we introduce a framework for understanding the relationship between memory and visual prediction and review the two classes of mechanisms that the visual system relies on to create future predictions. We also discuss the principles that define the mapping from predictive computations to predictive mechanisms and how downstream brain areas interpret the predictive signals computed by the visual system.
    Print ISSN: 2374-4642
    Electronic ISSN: 2374-4650
    Topics: Medicine
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  • 68
    Publication Date: 2021-09-29
    Description: The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry–based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time.
    Print ISSN: 2327-056X
    Electronic ISSN: 2327-0578
    Topics: Medicine
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  • 69
    Publication Date: 2021-09-29
    Description: The pervasive effects of the current coronavirus disease 2019 pandemic are but one reason for educators to refocus their efforts on virology teaching. Additionally, it is critical to understand how viruses function and to elucidate the relationship between virus and host. An understanding of current virology education may improve pedagogical approaches for educating our students and trainees. Faculty who teach undergraduate microbiology indicate that approximately 10% of the course content features viruses; stand-alone virology courses are infrequently offered to undergraduates. Fortunately, virology taught to undergraduates includes foundational material; several approaches for delivery of lecture- and lab-based content exist. At the graduate education level, there is growing appreciation that an emphasis on logic, reasoning, inference, and statistics must be reintroduced into the curriculum to create a generation of scientists who have a greater capacity for creativity and innovation. Educators also need to remove barriers to student success, at all levels of education.
    Print ISSN: 2327-056X
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    Topics: Medicine
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  • 70
    Publication Date: 2021-09-21
    Description: Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 71
    Publication Date: 2021-09-21
    Description: Neural crest stem/progenitor cells arise early during vertebrate embryogenesis at the border of the forming central nervous system. They subsequently migrate throughout the body, eventually differentiating into diverse cell types ranging from neurons and glia of the peripheral nervous system to bones of the face, portions of the heart, and pigmentation of the skin. Along the body axis, the neural crest is heterogeneous, with different subpopulations arising in the head, neck, trunk, and tail regions, each characterized by distinct migratory patterns and developmental potential. Modern genomic approaches like single-cell RNA- and ATAC-sequencing (seq) have greatly enhanced our understanding of cell lineage trajectories and gene regulatory circuitry underlying the developmental progression of neural crest cells. Here, we discuss how genomic approaches have provided new insights into old questions in neural crest biology by elucidating transcriptional and posttranscriptional mechanisms that govern neural crest formation and the establishment of axial level identity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 72
    Publication Date: 2021-08-30
    Description: Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 73
    Publication Date: 2021-08-31
    Description: Sexual selection has the potential to decrease mean fitness in a population through an array of costs to nonsexual fitness. These costs may be offset when sexual selection favors individuals with high nonsexual fitness, causing the alignment of sexual and natural selection. We review the many laboratory experiments that have manipulated mating systems aimed at quantifying the net effects of sexual selection on mean fitness. These must be interpreted in light of population history and the diversity of ways manipulations have altered sexual interactions, sexual conflict, and sexual and natural selection. Theory and data suggest a net benefit is more likely when sexually concordant genetic variation is enhanced and that ecological context can mediate the relative importance of these different effects. Comparative studies have independently examined the consequences of sexual selection for population/species persistence. These provide little indication of a benefit, and interpreting these higher-level responses is challenging. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 74
    Publication Date: 2021-08-31
    Description: Transcriptional deregulation is a key driver of acute myeloid leukemia (AML), a heterogeneous blood cancer with poor survival rates. Polycomb group (PcG) and Trithorax group (TrxG) genes, originally identified in Drosophila melanogaster several decades ago as master regulators of cellular identity and epigenetic memory, not only are important in mammalian development but also play a key role in AML disease biology. In addition to their classical canonical antagonistic transcriptional functions, noncanonical synergistic and nontranscriptional functions of PcG and TrxG are emerging. Here, we review the biochemical properties of major mammalian PcG and TrxG complexes and their roles in AML disease biology, including disease maintenance as well as drug resistance. We summarize current efforts on targeting PcG and TrxG for treatment of AML and propose rational synthetic lethality and drug-induced antagonistic pleiotropy options involving PcG and TrxG as potential new therapeutic avenues for treatment of AML.
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
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  • 75
    Publication Date: 2021-08-30
    Description: Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder that involves dysregulation of many cellular and molecular processes. It is notoriously difficult to develop therapeutics for AD due to its complex nature. Nevertheless, recent advancements in imaging technology and the development of innovative experimental techniques have allowed researchers to perform in-depth analyses to uncover the pathogenic mechanisms of AD. An important consideration when studying late-onset AD is its major genetic risk factor, apolipoprotein E4 (apoE4). Although the exact mechanisms underlying apoE4 effects on AD initiation and progression are not fully understood, recent studies have revealed critical insights into the apoE4-induced deficits that occur in AD. In this review, we highlight notable studies that detail apoE4 effects on prominent AD pathologies, including amyloid-β, tau pathology, neuroinflammation, and neural network dysfunction. We also discuss evidence that defines the physiological functions of apoE and outlines how these functions are disrupted in apoE4-related AD. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    Print ISSN: 1553-4006
    Electronic ISSN: 1553-4014
    Topics: Medicine
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  • 76