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The Role of Hybridization in Species Formation and Persistence CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-04 Joshua V. Peñalba, Anna Runemark, Joana I. Meier, Pooja Singh, Guinevere O.U. Wogan, Rosa Sánchez-Guillén, James Mallet, Sina J. Rometsch, Mitra Menon, Ole Seehausen, Jonna Kulmuni, Ricardo J. Pereira
Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some of the most diverse clades across the tree of life
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The Astrocyte: Metabolic Hub of the Brain CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-04 L. Felipe Barros, Stefanie Schirmeier, Bruno Weber
Astrocytic metabolism has taken center stage. Interposed between the neuron and the vasculature, astrocytes exert control over the fluxes of energy and building blocks required for neuronal activity and plasticity. They are also key to local detoxification and waste recycling. Whereas neurons are metabolically rigid, astrocytes can switch between different metabolic profiles according to local demand
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Microglia in Health and Diseases: Integrative Hubs of the Central Nervous System (CNS) CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-04 Amanda Sierra, Veronique E. Miron, Rosa C. Paolicelli, Richard M. Ransohoff
Microglia are usually referred to as “the innate immune cells of the brain,” “the resident macrophages of the central nervous system” (CNS), or “CNS parenchymal macrophages.” These labels allude to their inherent immune function, related to their macrophage lineage. However, beyond their classic innate immune responses, microglia also play physiological roles crucial for proper brain development and
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Protein Design Using Structure-Prediction Networks: AlphaFold and RoseTTAFold as Protein Structure Foundation Models CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-04 Jue Wang, Joseph L. Watson, Sidney L. Lisanza
Designing proteins with tailored structures and functions is a long-standing goal in bioengineering. Recently, deep learning advances have enabled protein structure prediction at near-experimental accuracy, which has catalyzed progress in protein design as well. We review recent studies that use structure-prediction neural networks to design proteins, via approaches such as activation maximization
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Characterizing Large-Scale Human Circuit Development with In Vivo Neuroimaging CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-04 Tomoki Arichi
Large-scale coordinated patterns of neural activity are crucial for the integration of information in the human brain and to enable complex and flexible human behavior across the life span. Through recent advances in noninvasive functional magnetic resonance imaging (fMRI) methods, it is now possible to study this activity and how it emerges in the living fetal brain across the second half of human
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Agritech to Tame the Nitrogen Cycle CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-01 Lisa Y. Stein
While the Haber–Bosch process for N-fixation has enabled a steady food supply for half of humanity, substantial use of synthetic fertilizers has caused a radical unevenness in the global N-cycle. The resulting increases in nitrate production and greenhouse gas (GHG) emissions have contributed to eutrophication of both ground and surface waters, the growth of oxygen minimum zones in coastal regions
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Features, Fates, and Functions of Oligodendrocyte Precursor Cells CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-01 Robert A. Hill, Akiko Nishiyama, Ethan G. Hughes
Oligodendrocyte precursor cells (OPCs) are a central nervous system resident population of glia with a distinct molecular identity and an ever-increasing list of functions. OPCs generate oligodendrocytes throughout development and across the life span in most regions of the brain and spinal cord. This process involves a complex coordination of molecular checkpoints and biophysical cues from the environment
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Remyelination in the Central Nervous System CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-01 Robin J.M. Franklin, Benedetta Bodini, Steven A. Goldman
The inability of the mammalian central nervous system (CNS) to undergo spontaneous regeneration has long been regarded as a central tenet of neurobiology. However, while this is largely true of the neuronal elements of the adult mammalian CNS, save for discrete populations of granule neurons, the same is not true of its glial elements. In particular, the loss of oligodendrocytes, which results in demyelination
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Building Representation Learning Models for Antibody Comprehension CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-01 Justin Barton, Aretas Gaspariunas, Jacob D. Galson, Jinwoo Leem
Antibodies are versatile proteins with both the capacity to bind a broad range of targets and a proven track record as some of the most successful therapeutics. However, the development of novel antibody therapeutics is a lengthy and costly process. It is challenging to predict the functional and biophysical properties of antibodies from their amino acid sequence alone, requiring numerous experiments
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Variability in Neural Circuit Formation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-01 Kevin J. Mitchell
The study of neural development is usually concerned with the question of how nervous systems get put together. Variation in these processes is usually of interest as a means of revealing these normative mechanisms. However, variation itself can be an object of study and is of interest from multiple angles. First, the nature of variation in both the processes and the outcomes of neural development
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Structural Variants and Speciation: Multiple Processes at Play CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-03-01 Emma L. Berdan, Thomas G. Aubier, Salvatore Cozzolino, Rui Faria, Jeffrey L. Feder, Mabel D. Giménez, Mathieu Joron, Jeremy B. Searle, Claire Mérot
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although
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Predictability, an Orrery, and a Speciation Machine: Quest for a Standard Model of Speciation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-12 Marius Roesti, Hannes Roesti, Ina Satokangas, Janette Boughman, Samridhi Chaturvedi, Jochen B.W. Wolf, R. Brian Langerhans
Accurate predictions are commonly taken as a hallmark of strong scientific understanding. Yet, we do not seem capable today of making many accurate predictions about biological speciation. Why? What limits predictability in general, what exactly is the function and value of predictions, and how might we go about predicting new species? Inspired by an orrery used to explain solar eclipses, we address
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How Important Is Sexual Isolation to Speciation? CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-12 Kerry L. Shaw, Christopher R. Cooney, Tamra C. Mendelson, Michael G. Ritchie, Natalie S. Roberts, Leeban H. Yusuf
A central role for sexual isolation in the formation of new species and establishment of species boundaries has been noticed since Darwin and is frequently emphasized in the modern literature on speciation. However, an objective evaluation of when and how sexual isolation plays a role in speciation has been carried out in few taxa. We discuss three approaches for assessing the importance of sexual
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Astrocyte Regulation of Synapse Formation, Maturation, and Elimination CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-12 Won-Suk Chung, Katherine T. Baldwin, Nicola J. Allen
Astrocytes play an integral role in the development, maturation, and refinement of neuronal circuits. Astrocytes secrete proteins and lipids that instruct the formation of new synapses and induce the maturation of existing synapses. Through contact-mediated signaling, astrocytes can regulate the formation and state of synapses within their domain. Through phagocytosis, astrocytes participate in the
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Astrocyte Regulation of Cerebral Blood Flow in Health and Disease CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Anusha Mishra, Grant R. Gordon, Brian A. MacVicar, Eric A. Newman
Astrocytes play an important role in controlling microvascular diameter and regulating local cerebral blood flow (CBF) in several physiological and pathological scenarios. Neurotransmitters released from active neurons evoke Ca2+ increases in astrocytes, leading to the release of vasoactive metabolites of arachidonic acid (AA) from astrocyte endfeet. Synthesis of prostaglandin E2 (PGE2) and epoxyeicosatrienoic
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Petabase-Scale Homology Search for Structure Prediction CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger
The recent CASP15 competition highlighted the critical role of multiple sequence alignments (MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2-based prediction methods. To push the boundaries of MSA utilization, we conducted a petabase-scale search of the Sequence Read Archive (SRA), resulting in gigabytes of aligned homologs for CASP15 targets. These were
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Genetic Coupling of Mate Recognition Systems in the Genomic Era CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Michael G. Ritchie, Roger K. Butlin
The concept of “genetic coupling” in mate recognition systems arose in the 1960s as a potential mechanism to maintain coordination between signals and receivers during evolutionary divergence. At its most basic it proposed that the same genes might influence trait and preference, and therefore mutations could result in coordinated changes in both traits. Since then, the concept has expanded in scope
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Cell Adhesion Molecule Signaling at the Synapse: Beyond the Scaffold CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Ben Verpoort, Joris de Wit
Synapses are specialized intercellular junctions connecting pre- and postsynaptic neurons into functional neural circuits. Synaptic cell adhesion molecules (CAMs) constitute key players in synapse development that engage in homo- or heterophilic interactions across the synaptic cleft. Decades of research have identified numerous synaptic CAMs, mapped their trans-synaptic interactions, and determined
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The Biology of Lipids CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Robert G. Parton, Kai Simons
Lipids are the defining features of cellular membranes. They act collectively to form a variety of different structures, and understanding their complex behavior represents an early example of systems biology. A multidisciplinary approach is needed to analyse the functions of lipids in biological systems, and new work is providing fascinating insights into their roles in membrane biology, metabolism
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Reactive Astrocytes and Emerging Roles in Central Nervous System (CNS) Disorders CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Shane A. Liddelow, Michelle L. Olsen, Michael V. Sofroniew
In addition to their many functions in the healthy central nervous system (CNS), astrocytes respond to CNS damage and disease through a process called “reactivity.” Recent evidence reveals that astrocyte reactivity is a heterogeneous spectrum of potential changes that occur in a context-specific manner. These changes are determined by diverse signaling events and vary not only with the nature and severity
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Coevolutionary Interactions between Sexual and Habitat Isolation during Reinforcement CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-05 Roman Yukilevich, Fumio Aoki, Scott Egan, Linyi Zhang
Speciation often involves the evolution of multiple genetic-based barriers to gene flow (i.e., “coupling”). However, barriers may exhibit a diversity of evolutionary interactions during speciation. These dynamics are important in reinforcement, where selection may favor different prezygotic isolating barriers to avoid maladaptive hybridization. Here we study the interaction between evolution of sexual
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Photosynthesis 2.0: Realizing New-to-Nature CO2-Fixation to Overcome the Limits of Natural Metabolism CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-01 Tobias J. Erb
Synthetic biology provides opportunities to realize new-to-nature CO2-fixation metabolisms to overcome the limitations of natural photosynthesis. Two different strategies are currently being pursued: One is to realize engineered plants that feature carbon-neutral or carbon-negative (i.e., CO2-fixing) photorespiration metabolism, such as the tatronyl-CoA (TaCo) pathway, to boost CO2-uptake rates of
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Is Novelty Predictable? CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-01 Clara Fannjiang, Jennifer Listgarten
Machine learning–based design has gained traction in the sciences, most notably in the design of small molecules, materials, and proteins, with societal applications ranging from drug development and plastic degradation to carbon sequestration. When designing objects to achieve novel property values with machine learning, one faces a fundamental challenge: how to push past the frontier of current knowledge
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Mapping the Retina onto the Brain CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-01 Daniel Kerschensteiner, Marla B. Feller
Vision begins in the retina, which extracts salient features from the environment and encodes them in the spike trains of retinal ganglion cells (RGCs), the output neurons of the eye. RGC axons innervate diverse brain areas (>50 in mice) to support perception, guide behavior, and mediate influences of light on physiology and internal states. In recent years, complete lists of RGC types (∼45 in mice)
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Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-01 Kira Delmore, Hannah Justen, Kathleen M. Kay, Jun Kitano, Leonie C. Moyle, Rike Stelkens, Matthew A. Streisfeld, Yo Y. Yamasaki, Joseph Ross
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances
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Genetics and the Evolution of Prezygotic Isolation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-02-01 Richard M. Merrill, Henry Arenas-Castro, Anna F. Feller, Julia Harenčár, Matteo Rossi, Matthew A. Streisfeld, Kathleen M. Kay
The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow
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Peripheral Nervous System (PNS) Myelin Diseases CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-22 Steven S. Scherer, John Svaren
This is a review of inherited and acquired causes of human demyelinating neuropathies and a subset of disorders that affect axon–Schwann cell interactions. Nearly all inherited demyelinating neuropathies are caused by mutations in genes that are expressed by myelinating Schwann cells, affecting diverse functions in a cell-autonomous manner. The most common acquired demyelinating neuropathies are Guillain–Barré
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Endoplasmic Reticulum Membrane Homeostasis and the Unfolded Protein Response CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-22 Robert Ernst, Mike F. Renne, Aamna Jain, Alexander von der Malsburg
The endoplasmic reticulum (ER) is the key organelle for membrane biogenesis. Most lipids are synthesized in the ER, and most membrane proteins are first inserted into the ER membrane before they are transported to their target organelle. The composition and properties of the ER membrane must be carefully controlled to provide a suitable environment for the insertion and folding of membrane proteins
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Membrane Epilipidome—Lipid Modifications, Their Dynamics, and Functional Significance CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-22 Sider Penkov, Maria Fedorova
Lipids are characterized by extremely high structural diversity translated into a wide range of physicochemical properties. As such, lipids are vital for many different functions including organization of cellular and organelle membranes, control of cellular and organismal energy metabolism, as well as mediating multiple signaling pathways. To maintain the lipid chemical diversity and to achieve rapid
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Fisher's Geometric Model as a Tool to Study Speciation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-22 Hilde Schneemann, Bianca De Sanctis, John J. Welch
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric
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Schwann Cells as Orchestrators of Nerve Repair: Implications for Tissue Regeneration and Pathologies CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-10 Ruth M. Stassart, Jose A. Gomez-Sanchez, Alison C. Lloyd
Peripheral nerves exist in a stable state in adulthood providing a rapid bidirectional signaling system to control tissue structure and function. However, following injury, peripheral nerves can regenerate much more effectively than those of the central nervous system (CNS). This multicellular process is coordinated by peripheral glia, in particular Schwann cells, which have multiple roles in stimulating
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Coupling of Barriers to Gene Exchange: Causes and Consequences CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-08 Erik B. Dopman, Kerry L. Shaw, Maria R. Servedio, Roger K. Butlin, Carole M. Smadja
Coupling has emerged as a concept to describe the transition from differentiated populations to newly evolved species through the strengthening of reproductive isolation. However, the term has been used in multiple ways, and relevant processes have sometimes not been clearly distinguished. Here, we synthesize existing uses of the concept of coupling and find three main perspectives: (1) coupling as
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Transformation of Plantation Forestry Productivity for Climate Change Mitigation and Adaptation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-01 Mike May, Stanley Hirsch, Miron Abramson
The protection of natural forests as the major land-based biotic sink of carbon is regarded as a priority for climate action, and zero deforestation is an accepted global imperative. Sustainable intensification of plantation forestry will be essential to meet escalating, shifting, and diversifying demand for forest products if logging pressure on natural forests is to be decreased. Substitution strategies
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Development and Evolution of Thalamocortical Connectivity CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-01 Zoltán Molnár, Kenneth Y. Kwan
Conscious perception in mammals depends on precise circuit connectivity between cerebral cortex and thalamus; the evolution and development of these structures are closely linked. During the wiring of reciprocal thalamus–cortex connections, thalamocortical axons (TCAs) first navigate forebrain regions that had undergone substantial evolutionary modifications. In particular, the organization of the
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Glia as Functional Barriers and Signaling Intermediaries CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-01 Vilaiwan M. Fernandes, Vanessa Auld, Christian Klämbt
Glia play a crucial role in providing metabolic support to neurons across different species. To do so, glial cells isolate distinct neuronal compartments from systemic signals and selectively transport specific metabolites and ions to support neuronal development and facilitate neuronal function. Because of their function as barriers, glial cells occupy privileged positions within the nervous system
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Endocytic Roles of Glycans on Proteins and Lipids CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-01 Ludger Johannes, Massiullah Shafaq-Zadah, Estelle Dransart, Christian Wunder, Hakon Leffler
Most cell surface proteins are decorated by glycans, and the plasma membrane is rich in glycosylated lipids. The mechanisms by which the enormous complexity of these glycan structures on proteins and lipids is exploited to control glycoprotein activity by setting their cell surface residence time and the ways by which they are taken up into cells are still under active investigation. Here, two mechanisms
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The Sensory Ecology of Speciation CSH Perspect. Biol. (IF 7.2) Pub Date : 2024-01-01 Denise Dalbosco Dell'Aglio, David F. Rivas-Sánchez, Daniel Shane Wright, Richard M. Merrill, Stephen H. Montgomery
In this work, we explore the potential influence of sensory ecology on speciation, including but not limited to the concept of sensory drive, which concerns the coevolution of signals and sensory systems with the local environment. The sensory environment can influence individual fitness in a variety of ways, thereby affecting the evolution of both pre- and postmating reproductive isolation. Previous
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The Ecology of Hybrid Incompatibilities CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-27 Ken A. Thompson, Yaniv Brandvain, Jenn M. Coughlan, Kira E. Delmore, Hannah Justen, Catherine R. Linnen, Daniel Ortiz-Barrientos, Catherine A. Rushworth, Hilde Schneemann, Molly Schumer, Rike Stelkens
Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky–Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based
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Synthesis and Scope of the Role of Postmating Prezygotic Isolation in Speciation CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-27 Martin D. Garlovsky, Emma Whittington, Tomas Albrecht, Henry Arenas-Castro, Dean M. Castillo, Graeme L. Keais, Erica L. Larson, Leonie C. Moyle, Melissa Plakke, Radka Reifová, Rhonda R. Snook, Murielle Ålund, Alexandra A.-T. Weber
How barriers to gene flow arise and are maintained are key questions in evolutionary biology. Speciation research has mainly focused on barriers that occur either before mating or after zygote formation. In comparison, postmating prezygotic (PMPZ) isolation—a barrier that acts after gamete release but before zygote formation—is less frequently investigated but may hold a unique role in generating biodiversity
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Phospholipase Modulation of Synaptic Membrane Landscape: Driving Force Behind Memory Formation? CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-27 Tristan P. Wallis, Frédéric A. Meunier
The synapse is the communication unit of the brain, linking billions of neurons through trillions of synaptic connections. The lipid landscape of the synaptic membrane underpins neurotransmitter release through the exocytic fusion of neurotransmitter-containing vesicles, endocytic recycling of these synaptic vesicles, and the postsynaptic response following binding of the neurotransmitter to specialized
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Overcoming Obstacles to Gene-Edited Solutions to Climate Challenges CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-27 L. Val Giddings
Gene editing and genetic modification hold enormous potential to deliver solutions to multiple climate change challenges. The most important rate-limiting obstacles impeding their development and deployment are not technical, but rather counterproductive policies and regulations. These are driven in part by the mistaken apprehension of widespread public opposition. These obstacles are described and
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Engineering Proteins Using Statistical Models of Coevolutionary Sequence Information CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-18 Jerry C. Dinan, James W. McCormick, Kimberly A. Reynolds
Homologous protein sequences are wonderfully diverse, indicating many possible evolutionary “solutions” to the encoding of function. Consequently, one can construct statistical models of protein sequence by analyzing amino acid frequency across a large multiple sequence alignment. A central premise is that covariance between amino acid positions reflects coevolution due to a shared functional or biophysical
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An Agrigenomics Trifecta: Greenhouse Gas Drawdown, Food Security, and New Drugs CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-18 Charles DeLisi
An abundance of data, including decades of greenhouse gas (GHG) emission rates, atmospheric concentrations, and global average temperatures, is sufficient to allow a strictly empirical evaluation of the U.S. plan for controlling GHGs. This article presents an analysis, based solely on such data, that shows that the difference between atmospheric GHG levels that will be reached if current trends continue
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Engineering Crassulacean Acid Metabolism in C3 and C4 Plants CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-05 Xiaohan Yang, Yang Liu, Guoliang Yuan, David J. Weston, Gerald A. Tuskan
Carbon dioxide (CO2) is a major greenhouse gas contributing to changing climatic conditions, which is a grand challenge affecting the security of food, energy, and environment. Photosynthesis plays the central role in plant-based CO2 reduction. Plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C3 or C4 photosynthesis. Therefore
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Environmental Impacts of Machine Learning Applications in Protein Science CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-01 Loïc Lannelongue, Michael Inouye
Computing tools and machine learning models play an increasingly important role in biology and are now an essential part of discoveries in protein science. The growing energy needs of modern algorithms have raised concerns in the computational science community in light of the climate emergency. In this work, we summarize the different ways in which protein science can negatively impact the environment
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Convergent Circuit Computation for Categorization in the Brains of Primates and Songbirds CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-01 Andreas Nieder
Categorization is crucial for behavioral flexibility because it enables animals to group stimuli into meaningful classes that can easily be generalized to new circumstances. A most abstract quantitative category is set size, the number of elements in a set. This review explores how categorical number representations are realized by the operations of excitatory and inhibitory neurons in associative
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Quantitative Analyses of Coupling in Hybrid Zones CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-01 Thomas J. Firneno, Jr., Georgy Semenov, Erik B. Dopman, Scott A. Taylor, Erica L. Larson, Zachariah Gompert
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations
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Anthropogenic Change and the Process of Speciation CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-01 Murielle Ålund, Meredith Cenzer, Nicolas Bierne, Janette W. Boughman, José Cerca, Mattheau S. Comerford, Alessandro Culicchi, Brian Langerhans, S. Eryn McFarlane, Markus H. Möst, Henry North, Anna Qvarnström, Mark Ravinet, Richard Svanbäck, Scott A. Taylor
Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging
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Seeing the Membrane from Both Sides Now: Lipid Asymmetry and Its Strange Consequences CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-01 Milka Doktorova, Ilya Levental, Frederick A. Heberle
Almost all biomembranes are constructed as lipid bilayers and, in almost all of these, the two opposing monolayers (leaflets) have distinct lipid compositions. This lipid asymmetry arises through the concerted action of a suite of energy-dependent enzymes that maintain living bilayers in a far-from-equilibrium steady-state. Recent discoveries reveal that lipid compositional asymmetry imparts biophysical
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Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-12-01 Masaaki Uematsu, Jeremy M. Baskin
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the
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Direct Methane Removal from Air by Aerobic Methanotrophs CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-11-03 Mary E. Lidstrom
The rapid pace of climate change has created great urgency for short-term mitigation strategies. Appropriately, the long-term target for intervening in global warming is CO2, but experts suggest that methane should be a key short-term target. Methane has a warming impact 34 times greater than CO2 on a 100-year timescale, and 86 times greater on a 20-year timescale, and its short half-life in the atmosphere
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Optimizing Crop Plant Stomatal Density to Mitigate and Adapt to Climate Change CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-11-03 Julie Gray, Jessica Dunn
Plants take up carbon dioxide, and lose water, through pores on their leaf surfaces called stomata. We have a good understanding of the biochemical signals that control the production of stomata, and over the past decade, these have been manipulated to produce crops with fewer stomata. Crops with abnormally low stomatal densities require less water to produce the same yield and have enhanced drought
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Exploring the Protein Sequence Space with Global Generative Models CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-11-01 Sergio Romero-Romero, Sebastian Lindner, Noelia Ferruz
Recent advancements in specialized large-scale architectures for training images and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT-4, have demonstrated exceptional capabilities in processing, translating, and generating human language. These breakthroughs have also been reflected in protein research
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The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-11-01 Sarah A. Shelby, Sarah L. Veatch
Several groups have recently reported evidence for the emergence of domains in cell plasma membranes when membrane proteins are organized by ligand binding or assembly of membrane proximal scaffolds. These domains recruit and retain components that favor the liquid-ordered phase, adding to a decades-old literature interrogating the contribution of membrane phase separation in plasma membrane organization
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The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-11-01 Kay Lucek, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja Marie Westram, Rui Faria
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has
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Cholesterol, Eukaryotic Lipid Domains, and an Evolutionary Perspective of Transmembrane Signaling CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-11-01 Yan Shi, Hefei Ruan, Yanni Xu, Chunlin Zou
Transmembrane signaling is essential for complex life forms. Communication across a bilayer lipid barrier is elaborately organized to convey precision and to fine-tune strength. Looking back, the steps that it has taken to enable this seemingly mundane errand are breathtaking, and with our survivorship bias, Darwinian. While this review is to discuss eukaryotic membranes in biological functions for
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Microbial Catalysis for CO2 Sequestration: A Geobiological Approach CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-10-03 Martin Van Den Berghe, Nathan G. Walworth, Neil C. Dalvie, Chris L. Dupont, Michael Springer, M. Grace Andrews, Stephen J. Romaniello, David A. Hutchins, Francesc Montserrat, Pamela A. Silver, Kenneth H. Nealson
One of the greatest threats facing the planet is the continued increase in excess greenhouse gasses, with CO2 being the primary driver due to its rapid increase in only a century. Excess CO2 is exacerbating known climate tipping points that will have cascading local and global effects including loss of biodiversity, global warming, and climate migration. However, global reduction of CO2 emissions is
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Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-10-01 Radka Reifová, S. Lorena Ament-Velásquez, Yann Bourgeois, Jenn Coughlan, Jonna Kulmuni, Agnieszka P. Lipinska, Genta Okude, Laurie Stevison, Kohta Yoshida, Jun Kitano
Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky–Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic
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A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-10-01 Satyajit Mayor, Abrar Bhat, Akihiro Kusumi
The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for
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How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs) CSH Perspect. Biol. (IF 7.2) Pub Date : 2023-10-01 Mykhailo Girych, Waldemar Kulig, Giray Enkavi, Ilpo Vattulainen
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized