October 2021

Research articles

    1. Developmental Biology
    2. Genetics and Genomics

    Paths and pathways that generate cell-type heterogeneity and developmental progression in hematopoiesis

    Juliet R Girard et al.
    A combination of mRNA sequencing and genetic analysis reveals mechanisms that govern the development of distinct differentiated blood cell types from hematopoietic progenitors.
    1. Cell Biology

    Growth-dependent signals drive an increase in early G1 cyclin concentration to link cell cycle entry with cell growth

    Robert A Sommer et al.
    A G1 cyclin shows key properties expected of a protein that could link cell cycle progression to cell growth.
    1. Neuroscience

    The decoy SNARE Tomosyn sets tonic versus phasic release properties and is required for homeostatic synaptic plasticity

    Chad W Sauvola et al.
    Loss of the decoy SNARE Tomosyn enhances synaptic vesicle docking and neurotransmitter release and regulates release and plasticity differences between tonic and phasic motoneurons in Drosophila.
    1. Neuroscience

    Causal roles of prefrontal cortex during spontaneous perceptual switching are determined by brain state dynamics

    Takamitsu Watanabe
    Prefrontal causal roles in bistable perception are dynamically changing and determined by the brain state to which the whole-brain activity pattern belongs.
    1. Cell Biology

    Genetically engineered mice for combinatorial cardiovascular optobiology

    Frank K Lee et al.
    A unique toolbox of novel mouse lines expressing optical effectors and sensors in cardiovascular, smooth muscle, and additional lineages allows extensive in vivo and ex vivo analysis of complex biological systems.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Piezo1 ion channels inherently function as independent mechanotransducers

    Amanda H Lewis, Jörg Grandl
    Mechanically activated Piezo1 ion channels, at physiologically relevant densities, behave as independent mechanotransducers, which we propose is essential for homogenous transduction of forces across the entire cell membrane.
    1. Neuroscience

    Humans use forward thinking to exploit social controllability

    Soojung Na et al.
    People use vmPFC-dependent forward thinking to guide social choices and exploit the controllability of social environments, expanding the role of this neurocomputational mechanism beyond spatial and cognitive mapping.
    1. Cell Biology

    Genetic, cellular, and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore

    Evgeniya Trofimenko et al.
    Cationic cell-penetrating peptides (CPPs) enter cells through ~2 (–5)-nm-wide water pores induced by the strong negative plasma membrane potential that CPPs and the activity of potassium channels generate.
    1. Computational and Systems Biology
    2. Neuroscience

    Evolving interpretable plasticity for spiking networks

    Jakob Jordan et al.
    Artificial evolution discovers biophysically plausible plasticity rules for spiking networks that perform competitively with and even outperform labor-intensive human-designed models in various learning scenarios, while providing new views on experimental data.
    1. Cell Biology
    2. Physics of Living Systems

    Phagocytic ‘teeth’ and myosin-II ‘jaw’ power target constriction during phagocytosis

    Daan Vorselen et al.
    During ingestion of antibody-coated targets, phagocytes probe and deform the target via Arp2/3-dependent protrusions and myosin-dependent constriction during cup closure.
    1. Chromosomes and Gene Expression
    2. Medicine

    Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia

    Tamara Garrido-Gomez et al.
    The in vivo transcriptomic fingerprint encoding defective decidualization comprises 120 genes associated with an imbalance hormonal signaling in the decidual endometria of women who developed severe preeclampsia.
    1. Cell Biology

    6-Phosphogluconate dehydrogenase (6PGD), a key checkpoint in reprogramming of regulatory T cells metabolism and function

    Saeed Daneshmandi et al.
    6-Phosphogluconate dehydrogenase controls regulatory T cells metabolism with shifts to Th1, Th2, and Th17 phenotypes.
    1. Cancer Biology
    2. Cell Biology

    RNF43 inhibits WNT5A-driven signaling and suppresses melanoma invasion and resistance to the targeted therapy

    Tomasz Radaszkiewicz et al.
    RNF43 interacts with receptor complexes of the Wnt/PCP signaling and its enzymatic activity results in the reduced cells sensitivity to WNT5A what translates in melanoma into decreased invasive properties and increased response to targeted therapies of this skin cancer.
    1. Neuroscience

    Evidence for a deep, distributed and dynamic code for animacy in human ventral anterior temporal cortex

    Timothy T Rogers et al.
    Signals recorded directly from human anterior temporal cortex reveal that the brain represents animacy information using a distributed code that changes radically as a stimulus is processed, as predicted by an artificial neural network model.
    1. Cell Biology

    Surface-associated antigen induces permeabilization of primary mouse B-cells and lysosome exocytosis facilitating antigen uptake and presentation to T-cells

    Fernando Y Maeda et al.
    The strength by which mouse B-cells bind surface-associated antigen determines how much their plasma membrane is permeabilized and also the extent of a resealing response involving lysosomal exocytosis, which promotes antigen extraction for intracellular processing and T-cell presentation.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD

    Ginto George et al.
    Biochemical analysis reveals the entire route of oligosaccharide processing from M9 to M8B and then to oligosaccharides exposing the α1,6-linked mannosyl residue (M7A, M6, and M5), and the enzymes (EDEM2 and EDEM3/1) responsible for endoplasmic reticulum-associated degradation of misfolded glycoproteins.
    1. Biochemistry and Chemical Biology

    Fusion of tethered membranes can be driven by Sec18/NSF and Sec17/αSNAP without HOPS

    Hongki Song, William T Wickner
    The coordinate activity of Sec17/SNAP and Sec18/NSF for membrane fusion is not limited to systems with homotypic fusion and vacuole protein sorting (HOPS), the lysosomal/vacuolar tethering, and SNARE assembly complex.
    1. Neuroscience

    Plasticity of olfactory bulb inputs mediated by dendritic NMDA-spikes in rodent piriform cortex

    Amit Kumar et al.
    NMDA-spikes mediate plasticity of lateral olfactory tract inputs carrying direct odor information to the piriform cortex.
    1. Cell Biology
    2. Immunology and Inflammation

    Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures

    Shannon Rausser et al.
    A high-throughput mitochondrial phenotyping approach quantifies mitochondrial features among purified human immune cell subtypes and provides foundational knowledge to map inter- and intra-individual variation in mitochondrial energetics with high biological specificity.
    1. Ecology

    Echolocating toothed whales use ultra-fast echo-kinetic responses to track evasive prey

    Heather Vance et al.
    Echolocating toothed whales can detect and react to sudden prey movements during close approaches with speeds similar to ultra-fast tracking responses in human vision.
    1. Medicine

    Infrared molecular fingerprinting of blood-based liquid biopsies for the detection of cancer

    Marinus Huber et al.
    The combination of molecular infrared fingerprinting and machine learning enables the detection of breast, bladder, prostate, and lung cancer based on liquid blood serum and plasma, providing a general framework for the minimally invasive investigation of oncological conditions.
    1. Neuroscience

    Auditory sensory deprivation induced by noise exposure exacerbates cognitive decline in a mouse model of Alzheimer’s disease

    Fabiola Paciello et al.
    Central damage and sensory deprivation caused by noise-induced hearing loss in the pre-symptomatic Alzheimer's disease (AD) phase can compromise auditory cortex-hippocampal circuitry, targeting common pathogenetic pathways, thereby accelerating onset and progression of AD phenotype.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate

    Thomas Hackl et al.
    Mutualistic viruses called virophages are common genome inhabitants of a marine protist, where they may protect host populations from giant viruses.
    1. Neuroscience

    Septal cholinergic input to CA2 hippocampal region controls social novelty discrimination via nicotinic receptor-mediated disinhibition

    Domenico Pimpinella et al.
    Acetylcholine, released from cholinergic fibers originating from the medial septum, shapes social memory, and controls the CA2 hippocampal circuit via nicotinic receptors localized on GABAergic interneurons.
    1. Structural Biology and Molecular Biophysics

    Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8

    Lukas M Langer et al.
    Structures of human SMG1-9 and SMG1-8-9 reveal how the SMG1 kinase active site is targeted by a specific inhibitor and provide insights into the regulation of the SMG1-8-9 kinase complex in nonsense-mediated mRNA decay.
    1. Developmental Biology

    The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling

    Yanyan Ding et al.
    A new zebrafish RBC aggregation model is developed to explore the dynamic process and the underlying regulatory mechanisms in blood clot formation.
    1. Cell Biology

    Electron cryo-tomography reveals the subcellular architecture of growing axons in human brain organoids

    Patrick C Hoffmann et al.
    Combining cerebral organoid technology with cryo-correlative microscopy reveals the organization of cytoskeleton, membrane compartments, and protein synthesis machinery contributing to the rapid expansion of developing human axons.
    1. Neuroscience

    Visual pursuit behavior in mice maintains the pursued prey on the retinal region with least optic flow

    Carl D Holmgren et al.
    Digital reconstruction of environment combined with eye and head-tracking enabled the process of prey-detection and capture to be seen from the freely moving mouse’s point-of-view and shows the exact visual-field and retinal location mice use when chasing prey and the advantage.
    1. Cell Biology
    2. Developmental Biology

    Fascin limits Myosin activity within Drosophila border cells to control substrate stiffness and promote migration

    Maureen C Lamb et al.
    Collectively migrating cells control their stiffness by Fascin-dependent control of Myosin activity, and this migratory cell stiffness regulates Myosin activity and stiffness within the cellular substrate to ultimately promote migration.
    1. Cell Biology
    2. Developmental Biology

    Patched 1 reduces the accessibility of cholesterol in the outer leaflet of membranes

    Maia Kinnebrew et al.
    Cholesterol accessibility in the plasma membrane can be controlled by proteins and function as a signaling messenger in cell-cell communication pathways.
    1. Cell Biology
    2. Microbiology and Infectious Disease

    The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle

    Deike J Omnus et al.
    A proteomics-based approach identifies novel substrate proteins of the Lon protease in Caulobacter crescentus and reveals a critical role of Lon in regulating flagella assembly and stalk biogenesis during the cell cycle.
    1. Neuroscience

    Astrocyte GluN2C NMDA receptors control basal synaptic strengths of hippocampal CA1 pyramidal neurons in the stratum radiatum

    Peter H Chipman et al.
    Electrophysiology experiments with genetic and pharmacological manipulations identify a role for astrocyte GluN2C NMDA receptors in maintaining the broad range of presynaptic strengths, which is suggested by numerical simulations to enhance the expression of synaptic plasticity.
    1. Microbiology and Infectious Disease

    Effect of SARS-CoV-2 proteins on vascular permeability

    Rossana Rauti et al.
    A specific SARS-CoV-2 proteins that affect the vascular permeability and impairs the functionality of other significant organs has been identified.
    1. Immunology and Inflammation

    Protein kinase Cδ is essential for the IgG response against T-cell-independent type 2 antigens and commensal bacteria

    Saori Fukao et al.
    Protein kinase Cδ, a kinase downstream of B-cell antigen receptor, is found to be essential for class switching to and production of IgG in the T-cell-independent type 2 immune response and for regulation of gut-residing bacteria.
    1. Neuroscience

    Subpopulations of neurons in lOFC encode previous and current rewards at time of choice

    David L Hocker et al.
    A distinct subpopulation of neurons in the rat orbitofrontal cortex encodes reward history at the time of choice, providing a potential neural substrate by which reward history may influence decisions.
    1. Evolutionary Biology
    2. Neuroscience

    Molecular reconstruction of recurrent evolutionary switching in olfactory receptor specificity

    Lucia L Prieto-Godino et al.
    A 'hotspot' position in an olfactory receptor protein family underlies changes in odor tuning in different receptors at different times during evolution.
    1. Physics of Living Systems

    Physical observables to determine the nature of membrane-less cellular sub-compartments

    Mathias L Heltberg et al.
    Two competing descriptions of membrane-less sub-compartments, liquid droplets and polymer binding aggregates, can be cast into a common theoretical framework and tested through single-particle tracking experiments.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Short-chain fatty acids activate acetyltransferase p300

    Sydney P Thomas, John M Denu
    At most physiological concentrations, the short-chain fatty acids propionate and butyrate affect histone acetylation by modifying and activating the acetyltransferase p300/CBP, rather than by inhibiting histone deacetylases.
    1. Cell Biology
    2. Immunology and Inflammation

    Intestinal goblet cells sample and deliver lumenal antigens by regulated endocytic uptake and transcytosis

    Jenny K Gustafsson et al.
    Goblet cells use distinct receptors and signaling pathways to independently perform mucus secretion and endocytosis of fluid-phase cargo with atypical trafficking to deliver lumenal substances to the immune system.
    1. Developmental Biology

    mTORC1-induced retinal progenitor cell overproliferation leads to accelerated mitotic aging and degeneration of descendent Müller glia

    Soyeon Lim et al.
    Comprehensive mouse genetic analyses show, by having mTORC1 constitutively active, a RPC divides and exhausts mitotic capacity faster than neighboring RPCs, and thus produces retinal cells that degenerate with aging-related changes in the mature mouse retina.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk

    Jessamyn I Perlmutter et al.
    An endosymbiont transgene in Drosophila melanogaster exhibits remarkable phenotypic sensitivity, including to synonymous codon changes.
    1. Cell Biology
    2. Developmental Biology

    Ciliary Hedgehog signaling regulates cell survival to build the facial midline

    Shaun R Abrams, Jeremy F Reiter
    Genetic analysis identifies the origins of midface defects in mouse models of ciliopathies, revealing a role for ciliary Hedgehog signaling in cell survival.
    1. Epidemiology and Global Health

    Identifying Plasmodium falciparum transmission patterns through parasite prevalence and entomological inoculation rate

    Benjamin Amoah et al.
    Estimating fine-scale spatiotemporal patterns of Plasmodium falciparum transmission showed an association between entomological inoculation rate and parasite prevalence that emphasizes the value of both measures in malaria surveillance.
    1. Neuroscience

    Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent

    Leonhard Waschke et al.
    Waschke and colleagues demonstrate that aperiodic EEG activity not only captures subtle attention-related changes in brain signals but also tracks 1/f-like sensory input.
    1. Cell Biology
    2. Developmental Biology

    Sex determination gene transformer regulates the male-female difference in Drosophila fat storage via the adipokinetic hormone pathway

    Lianna W Wat et al.
    Drosophila females store more fat than males because the presence of a functional Transformer protein in females limits adipokinetic hormone production and pathway activity.
    1. Neuroscience

    Disturbed retinoid metabolism upon loss of rlbp1a impairs cone function and leads to subretinal lipid deposits and photoreceptor degeneration in the zebrafish retina

    Domino K Schlegel et al.
    The retinoid-binding protein RLBP1 in the retinal pigment epithelium is crucially involved in cone photoreceptor visual pigment recycling and mimics the human eye disease with retinal lipid deposits when mutated.
    1. Genetics and Genomics

    Sequence features of retrotransposons allow for epigenetic variability

    Kevin R Costello et al.
    Variably methylated retrotransposons have an underlying sequence that allows them to escape KAP1-mediated silencing and recruit ZF-CxxC proteins.
    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics

    5′-Modifications improve potency and efficacy of DNA donors for precision genome editing

    Krishna S Ghanta et al.
    Chemically modifying the 5´ends of donor DNA improves the efficiency of homology-directed repair and suppresses end-joining reactions, which will facilitate precise gene editing.
    1. Neuroscience

    Finger somatotopy is preserved after tetraplegia but deteriorates over time

    Sanne Kikkert et al.
    Hand somatotopy can be preserved in the primary somatosensory cortex of tetraplegic patients, despite the absence of sensorimotor function and periphery-brain communication, but deteriorates over years after injury.
    1. Cell Biology
    2. Medicine

    An experimental test of the effects of redacting grant applicant identifiers on peer review outcomes

    Richard K Nakamura et al.
    Redaction, intended to obscure personal and institutional identity, reduced the gap between Black vs. White applicants in simulated review of real NIH scientific grant applications, thus providing qualified support for double-blinded models of peer review.
    1. Medicine
    2. Neuroscience

    scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution

    Bilge E Öztürk et al.
    A transcriptome-based pipeline (scAAVengr) quantifies and ranks competing adeno-associated viral vectors in primate retina, and mouse brain, heart, and liver, simultaneously and across all cell types, in the same animal, with single-cell resolution.
    1. Neuroscience

    Mechanical overstimulation causes acute injury and synapse loss followed by fast recovery in lateral-line neuromasts of larval zebrafish

    Melanie Holmgren et al.
    Mechanically induced injury of zebrafish lateral-line organs shares key features of damage observed in noise-exposed mammalian ears, such as inflammation and synapse loss, yet, unlike mammals, rapidly repairs following damage.
    1. Cell Biology
    2. Stem Cells and Regenerative Medicine

    Human Erbb2-induced Erk activity robustly stimulates cycling and functional remodeling of rat and human cardiomyocytes

    Nicholas Strash et al.
    Comparative analysis of cardiac mitogenic pathways identified a potent human gene that is effective at driving in vitro cell cycle activation across species and cell culture systems.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy

    Paul Fischer et al.
    UV-Vis- and IR-spectroscopy provides insights into the light-induced enzyme activity of a rhodopsin guanylyl cyclase by tracking the substrate turnover with atomic resolution in real-time and correlating it with the structural changes of the protein.
    1. Microbiology and Infectious Disease

    Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius

    Alan M O'Neill et al.
    The discovery and development of a feline skin commensal bacterium for bacteriotherapy against skin disease, that could benefit patients due to established low cytotoxicity, broad-spectrum antimicrobial activity and anti-inflammatory activity.
    1. Neuroscience

    Learning differentially shapes prefrontal and hippocampal activity during classical conditioning

    Jan L Klee et al.
    CA1 and PFC bridge the temporal gap between cue and reward delivery during trace conditioning according to different underlying coding principles and task-related activity is reactivated during awake Sharp-Wave Ripples.
    1. Genetics and Genomics
    2. Neuroscience

    The structure of behavioral variation within a genotype

    Zachary Werkhoven et al.
    Multidimensional analysis of data from high-throughput behavioral assays reveals many independent axes of behavioral variation among inbred animals reared in the same environment.
    1. Cell Biology
    2. Neuroscience

    Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain

    Shahzad S Khan et al.
    Striatal cholinergic interneurons and astrocytes lose cilia and show dysregulation of Hedgehog signaling in mice with a Parkinson's disease-associated, G2019S LRRK2 mutation or upon loss of PPM1H phosphatase specific for LRRK2-phosphorylated Rab GTPases.
    1. Cell Biology

    Collagen polarization promotes epithelial elongation by stimulating locoregional cell proliferation

    Hiroko Katsuno-Kambe et al.
    Integrin- and ERK signaling stimulates mammary epithelial cell proliferation when extracellular collagen condenses, causing asymmetric growth of multicellular aggregates that is necessary for elongation during branching morphogenesis.
    1. Biochemistry and Chemical Biology
    2. Medicine

    Early prediction of in-hospital death of COVID-19 patients: a machine-learning model based on age, blood analyses, and chest x-ray score

    Emirena Garrafa et al.
    An early-warning model able to predict in-hospital mortality in patients affected by COVID-19 was developed and validated using common and economic tools.
    1. Ecology
    2. Microbiology and Infectious Disease

    Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms

    Matt Lloyd Jones et al.
    Resident members of natural bacterial communities limit the growth of non-resident bacteria primarily by increasing overall community growth.
    1. Immunology and Inflammation

    Different B cell subpopulations show distinct patterns in their IgH repertoire metrics

    Marie Ghraichy et al.
    IgH repertoires of physically sorted and bioinformatically selected B cell subpopulations overlap and are characterised by distinct repertoire characteristics, while certain repertoire features correlate with the position of the constant region on the IgH locus.
    1. Immunology and Inflammation

    Susceptibility rhythm to bacterial endotoxin in myeloid clock-knockout mice

    Veronika Lang et al.
    Circadian clocks in murine myeloid cells are dispensable for circadian cytokine function, trafficking and endotoxic shock in response to LPS in vivo.
    1. Neuroscience

    Cell and circuit origins of fast network oscillations in the mammalian main olfactory bulb

    Shawn D Burton, Nathaniel N Urban
    Fast network oscillations in the mammalian main olfactory bulb emerge from the dense synchronization of gamma-frequency firing among resonant tufted cells.
    1. Neuroscience

    Neuronal sequences during theta rely on behavior-dependent spatial maps

    Eloy Parra-Barrero et al.
    A computational framework and analysis of rodent CA1 data reveals that theta oscillations sequentially sweep through the past, present, and future at a spatial scale that varies with the characteristic speed of the animal.
    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107

    Holly Fowle et al.
    Molecular, cellular, and computational analyses reveal key insights into PP2A/B55α's mechanisms of substrate recruitment and active site engagement, and facilitate identification/validation of new substrates, a step towards understanding PP2A/B55α's role in multiple cellular processes.
    1. Neuroscience

    The OpenNeuro resource for sharing of neuroscience data

    Christopher J Markiewicz et al.
    OpenNeuro is a data sharing archive that provides a platform for the free and open sharing of a broad range of neuroscience data types.
    1. Neuroscience

    Excitatory and inhibitory receptors utilize distinct post- and trans-synaptic mechanisms in vivo

    Taisuke Miyazaki et al.
    Excitatory and inhibitory postsynaptic receptors are maintained at corresponded postsynaptic sites with the different dependency of presynaptic neurons in the mature mammalian brain.
    1. Neuroscience

    Visualizing synaptic plasticity in vivo by large-scale imaging of endogenous AMPA receptors

    Austin R Graves et al.
    A knockin mouse line was made to label endogenous AMPA receptors, enabling direct observation of synaptic plasticity in behaving animals with single-synapse resolution across the entire brain.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel

    Cathrine Bergh et al.
    Computational models of gating processes in an ion channel show how stability shifts upon ligand-binding and mutations are reproduced, which highlights mechanistic details and proposes a new role for symmetry in gating.
    1. Neuroscience

    Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice

    Julia A Kuhn et al.
    Intrathecal injection of CSF1 induces greater upregulation of spinal microglial genes in male versus female mice, however, Treg depletion enhances microglial activation and restores pain hypersensitivity in the female mice.
    1. Genetics and Genomics

    Ssl2/TFIIH function in transcription start site scanning by RNA polymerase II in Saccharomyces cerevisiae

    Tingting Zhao et al.
    Ssl2 processivity determines the window for transcription start site selection during promoter scanning by RNA polymerase II in Saccharomyces cerevisiae.
    1. Immunology and Inflammation

    Sepsis leads to lasting changes in phenotype and function of memory CD8 T cells

    Isaac J Jensen et al.
    Sepsis leads to lasting changes in the composition of the pre-existing memory CD8 T cell compartment leading to altered localization, changes in their transcriptional landscape and chromatin accessibility, differential function, and reduced capacity to control infection.
    1. Computational and Systems Biology
    2. Epidemiology and Global Health

    Emerging dynamics from high-resolution spatial numerical epidemics

    Olivier Thomine et al.
    Countrywide agent-based simulations with building-level resolution reveal the importance of demographic repartition and population density on epidemic dynamics of respiratory infections.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

    Zelin Liu et al.
    Accurate identification and quantification of various circRNA isoforms.
    1. Neuroscience

    An open-source, high-performance tool for automated sleep staging

    Raphael Vallat, Matthew P Walker
    A robust automatic sleep-staging algorithm offers a high level of accuracy matching that of typical human interscorer agreement.
    1. Neuroscience

    Skipping ahead: A circuit for representing the past, present, and future

    Jennifer C Robinson, Mark P Brandon
    A circuit between the hippocampus, nucleus reunions, and prefrontal cortex organizes information about the past, present, and future into alternating theta sequences.
    1. Neuroscience

    The generation of cortical novelty responses through inhibitory plasticity

    Auguste Schulz et al.
    Inhibitory synaptic plasticity provides a flexible and biologically plausible circuit mechanism to detect the novelty of bottom-up stimuli and to generate stimulus-specific adaptation.
    1. Cell Biology
    2. Developmental Biology

    SLC1A5 provides glutamine and asparagine necessary for bone development in mice

    Deepika Sharma et al.
    Osteoblasts utilize an elegant mechanism by which they obtain and subsequently synthesize the requisite amino acids to support osteoblast differentiation and bone formation.
    1. Computational and Systems Biology

    Simplifying the development of portable, scalable, and reproducible workflows

    Stephen R Piccolo et al.
    Descriptions, examples, and tools to enable biologists to use the Common Workflow Language for data processing and to facilitate computational reproducibility.
    1. Neuroscience

    Neuronal activity in dorsal anterior cingulate cortex during economic choices under variable action costs

    Xinying Cai, Camillo Padoa-Schioppa
    In economic choices under variable action costs, in contrast to the orbitofrontal cortex, dorsal anterior cingulate cortex represents not pre-decision but post-decision variables, thus might inform subsequent actions based on reward and effort associated with the choice outcomes.
    1. Developmental Biology
    2. Genetics and Genomics

    Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development

    Scott A Rankin et al.
    Epistatic analysis in Xenopus and mouse embryos reveals an evolutionarily conserved gene regulatory network downstream of the transcription factor Tbx5 and retinoic acid that coordinates cardiac and pulmonary development.
    1. Developmental Biology
    2. Plant Biology

    Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways

    Jenia Schlegel et al.
    Plant meristem size and shape is controlled by two intertwined regional feedback signals that are mediated by secreted peptides.
    1. Evolutionary Biology
    2. Physics of Living Systems

    Evolution of irreversible somatic differentiation

    Yuanxiao Gao et al.
    Irreversible differentiation into somatic cells is evolutionarily optimal if changing cell phenotype is costly, a few somatic cells already improve the organism's performance, and the organism is large enough.
    1. Genetics and Genomics

    Utility of polygenic embryo screening for disease depends on the selection strategy

    Todd Lencz et al.
    Preimplantation screening of embryos using polygenic risk scores may substantially reduce risk for a given complex disease, but this effect depends on several quantifiable factors and raises significant ethical issues.
    1. Evolutionary Biology

    Decreased recent adaptation at human mendelian disease genes as a possible consequence of interference between advantageous and deleterious variants

    Chenlu Di et al.
    Harmful genetic variants at mendelian disease genes slow down adaptation, by interfering with the spread of adaptive variants in a population.
    1. Biochemistry and Chemical Biology
    2. Ecology

    Secondary metabolites of Hülle cells mediate protection of fungal reproductive and overwintering structures against fungivorous animals

    Li Liu et al.
    Xanthones produced by the filamentous fungus Aspergillus nidulans protect its sexual structures from predation by arthropods.
    1. Cell Biology
    2. Physics of Living Systems

    Quantitative theory for the diffusive dynamics of liquid condensates

    Lars Hubatsch et al.
    Dynamical properties of liquid condensates can be quantitatively assessed by combining phase separation theory and photobleaching, which opens new avenues to understand their physicochemical properties and functioning.
    1. Immunology and Inflammation

    IRAK1-dependent Regnase-1-14-3-3 complex formation controls Regnase-1-mediated mRNA decay

    Kotaro Akaki et al.
    Regnase-1, an RNase suppressing proinflammatory mRNAs, interacts with 14-3-3, which diminishes cytokine mRNA recognition and the nuclear-cytoplasmic shuttling of Regnase-1 under inflammatory conditions.
    1. Microbiology and Infectious Disease

    Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection

    Karthik Hullahalli, Matthew K Waldor
    During Escherichia coli systemic infection, the replication of a minuscule fraction of the inoculum drives organ-specific clearance failures, systemic dissemination, and stochastic infection outcomes.
    1. Biochemistry and Chemical Biology
    2. Cancer Biology

    USP28 deletion and small-molecule inhibition destabilizes c-MYC and elicits regression of squamous cell lung carcinoma

    E Josue Ruiz et al.
    Deletion and small-molecule inhibition of ubiquitin-specific protease 28 destabilizes the oncogenes c-MYC, c-JUN, and Δp63, and elicits regression of squamous cell lung carcinoma, a major cancer type with currently limited treatment options.
    1. Neuroscience

    Switch-like and persistent memory formation in individual Drosophila larvae

    Amanda Lesar et al.
    A new computer controlled behavioral assay and integrated training chamber for individual Drosophila larvae shows that larvae learn all at once and create long-term memories that last overnight.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Linking functional and molecular mechanisms of host resilience to malaria infection

    Tsukushi Kamiya et al.
    With a data-driven mathematical modelling approach, within-host ecological information alone can provide clues on the mechanistic basis of diverse malaria infection outcomes.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status

    Jason Neidleman et al.
    COVID-19 mRNA vaccine-elicited T cells recognize variants of concern and phenotypically differ depending on number of vaccine doses and prior SARS-CoV-2 infection status.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Pathway dynamics can delineate the sources of transcriptional noise in gene expression

    Lucy Ham et al.
    There are fundamental limits to what can be learned about the origins of transcriptional noise from gene expression data alone, which can be overcome by simultaneously quantifying the abundances of linked molecular species.
    1. Cell Biology

    Protein phosphatase 1 in association with Bud14 inhibits mitotic exit in Saccharomyces cerevisiae

    Dilara Kocakaplan et al.
    PP1-Bud14 is a novel Spindle Position Checkpoint component.
    1. Immunology and Inflammation

    IFN-γ mediates Paneth cell death via suppression of mTOR

    Alessandra Araujo et al.
    A major Th1 cytokine IFN-γ mediates mitochondrial damage that leads to mTORC1 inhibition and Paneth cells death.
    1. Biochemistry and Chemical Biology

    A pre-screening strategy to assess resected tumor margins by imaging cytoplasmic viscosity and hypoxia

    Hui Huang et al.
    A fluorescence-based pre-screening strategy allows high-throughput, convenient, and fast gross assessment of resected tumor margins by imaging cytoplasmic viscosity and hypoxia.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Fibrinogen αC-subregions critically contribute blood clot fibre growth, mechanical stability, and resistance to fibrinolysis

    Helen R McPherson et al.
    Fibrinogen, a key protein involved in blood coagulation, contains a disordered and previously poorly characterised region called αC that plays a critical role in fibrin fibre growth and clot stability.
    1. Structural Biology and Molecular Biophysics

    Transcription initiation at a consensus bacterial promoter proceeds via a ‘bind-unwind-load-and-lock’ mechanism

    Abhishek Mazumder et al.
    Single-molecule fluorescence experiments reveal transcription initiation proceeds via a 'bind-unwind-load-and-lock' mechanism where promoter DNA unwinds outside the RNA polymerase (RNAP) cleft, the unwound template-DNA loads into the cleft, and RNAP 'locks' the template-DNA by closing the RNAP clamp module.
    1. Ecology

    A beta-glucosidase of an insect herbivore determines both toxicity and deterrence of a dandelion defense metabolite

    Meret Huber et al.
    An insect digestive enzyme metabolizes a plant defense compound and thereby modulates herbivore performance and host plant choice, which in turn may alter plant defense evolution in nature.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs

    Nicholas O Burton et al.
    Intergenerational adaptations to stress play a critical role in organismal responses to changing environments and are largely lost or erased after one generation.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    TAZ inhibits glucocorticoid receptor and coordinates hepatic glucose homeostasis in normal physiological states

    Simiao Xu et al.
    Hepatic TAZ coordinates the differential expression of gluconeogenic genes in the fasted and fed states by inhibiting glucocorticoid receptor.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

    William N Zagotta et al.
    Time-resolved transition metal ion fluorescence resonance energy transfer using a fluorescent, noncanonical amino acid donor and metal ion acceptor measures distances and distance distributions in proteins, allowing the equilibrium distributions among conformational states to be accurately determined.
    1. Neuroscience

    Memory recall involves a transient break in excitatory-inhibitory balance

    Renée S Koolschijn et al.
    Hippocampal activity during memory recall predicts a transient increase in the ratio between neocortical glutamate and GABA, thereby allowing otherwise dormant memories to be released.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Retinoic acid signaling is directly activated in cardiomyocytes and protects mouse hearts from apoptosis after myocardial infarction

    Fabio Da Silva et al.
    Lineage tracing and genetic experiments resolve a long-standing controversy by showing that retinoic acid signaling is active in cardiomyocytes, both during development and after myocardial infarction, and protects damaged hearts from apoptosis.
    1. Cell Biology
    2. Developmental Biology

    Duox-generated reactive oxygen species activate ATR/Chk1 to induce G2 arrest in Drosophila tracheoblasts

    Amrutha Kizhedathu et al.
    Reactive oxygen species can activate the ATR/Chk1 pathway in the absence of detectable DNA damage and without a requirement for DNA damage response proteins.
    1. Neuroscience

    Neuropsychological evidence of multi-domain network hubs in the human thalamus

    Kai Hwang et al.
    Lesions to the anterior-medio-dorsal thalamus cause widespread behavioral impairments across multiple cognitive domains, suggesting that thalamic hubs are critical for interconnecting diverse cognitive processes.
    1. Evolutionary Biology

    Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

    Katelyn Mika et al.
    Comparative studies of gene expression in the uterus during pregnancy identifies new genes important for pregnancy and associated with complications such as preterm birth.
    1. Medicine

    Modulation of fracture healing by the transient accumulation of senescent cells

    Dominik Saul et al.
    Senescent cells accumulate in the fracture callus and a reduction in the number of these cells accelerates fracture healing in mice.
    1. Neuroscience

    Experience-dependent weakening of callosal synaptic connections in the absence of postsynaptic FMRP

    Zhe Zhang et al.
    Postnatal, postsynaptic loss of FMRP specifically weakens callosal synaptic inputs onto L2/3 pyramidal neurons, in requirement ofnormal sensory experience, through downregulating AMPA receptor transmission and without affecting local synaptic inputs during cortical circuit development.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    The mammalian rod synaptic ribbon is essential for Cav channel facilitation and ultrafast synaptic vesicle fusion

    Chad Paul Grabner, Tobias Moser
    The mouse rod photoreceptor ribbon creates a large number of releasable vesicles with uniform release kinetics.
    1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    Inhibition of SARS-CoV-2 polymerase by nucleotide analogs from a single-molecule perspective

    Mona Seifert et al.
    High-throughput and ultra-stable magnetic tweezers reveal that Remdesivir induces a long-lived backtrack pause upon incorporation by the coronavirus polymerase, and SARS-CoV-2 is able to evade interferon-induced antiviral ddhCTP.
    1. Microbiology and Infectious Disease

    The East Asian gut microbiome is distinct from colocalized White subjects and connected to metabolic health

    Qi Yan Ang et al.
    The gut microbiota of East Asians is distinct, dissociated from body mass, and self-sustains compared to White subjects from the same region, and therein may underpin a key health disparity.
    1. Neuroscience

    NHE6 depletion corrects ApoE4-mediated synaptic impairments and reduces amyloid plaque load

    Theresa Pohlkamp et al.
    Genetic disruption of sodium-hydrogen exchanger 6 (NHE6) reduces amyloid plaques in humanized Alzheimer's disease mouse models and restores normal synaptic responses to neuromodulatory input in humanized ApoE4-expressing animals.
    1. Developmental Biology

    A functional genetic toolbox for human tissue-derived organoids

    Dawei Sun et al.
    To facilitate human developmental biology research, CRISPR-mediated homologous recombination, tightly inducible gene knockdowns (CRISPRi) and overexpression (CRISPRa) have been efficiently applied to human organoids.
    1. Neuroscience

    Closed-loop auditory stimulation method to modulate sleep slow waves and motor learning performance in rats

    Carlos G Moreira et al.
    Delivery of auditory triggers as unique slow waves-targeting approach yields efficient, stable, and precise modulation of slow-wave activity in rats.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Divergent acyl carrier protein decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis in malaria parasites

    Seyi Falekun et al.
    Malaria parasites have simplified and adapted their mitochondrial metabolism to lack fatty acid synthesis but retain an unusual acyl carrier protein required for stability of the core iron-sulfur cluster biogenesis complex.
    1. Biochemistry and Chemical Biology
    2. Neuroscience

    AKAP79 enables calcineurin to directly suppress protein kinase A activity

    Timothy W Church et al.
    Discovery of a non-canonical mechanism for decreasing protein kinase A activity that does not require lowering of cyclic AMP.
    1. Neuroscience

    Bayesian inference of population prevalence

    Robin AA Ince et al.
    Bayesian estimation of the proportion of the population that would show an effect in an experiment provides a broadly applicable alternative to standard null hypothesis tests on the population mean with several advantages.
    1. Neuroscience

    Calcium dependence of neurotransmitter release at a high fidelity synapse

    Abdelmoneim Eshra et al.
    The Ca2+-dependence of vesicle priming, fusion, and replenishment at cerebellar mossy fiber boutons show a prominent Ca2+-dependent priming step, a shallow non-saturating dose-response curve up to 50 µM, and little Ca2+-dependence of sustained vesicle replenishment.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Two different cell-cycle processes determine the timing of cell division in Escherichia coli

    Alexandra Colin et al.
    Chromosome replication and a different inter-division process both contribute to division control during unperturbed growth, but if division is delayed by increasing cell width the inter-division process becomes solely rate-limiting.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Visualizing formation of the active site in the mitochondrial ribosome

    Viswanathan Chandrasekaran et al.
    GTPBP7, NSUN4, and MTERF4 facilitate maturation of the peptidyl transferase center of the mitochondrial ribosome.
    1. Developmental Biology
    2. Neuroscience

    Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation

    Maria-Daniela Cirnaru et al.
    RNAseq and ATACseq are utilized to identify transcription factors participating in striatal compartmentation into striosome and matrix, and roles for Stat1, Olig2, and Foxf2 are validated in vitro and in vivo.
    1. Neuroscience

    Modelling the neural code in large populations of correlated neurons

    Sacha Sokoloski et al.
    The proposed techniques enable researchers to disentangle the statistical features of neural population responses, and rigorously quantify how these features carry information about stimuli and experimental variables.
    1. Neuroscience

    Dynamic dichotomy of accumbal population activity underlies cocaine sensitization

    Ruud van Zessen et al.
    Cocaine elicits opposing activity changes in D1R vs D2R spiny projection neurons of the nucleus accumbens with much variability, subsequent recruitment of a subset of D1R neurons drives behavioral sensitization.
    1. Immunology and Inflammation

    Microglia and CD206+ border-associated mouse macrophages maintain their embryonic origin during Alzheimer’s disease

    Xiaoting Wu et al.
    Inducible fate-mapping analysis demonstrates that neither microglia, CD11c+ activated microglia nor border-associated macrophages are replenished by bone marrow-derived cells in Alzheimer’s disease.
    1. Neuroscience

    Neural excitability and sensory input determine intensity perception with opposing directions in initial cortical responses

    Tilman Stephani et al.
    Larger evoked responses during initial cortical processing may reflect states of lower excitability.
    1. Chromosomes and Gene Expression

    DDK/Hsk1 phosphorylates and targets fission yeast histone deacetylase Hst4 for degradation to stabilize stalled DNA replication forks

    Shalini Aricthota, Devyani Haldar
    Sirtuin, Hst4 is a novel DDK kinase target, which is modified and degraded in response to replication stress, increasing H3K56 acetylation, to stabilize DNA replication forks via fork protection complex which maintains genome stability and has potential in cancer therapeutics.
    1. Developmental Biology

    Cell-to-cell heterogeneity in Sox2 and Bra expression guides progenitor motility and destiny

    Michèle Romanos et al.
    Spatial variations of transcription factor expression regulate the choice of progenitors to stay in their niche or to migrate into neural and mesodermal tissues.
    1. Cell Biology

    Protective mitochondrial fission induced by stress-responsive protein GJA1-20k

    Daisuke Shimura et al.
    Stress-induced alternative translation of an otherwise common gap junction protein generates an isoform that orchestrates protective mitochondrial fission and organ protection during anticipated ischemia.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    A sex-specific evolutionary interaction between ADCY9 and CETP

    Isabel Gamache et al.
    Genomics-based evidence support population- and sex-specific selection of an epistatic interaction between genetic variants in ADCY9 and CETP, genes of pharmacogenetic importance in cardiovascular diseases.
    1. Developmental Biology

    Visually induced changes in cytokine production in the chick choroid

    Jody A Summers, Elizabeth Martinez
    IL-6 gene and protein expression are rapidly and transiently upregulated in the choroid in response to myopic defocus, as a result of prior form deprivation or treatment with +15 D lenses in a nitric oxide-dependent manner.
    1. Cell Biology
    2. Developmental Biology

    3D cell neighbour dynamics in growing pseudostratified epithelia

    Harold Fernando Gómez et al.
    The 3D shape and dynamic organization of epithelial cells are far more complex than previously believed, but can be explained with simple physical principles based on lateral surface energy minimisation.
    1. Immunology and Inflammation

    Redefining innate natural antibodies as important contributors to anti-tumor immunity

    Kavita Rawat et al.
    Natural antibodies play a fundamental role in anti-cancer immunity.
    1. Developmental Biology
    2. Medicine

    β-Catenin-NF-κB-CFTR interactions in cholangiocytes regulate inflammation and fibrosis during ductular reaction

    Shikai Hu et al.
    Ductular reaction often observed in chronic liver pathologies such as in cystic fibrosis could be due to disruption of a novel complex of β-catenin-NF-κB and CFTR in cholangiocytes, which leads to persistent nuclear translocation of p65 and NF-κB activation.
    1. Genetics and Genomics

    The transcription factor Xrp1 is required for PERK-mediated antioxidant gene induction in Drosophila

    Brian Brown et al.
    The transcription factor Xrp1 mediates a previously unrecognized branch of stress-response signaling, specifically as a downstream effector of eIF2alpha kinases.
    1. Cell Biology
    2. Developmental Biology

    Myogenin controls via AKAP6 non-centrosomal microtubule-organizing center formation at the nuclear envelope

    Robert Becker et al.
    Myogenin promotes centrosome attenuation and establishes the nuclear envelope as the dominant microtubule organization center via the scaffold protein AKAP6, which is required for the recruitment of centrosomal proteins.
    1. Genetics and Genomics
    2. Neuroscience

    Parallel functional testing identifies enhancers active in early postnatal mouse brain

    Jason T Lambert et al.
    Methods for screening hundreds of DNA sequences for enhancer activity have been extended for use in vivo, uncovering novel enhancer elements active in the early postnatal brain.
    1. Neuroscience

    Early life experience sets hard limits on motor learning as evidenced from artificial arm use

    Roni O Maimon-Mor et al.
    Biological- or artificial-arm experience during early development has a significant effect on artificial-arm motor control in adulthood, providing evidence for limited sensorimotor plasticity beyond childhood.
    1. Developmental Biology

    Y chromosome functions in mammalian spermatogenesis

    Jeremie Subrini, James Turner
    The mammalian Y chromosome has become specialised for male fertility, but exact functions of individual Y genes remain poorly understood, a knowledge gap that new approaches can bridge.
    1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    Single-cell growth inference of Corynebacterium glutamicum reveals asymptotically linear growth

    Joris JB Messelink et al.
    A novel bacterial single-cell growth mode is identified in C. glutamicum, which sheds light on its elongation dynamics and cell size regulation.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    microRNA-mediated regulation of microRNA machinery controls cell fate decisions

    Qiuying Liu et al.
    Genetic and biochemical analyses reveal that two stem-cell-specific microRNAs control stem cell fate decisions between pluripotency and differentiation through repressing Ago2, a key component of the microRNA machinery.
    1. Evolutionary Biology

    Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

    Christopher W Bakerlee et al.
    Experimentally evolved budding yeast populations reveal the role of contingency and chance in shaping the emergence and dynamics of pleiotropic effects of adaptation.
    1. Neuroscience

    Proof of concept for multiple nerve transfers to a single target muscle

    Matthias Luft et al.
    A murine model for a novel surgical concept demonstrates potential advances of neuroprosthetic interfacing.
    1. Cell Biology
    2. Developmental Biology

    Par3 cooperates with Sanpodo for the assembly of Notch clusters following asymmetric division of Drosophila sensory organ precursor cells

    Elise Houssin et al.
    Baz/Par3 and Sanpdo are required for clustering and activation of Notch receptors to allow intra-lineage private communication following asymmetric division of Drosophila epithelial cells.
    1. Cell Biology
    2. Neuroscience

    HIF1α stabilization in hypoxia is not oxidant-initiated

    Amit Kumar et al.
    The current findings address the redox regulation of hypoxia inducible factor 1α (HIF1α) stability in hypoxia by showing that cytosolic, mitochondrial or lipid ROS are not necessary for HIF1α stabilization in hypoxia.