journal
Journals Cold Spring Harbor Perspective...

Cold Spring Harbor Perspectives in Biology

https://read.qxmd.com/read/38346860/predictability-an-orrery-and-a-speciation-machine-quest-for-a-standard-model-of-speciation
#1
JOURNAL ARTICLE
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 these questions with a thought experiment in which we conceive an evolutionary speciation machine generating new species...
February 12, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38346859/how-important-is-sexual-isolation-to-speciation
#2
JOURNAL ARTICLE
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 isolation relative to other reproductive barriers, including the relative evolutionary rate of sexual trait differentiation, the relative strength of sexual isolation in sympatry, and the role of sexual isolation in the long-term persistence of diverging forms...
February 12, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38346858/astrocyte-regulation-of-synapse-formation-maturation-and-elimination
#3
JOURNAL ARTICLE
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 elimination of excess synaptic connections. In this work, we will review key findings on the molecular mechanisms of astrocyte-synapse interaction with a focus on astrocyte-secreted factors, contact-mediated mechanisms, and synapse elimination...
February 12, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316558/genetic-coupling-of-mate-recognition-systems-in-the-genomic-era
#4
JOURNAL ARTICLE
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 and is often used to include linkage or genetic correlation between recognition system components. Here we review evidence for genetic coupling, concentrating on proposed examples of a common genetic basis for signals and preferences...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316557/the-biology-of-lipids
#5
JOURNAL ARTICLE
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, signaling, subcellular dynamics and various disease processes.
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316556/cell-adhesion-molecule-signaling-at-the-synapse-beyond-the-scaffold
#6
JOURNAL ARTICLE
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 their role in orchestrating synaptic connectivity. However, surprisingly little is known about the molecular mechanisms that translate trans -synaptic adhesion into the assembly of pre- and postsynaptic compartments...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316555/petabase-scale-homology-search-for-structure-prediction
#7
JOURNAL ARTICLE
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 merged with default MSAs produced by ColabFold-search and provided to ColabFold-predict. By using SRA data, we achieved highly accurate predictions (GDT_TS > 70) for 66% of the non-easy targets, whereas using ColabFold-search default MSAs scored highly in only 52%...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316554/reactive-astrocytes-and-emerging-roles-in-central-nervous-system-cns-disorders
#8
JOURNAL ARTICLE
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 of different CNS insults but also with location in the CNS, genetic predispositions, age, and potentially also with "molecular memory" of previous reactivity events...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316553/astrocyte-regulation-of-cerebral-blood-flow-in-health-and-disease
#9
JOURNAL ARTICLE
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 acids (EETs) dilate blood vessels while 20-hydroxyeicosatetraenoic acid (20-HETE) constricts vessels...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316552/remyelination-in-the-central-nervous-system
#10
JOURNAL ARTICLE
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, triggers a spontaneous and often highly efficient regenerative response, remyelination, in which new oligodendrocytes are generated and myelin sheaths are restored to denuded axons...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38316551/coevolutionary-interactions-between-sexual-and-habitat-isolation-during-reinforcement
#11
JOURNAL ARTICLE
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 and habitat isolation. We first review the empirical literature where both barriers were explicitly considered, and then develop a population genetic model of reinforcement...
February 5, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38253418/variability-in-neural-circuit-formation
#12
JOURNAL ARTICLE
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 is relevant to our understanding of how these processes and outcomes are encoded in the genome. Second, variation in the wiring of the brain in humans may underlie variation in all kinds of psychological and behavioral traits, as well as neurodevelopmental disorders...
January 22, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38253417/peripheral-nervous-system-pns-myelin-diseases
#13
JOURNAL ARTICLE
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 syndrome and chronic, inflammatory demyelinating polyneuropathy, both of which are immune-mediated...
January 22, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38253416/membrane-epilipidome-lipid-modifications-their-dynamics-and-functional-significance
#14
JOURNAL ARTICLE
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 lipid remodeling required for the responsiveness and adaptability of cellular membranes, living systems make use of a network of chemical modifications of already existing lipids that complement the rather slow biosynthetic pathways...
January 22, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38253415/fisher-s-geometric-model-as-a-tool-to-study-speciation
#15
JOURNAL ARTICLE
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 model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa...
January 22, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38253414/endoplasmic-reticulum-membrane-homeostasis-and-the-unfolded-protein-response
#16
JOURNAL ARTICLE
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. The unfolded protein response (UPR) is a powerful signaling pathway that balances protein and lipid production in the ER...
January 22, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38199866/schwann-cells-as-orchestrators-of-nerve-repair-implications-for-tissue-regeneration-and-pathologies
#17
JOURNAL ARTICLE
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 and nurturing the regrowth of damaged axons back to their targets. Aside from the repair of damaged nerves themselves, nerve regenerative processes have been linked to the repair of other tissues and de novo innervation appears important in establishing an environment conducive for the development and spread of tumors...
January 10, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38191516/coupling-of-barriers-to-gene-exchange-causes-and-consequences
#18
JOURNAL ARTICLE
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 the build-up of linkage disequilibrium among loci underlying barriers to gene exchange, (2) coupling as the build-up of genome-wide linkage disequilibrium, and (3) coupling as the process generating a coincidence of distinct barrier effects...
January 8, 2024: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38151332/overcoming-obstacles-to-gene-edited-solutions-to-climate-challenges
#19
JOURNAL ARTICLE
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 solutions to overcoming them are presented.
December 27, 2023: Cold Spring Harbor Perspectives in Biology
https://read.qxmd.com/read/38151331/the-ecology-of-hybrid-incompatibilities
#20
JOURNAL ARTICLE
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 selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic...
December 27, 2023: Cold Spring Harbor Perspectives in Biology
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