April 2020

Research articles

    1. Neuroscience

    Principles of operation of a cerebellar learning circuit

    David J Herzfeld et al.
    Quantitative analysis of behavior coupled with computational modeling reveal the set of circuit-level principles that underlie cerebellar-dependent motor learning in smooth pursuit eye movements of monkeys across timescales.
    1. Cell Biology
    2. Computational and Systems Biology

    DASC, a sensitive classifier for measuring discrete early stages in clathrin-mediated endocytosis

    Xinxin Wang et al.
    A new user-intervention-free classification, using single-fluorescent markers, measures conventionally unmeasureable phenotypes in early stages during clathrin-mediated endocytosis.
    1. Developmental Biology
    2. Genetics and Genomics

    Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice

    Mohamed Mahgoub et al.
    The meiotic recombination landscape in vertebrates was re-engineered via the co-evolution of a dual histone H3K4/H3K36 methylation 'writer' PRDM9 and its 'reader' ZCWPW1 that facilitates efficient double strand break repair.
    1. Developmental Biology

    Yap-lin28a axis targets let7-Wnt pathway to restore progenitors for initiating regeneration

    Zhian Ye et al.
    Atoh1+ HC precursors survive post severe injury and activate the Yap-Lin28 pathway to restore progenitor for initiating regeneration.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    An advanced cell cycle tag toolbox reveals principles underlying temporal control of structure-selective nucleases

    Julia Bittmann et al.
    The development of an advanced cell cycle tag toolbox will enable a wide variety of cell cycle studies and shows post-replicative function of nucleases resolving replication/recombination structures.
    1. Physics of Living Systems

    Polar pattern formation induced by contact following locomotion in a multicellular system

    Masayuki Hayakawa et al.
    Transient cell-cell contact of eukaryotic cells, called contact following locomotion, causes cell density segregation, and its high-density region traveled as a band within the disordered background.
    1. Neuroscience

    Effects of fluorescent glutamate indicators on neurotransmitter diffusion and uptake

    Moritz Armbruster et al.
    Fluorescent glutamate indicators distort the time course of neurotransmitter diffusion and uptake by competing with transporters, an important caveat to consider when using iGluSnFR and its analogs.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    SKAP2 is required for defense against K. pneumoniae infection and neutrophil respiratory burst

    Giang T Nguyen et al.
    SKAP2 is critical for hematopoietic cell protection against Klebsiella infection in mouse lungs, for full phosphorylation of Src Family Kinases, Syk, and Pyk2, and for Klebsiella-induced reactive oxygen species production.
    1. Cancer Biology
    2. Physics of Living Systems

    Collective forces of tumor spheroids in three-dimensional biopolymer networks

    Christoph Mark et al.
    The forces that multicellular tumor aggregates exert on their environment lead to non-linear, scale-invariant tissue deformations far away from the tumor, which can be exploited to quantify its collective contractility.
    1. Cell Biology

    Asymmetric clustering of centrosomes defines the early evolution of tetraploid cells

    Nicolaas C Baudoin et al.
    Newly formed tetraploid cells rapidly lose extra centrosomes acquired upon tetraploidization via asymmetric centrosome clustering during cell division and selective advantage of tetraploid daughter cells that inherit a single centrosome.
    1. Neuroscience

    Probabilistic, spinally-gated control of bladder pressure and autonomous micturition by Barrington’s nucleus CRH neurons

    Hiroki Ito et al.
    Ponto-spinal CRH neurons in Barrington’s nucleus are a core component of an inferential circuit that regulates autonomous micturition and generates voids when the bladder is full.
    1. Developmental Biology
    2. Genetics and Genomics

    OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification

    Miruna Georgiana Ghinia Tegla et al.
    A retinal gene regulatory network prevents the formation of alternative cell fates from non-stochastic retinal progenitor cells.
    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network

    Isabella V Soluri et al.
    Mechanisms for shaping the chromatin accessibility landscape operate during development to regulate how embryonic patterning information is interpreted at the level of gene regulatory networks.
    1. Cell Biology
    2. Developmental Biology

    Maternal spindle transfer overcomes embryo developmental arrest caused by ooplasmic defects in mice

    Nuno Costa-Borges et al.
    Maternal spindle transfer is a feasible approach to enhance embryonic developmental of compromised oocytes, which can represent a new strategy for patients with forms of infertility refractory to current treatments.
    1. Neuroscience

    Loss of Doc2b does not influence transmission at Purkinje cell to deep nuclei synapses under physiological conditions

    Mehak M Khan, Wade G Regehr
    Eliminating the calcium-binding protein Doc2b does not alter transmission at a mature synapse under physiological conditions, counter to the prevailing view of Doc2b based on cultured neurons.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Divergent Cl- and H+ pathways underlie transport coupling and gating in CLC exchangers and channels

    Lilia Leisle et al.
    Combined simulations and electrophysiological experiments show that the CLC channels and exchangers form physically distinct and evolutionarily conserved pathways through which Cl- and H+ ions move when crossing biological membranes.
    1. Neuroscience

    Drosophila Synaptotagmin 7 negatively regulates synaptic vesicle release and replenishment in a dosage-dependent manner

    Zhuo Guan et al.
    Drosophila synaptotagmin 7 functions to restrict SV availability and release, but does not act as the Ca2+ sensor mediating the asynchronous release and facilitation remaining in synaptotagmin 1 mutants.
    1. Neuroscience

    Cerebellar Purkinje cell activity modulates aggressive behavior

    Skyler L Jackman et al.
    Optogenetic control of Purkinje cells in the cerebellar vermis enables bidirectional control of aggression.
    1. Chromosomes and Gene Expression

    Enhancement of homology-directed repair with chromatin donor templates in cells

    Grisel Cruz-Becerra, James T Kadonaga
    Precise genome editing by homology-directed repair occurs more efficiently with a chromatin donor template than with a naked DNA donor template.
    1. Cell Biology
    2. Immunology and Inflammation

    Rapamycin rejuvenates oral health in aging mice

    Jonathan Y An et al.
    Short-term treatment with rapamycin reverses periodontal bone loss, attenuates inflammation, and remodels the oral microbiome toward a more youthful state.
    1. Neuroscience

    Developmental loss of MeCP2 from VIP interneurons impairs cortical function and behavior

    James M Mossner et al.
    Loss of function of the Rett syndrome gene MeCP2 in a small but powerful interneuron population, the VIP cells, causes a unique combination of impairments in neural function and behavior.
    1. Immunology and Inflammation

    A delayed fractionated dose RTS,S AS01 vaccine regimen mediates protection via improved T follicular helper and B cell responses

    Suresh Pallikkuth et al.
    Circulating T follicular helper cells appear to be a promising biomarker candidate for monitoring vaccine efficacy in malaria vaccine trials.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Disease-associated mutations in the human TRPM3 render the channel overactive via two distinct mechanisms

    Siyuan Zhao et al.
    Disease-associated mutants of the TRPM3 ion channel are overactive, and they are inhibited by the antiepileptic medication primidone, offering a potential therapeutic intervention to treat this channelopathy.
    1. Developmental Biology
    2. Genetics and Genomics

    Disparate expression specificities coded by a shared Hox-C enhancer

    Steve W Miller, James W Posakony
    Tucked within a well-known story of diverging gene function is a single enhancer encoding two inseparable specificities that regulates two adjacent genes, each with different spatiotemporal expression patterns.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

    Anneke Dixie Kakebeen et al.
    Regenerating neural progenitors of the Xenopus tropicalis tail prioritize differentiation to motor neuron types earlier than proliferation, a decision partly regulated by the transcription factors Pbx3 and Meis1.
    1. Developmental Biology
    2. Evolutionary Biology

    Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure

    Sarah Jacquelyn Smith et al.
    A new morphological structure evolved through extreme changes in cell height requires novel connections to an extracellular matrix network, which predates the origin of structure.
    1. Biochemistry and Chemical Biology

    The dynamic interplay of host and viral enzymes in type III CRISPR-mediated cyclic nucleotide signalling

    Januka S Athukoralage et al.
    The dynamic interplay between type III CRISPR enzymes governs cyclic nucleotide levels and infection outcomes in virus-host conflict.
    1. Developmental Biology
    2. Genetics and Genomics

    Nuclear receptor Ftz-f1 promotes follicle maturation and ovulation partly via bHLH/PAS transcription factor Sim

    Elizabeth M Knapp et al.
    Genetic analyses illustrate the novel requirement of Ftz-f1 and Sim in adult Drosophila ovaries for regulating follicle cell differentiation and ovulation that is likely conserved in mammals.
    1. Chromosomes and Gene Expression

    Srsf10 and the minor spliceosome control tissue-specific and dynamic SR protein expression

    Stefan Meinke et al.
    Competition between minor and major splice sites in SRSF10 controls cell type-dependent expression of all SR-proteins and reveals a global impact of the minor spliceosome on major intron splicing.
    1. Human Biology and Medicine
    2. Immunology and Inflammation

    Kallikrein-kinin blockade in patients with COVID-19 to prevent acute respiratory distress syndrome

    Frank L van de Veerdonk et al.
    The kinin-kallikrein system is a crucial target for the treatment of COVID-19.
    1. Evolutionary Biology

    Convergent evolution of small molecule pheromones in Pristionchus nematodes

    Chuanfu Dong et al.
    Unexpected structural diversity of nematode small molecules, as revealed by high-resolution phylogenetic analysis, suggests recurrent biochemical innovation, a pattern that is probably typical across animals.
    1. Developmental Biology

    The Warburg Effect and lactate signaling augment Fgf-MAPK to promote sensory-neural development in the otic vesicle

    Husniye Kantarci et al.
    Glycolysis is locally enhanced and redirected in zebrafish to generate lactate, which functions as a signaling molecule to fully activate Fgf target genes required for proper sensory and neural development.
    1. Evolutionary Biology
    2. Genetics and Genomics

    The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family

    Aisling Y Coughlan et al.
    A family of homing genetic elements that look like inteins but work differently is the progenitor of the endonuclease that enables Saccharomyces cerevisiae to change its mating type.
    1. Neuroscience

    Differentiating between integration and non-integration strategies in perceptual decision making

    Gabriel M Stine et al.
    The determination that a decision-maker integrated evidence to form perceptual decisions is shown to be much more difficult than previously appreciated.
    1. Biochemistry and Chemical Biology

    A dynamic interaction between CD19 and the tetraspanin CD81 controls B cell co-receptor trafficking

    Katherine J Susa et al.
    The tetraspanin CD81 uses its ectodomain to export CD19, and the interaction of the two proteins is dynamically regulated by B cell activation state.
    1. Structural Biology and Molecular Biophysics

    Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A

    Cristina Olivieri et al.
    A combination of NMR, fluorescence, and molecular dynamics simulations reveals the recognition mechanism for the intrinsically disordered regulator of protein kinase A, highlighting the enzyme's nuclear export process.
    1. Chromosomes and Gene Expression

    A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans

    Kevin I Manage et al.
    SIMR-1 acts downstream of the piRNA pathway to promote siRNA amplification by the Mutator complex and localizes to perinuclear foci distinct from Mutator foci, P granules and Z granules.
    1. Genetics and Genomics
    2. Immunology and Inflammation

    Aire-dependent genes undergo Clp1-mediated 3’UTR shortening associated with higher transcript stability in the thymus

    Clotilde Guyon et al.
    The Aire-dependent genes show a preference for short 3’UTR transcript isoforms resulting in the escape from the post-transcriptional repression mediated by miRNAs in medullary thymic epithelial cells.
    1. Chromosomes and Gene Expression

    Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

    Anand Ranjan et al.
    Histone variant H2A.Z is deposited near transcription start sites by the chromatin remodeler SWR1 and seems to be removed by RNA polymerase II at an early stage of transcription elongation.
    1. Microbiology and Infectious Disease

    Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite

    Stephanie G Hays, Kimberley D Seed
    Genetic and molecular analyses identify and characterize an evolutionary battle over lysis timing wherein a bacteriophage delays lysis through lysis inhibition while a defensive phage satellite accelerates lysis.
    1. Neuroscience

    The switch-like expression of heme-regulated kinase 1 mediates neuronal proteostasis following proteasome inhibition

    Beatriz Alvarez-Castelao et al.
    In neurons, inhibition of the proteasome results in feedback inhibition of protein synthesis, mediated by heme-regulated kinase 1, which is optimized to act as both a sensor and an effector.
    1. Cancer Biology
    2. Human Biology and Medicine

    Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation

    Tim DD Somerville et al.
    A major consequence of ductal-to-squamous lineage transition in pancreatic cancer cells is to augment inflammation, which may explain the exceptionally poor clinical outcomes of squamous-subtype tumors.
    1. Cell Biology

    Serotonin signaling by maternal neurons upon stress ensures progeny survival

    Srijit Das et al.
    Neuronal serotonin release tunes transcription response times of Caenorhabditis elegans germ cells to promote the survival and stress resistance of future offspring.
    1. Neuroscience

    High-fat diet enhances starvation-induced hyperactivity via sensitizing hunger-sensing neurons in Drosophila

    Rui Huang et al.
    Fruit flies fed with high-fats diets are hyper-sensitive to a hunger hormone AKH and exhibit enhanced food-seeking behavior when starved.
    1. Neuroscience

    Optogenetic control of excitatory post-synaptic differentiation through neuroligin-1 tyrosine phosphorylation

    Mathieu Letellier et al.
    Orthogonal to traditional paradigms that manipulate neuroligin expression level, optogenetic stimulation of tyrosine phosphorylation highlights a role of the intracellular domain of endogenous neuroligin-1 in excitatory synaptic differentiation and potentiation.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    R-spondin signalling is essential for the maintenance and differentiation of mouse nephron progenitors

    Valerie PI Vidal et al.
    In the developing kidney, secreted molecules of the R-spondin family control progenitor cell proliferation and nephron formation by permitting WNT/β-catenin signalling.
    1. Neuroscience

    Pre-stimulus phase and amplitude regulation of phase-locked responses are maximized in the critical state

    Arthur-Ervin Avramiea et al.
    Critical networks show maximum pre-stimulus phase and amplitude regulation of stimulus-evoked responses.
    1. Neuroscience

    Opponent regulation of action performance and timing by striatonigral and striatopallidal pathways

    Konstantin I Bakhurin et al.
    Direct and indirect pathways in the basal ganglia have opposing effects not only on action performance but also on internal timing of expected reward delivery.
    1. Developmental Biology

    Nodal and planar cell polarity signaling cooperate to regulate zebrafish convergence and extension gastrulation movements

    Margot LK Williams, Lilianna Solnica-Krezel
    Nodal signaling regulates gastrulation cell behaviors largely in parallel with planar cell polarity signaling and is sufficient for ex vivo extension of embryonic explants.
    1. Neuroscience

    Spatiotemporally precise optogenetic activation of sensory neurons in freely walking Drosophila

    Brian D DeAngelis et al.
    A simple, computationally efficient method provides spatiotemporally precise optogenetic perturbations in freely walking Drosophila, revealing the asymmetries and region-specificity of behavioral programs evoked by activating mechanosensory and chemosensory neurons.
    1. Genetics and Genomics
    2. Neuroscience

    Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation

    Callison E Alcott et al.
    Partial reduction of CFIm25 protein levels leads to misregulated alternative polyadenylation in neurons and learning deficits.
    1. Cell Biology

    ERK3/MAPK6 controls IL-8 production and chemotaxis

    Katarzyna Bogucka et al.
    Understudied atypical MAPK, ERK3 controls epithelial secretome and chemotaxis.
    1. Genetics and Genomics
    2. Neuroscience

    Sex-determining genes distinctly regulate courtship capability and target preference via sexually dimorphic neurons

    Kenichi Ishii et al.
    Sex-specific characteristics of the fruit fly courtship behavior are not specified by a single binary switch, but as a combination of traits that are modularly specified by separable genetic switches.
    1. Genetics and Genomics
    2. Neuroscience

    A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord

    Aaron M Allen et al.
    A single-cell atlas of the adult fly VNC charts the types and properties of cells for future studies of brain development and function.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    EphA7 promotes myogenic differentiation via cell-cell contact

    Laura L Arnold et al.
    The juxtacrine signaling molecule EphA7, when expressed on terminally-differentiated myocytes, non-cell-autonomously induces adjacent myoblasts to also commit to terminal differentiation leading to rapid coordinated differentiation across the entire population.
    1. Genetics and Genomics
    2. Neuroscience

    Layered roles of fruitless isoforms in specification and function of male aggression-promoting neurons in Drosophila

    Margot Wohl et al.
    Male-type aggressive and courtship behaviors of the fruit flies are differentially specified by two sex-determining genes, providing a substrate for the evolution to sculpt these two behaviors independently.
    1. Cancer Biology

    Replication Study: A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

    John Kerwin et al.
    Editors' Summary: This Replication Study has reproduced some parts of the original paper but it also contains results that are not consistent with other parts of the original paper.
    1. Cell Biology
    2. Human Biology and Medicine

    Vascular permeability in retinopathy is regulated by VEGFR2 Y949 signaling to VE-cadherin

    Ross O Smith et al.
    Pathological vessel leakage in mouse retinopathy models depends on VE-cadherin Y685 phosphorylation status, which in turn is regulated by a signaling cascade originating with VEGFR2 Y949 phosphorylation.
    1. Neuroscience

    A discrete subtype of neural progenitor crucial for cortical folding in the gyrencephalic mammalian brain

    Naoyuki Matsumoto et al.
    Sonic hedgehog signaling is crucial for the self-renewal of outer radial glial cells and gyrus formation of the cerebral cortex in gyrencephalic mammals.
    1. Evolutionary Biology

    Phenotypic plasticity as a mechanism of cave colonization and adaptation

    Helena Bilandžija et al.
    Astyanax mexicanus surface-dwelling fish exposed to complete darkness develop many traits resembling cavefish adaptations by phenotypic plasticity in a single generation.
    1. Neuroscience

    Population coupling predicts the plasticity of stimulus responses in cortical circuits

    Yann Sweeney, Claudia Clopath
    Networks simulations and in vivo imaging suggest a stable backbone of stimulus representation formed by neurons with low population coupling, alongside a flexible substrate of neurons with high population coupling.
    1. Neuroscience

    A neuropeptide regulates fighting behavior in Drosophila melanogaster

    Fengming Wu et al.
    Dsk-expressing neurons function downstream of a subset of P1 neurons to control fighting behavior.
    1. Evolutionary Biology
    2. Genetics and Genomics

    The evolutionary history and genomics of European blackcap migration

    Kira Delmore et al.
    Variation in migration can evolve rapidly and traits that comprise this behaviour may be determined by standing variation at a few regulatory regions that are not common across taxonomic groups.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A single power stroke by ATP binding drives substrate translocation in a heterodimeric ABC transporter

    Erich Stefan et al.
    Single-turnover studies reveal quantitative insights into the inner mechanics and unfold hidden facets in the conformational coupling of ATP binding, hydrolysis, and substrate translocation by ABC transporters.
    1. Neuroscience

    Slo2 potassium channel function depends on RNA editing-regulated expression of a SCYL1 protein

    Long-Gang Niu et al.
    The pseudokinase protein SCYL1 is an evolutionarily conserved enhancer of Slo2 potassium channel activity.
    1. Microbiology and Infectious Disease

    Multimeric single-domain antibody complexes protect against bunyavirus infections

    Paul J Wichgers Schreur et al.
    Llama-derived single-domain antibodies, formatted as bispecific antibodies with human Fc domains, reduce and prevent bunyavirus-induced morbidity and mortality in mice upon prophylactic and therapeutic administration.
    1. Cell Biology
    2. Physics of Living Systems

    Centering and symmetry breaking in confined contracting actomyosin networks

    Niv Ierushalmi et al.
    Novel mechanisms for cellular centering and symmetry breaking involving persistent contractile actomyosin flows and their hydrodynamic interactions with the fluid cytosol are presented and studied using a minimal, reconstituted system.
    1. Cell Biology
    2. Human Biology and Medicine

    Activated αIIbβ3 on platelets mediates flow-dependent NETosis via SLC44A2

    Adela Constantinescu-Bercu et al.
    The interaction between activated αIIbβ3 on platelets and SLC44A2 on circulating neutrophils facilitates neutrophil capture and drives flow-dependent NETosis.
    1. Immunology and Inflammation

    Landscape mapping of shared antigenic epitopes and their cognate TCRs of tumor-infiltrating T lymphocytes in melanoma

    Kenji Murata et al.
    A library of the paired peptide/HLA multimers and artificial APCs allows for construction of a large database of class I-restricted peptides and cognate tumor-reactive TCR genes at an unprecedented scale.
    1. Physics of Living Systems

    Shape selection and mis-assembly in viral capsid formation by elastic frustration

    Carlos I Mendoza, David Reguera
    Nucleation, elasticity theory, and simulations were combined to construct a general phase diagram that elucidates the conditions for successful viral assembly and the key factors to prevent it.
    1. Neuroscience

    Reconfiguration of functional brain networks and metabolic cost converge during task performance

    Andreas Hahn et al.
    Cognitive performance is supported by symbiotic metabolic and neuro-vascular responses in task-specific brain networks.
    1. Neuroscience

    Dual orexin and MCH neuron-ablated mice display severe sleep attacks and cataplexy

    Chi Jung Hung et al.
    New transgenic mice, which can be ablated both orexin neurons and MCH neurons, showed new brain state and revealed functional interaction that MCH neurons have protective role in narcolepsy symptoms.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Progenitors oppositely polarize WNT activators and inhibitors to orchestrate tissue development

    Irina Matos et al.
    Progenitors establish a single-cell length WNT morphogen gradient to transmit signals directionally and differentially to neighbors.
    1. Neuroscience

    Distinct neural contributions to metacognition for detecting, but not discriminating visual stimuli

    Matan Mazor et al.
    Combining psychophysics and functional MRI reveals a qualitative asymmetry in neural engagement when reflecting on whether a stimulus is seen (detection) compared to reflecting on what a stimulus is (discrimination).
    1. Neuroscience

    Group III metabotropic glutamate receptors gate long-term potentiation and synaptic tagging/capture in rat hippocampal area CA2

    Ananya Dasgupta et al.
    Group III metabotropic glutamate receptor inhibition facilitates synaptic plasticity in the plasticity-resistant synapses of hippocampal area CA2, a brain region critical for social memory.
    1. Structural Biology and Molecular Biophysics

    A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl/H+ transport cycle

    Tanmay S Chavan et al.
    Crystallography together with electron-resonance spectroscopy, molecular-dynamics simulations, and transport measurements reveal the molecular details of protein conformational change, and how this change contributes to function in a CLC-type chloride/proton exchanger.
    1. Neuroscience

    Behavioral evidence for memory replay of video episodes in the macaque

    Shuzhen Zuo et al.
    Macaque monkeys temporally compress past experiences and use a forward-replay mechanism during judgment of temporal-order between episodes.
    1. Chromosomes and Gene Expression

    Centromere deletion in Cryptococcus deuterogattii leads to neocentromere formation and chromosome fusions

    Klaas Schotanus, Joseph Heitman
    Centromere deletion in Cryptococcus deuterogattii results in neocentromeres, which span actively expressed genes and at elevated temperatures cen10∆ mutants are unstable leading to chromosome fusion and silencing of the neocentromere.
    1. Neuroscience

    Low-frequency neural activity reflects rule-based chunking during speech listening

    Peiqing Jin et al.
    Neuroimaging reveals that the brain response to spoken language can be better explained by rule-based models than statistical models recently developed in artificial intelligence research.
    1. Developmental Biology

    A complex regulatory landscape involved in the development of mammalian external genitals

    Ana Rita Amândio et al.
    In vertebrates, large regulatory landscapes sometimes behave as coherent regulatory units, which may explain the lack of effect sometimes observed when single enhancer sequences are deleted in isolation.
    1. Human Biology and Medicine
    2. Immunology and Inflammation

    Yolk-sac-derived macrophages progressively expand in the mouse kidney with age

    Shintaro Ide et al.
    A combination of genetic fate-mapping and parabiotic experiments reveals the chronological expansion of yolk-sac-derived renal tissue-resident macrophages with age by cellular proliferation and recruitment from circulating progenitors.
    1. Biochemistry and Chemical Biology

    Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins

    Joury S van 't Klooster et al.
    Analysis of periprotein lipids by direct extraction of membrane proteins, using styrene-maleic acid polymers.
    1. Computational and Systems Biology

    A molecular view on the escape of lipoplexed DNA from the endosome

    Bart MH Bruininks et al.
    The molecular insight in lipoplex transfection mechanisms helps in the development of efficient and affordable gene delivery systems.
    1. Structural Biology and Molecular Biophysics

    Limited dishevelled/Axin oligomerization determines efficiency of Wnt/β-catenin signal transduction

    Wei Kan et al.
    In vitro and in cellulo characterization of oligomerization by the cytoplasmic Wnt effector dishevelled and its partner Axin provide new mechanistic principles for Wnt/β-catenin signaling.
    1. Developmental Biology

    Enhancer architecture sensitizes cell specific responses to Notch gene dose via a bind and discard mechanism

    Yi Kuang et al.
    DNA binding site architecture promotes Notch transcription complex degradation to sensitize developmental processes requiring long-duration signaling.
    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Charting the native architecture of Chlamydomonas thylakoid membranes with single-molecule precision

    Wojciech Wietrzynski et al.
    In situ cryo-electron tomography resolves individual photosynthetic complexes within native thylakoid membranes, revealing how thylakoid architecture sorts proteins into discrete membrane domains.
    1. Chromosomes and Gene Expression

    Telomere dysfunction cooperates with epigenetic alterations to impair murine embryonic stem cell fate commitment

    Mélanie Criqui et al.
    Cell lineage tracing and biochemical analysis of cell fate during murine stem cell differentiation demonstrates a specific cooperativity between perturbations in histone methylation and eroded telomeres that destabilize cell differentiation.
    1. Structural Biology and Molecular Biophysics

    Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans

    Jihee Hwang et al.
    RecO efficiently displaces SSB from ssDNA without consuming ATPs using its two DNA-binding sites, even though SSB binds to ssDNA approximately 300 times more strongly than RecO does.
    1. Neuroscience

    Primate homologs of mouse cortico-striatal circuits

    Joshua Henk Balsters et al.
    Connectivity fingerprint matching bridges the gap between mouse and primate neuroanatomy, addressing crucial questions surrounding brain evolution that likely impact translation across species.
    1. Chromosomes and Gene Expression
    2. Neuroscience

    The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth

    Baisakhi Mondal et al.
    Identification of the underlying molecular gene-regulatory mechanisms by which the histone deacetylase complex MiDAC controls neurite outgrowth.
    1. Plant Biology

    The biogenesis of CLEL peptides involves several processing events in consecutive compartments of the secretory pathway

    Nils Stührwohldt et al.
    Step-wise processing of plant peptide hormone precursors by subtilisin-like proteinases in consecutive compartments of the secretory pathway is required for formation and secretion of the bioactive peptides.
    1. Cell Biology

    RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia

    Gregory G Fuller et al.
    Under hypoxic stress, when cellular demand for energy relies entirely on glycolysis, the machinery for glycolysis binds RNA and phase separates into G bodies, leading to enhanced glycolysis rates.
    1. Developmental Biology

    The metalloproteinase Papp-aa controls epithelial cell quiescence-proliferation transition

    Chengdong Liu et al.
    Zinc metalloproteinase Papp-aa-mediated Igfbp5 proteolysis functions as a [Ca2+]-regulated molecular switch linking IGF signaling to epithelial cell proliferation and bone calcification.
    1. Epidemiology and Global Health

    Determinants of MDA impact and designing MDAs towards malaria elimination

    Bo Gao et al.
    The impact of mass intervention campaigns is determined by the interaction between implementation logistics, patterns of human mobility and how transmission risk is distributed over space.
    1. Neuroscience

    Stretching the skin immediately enhances perceived stiffness and gradually enhances the predictive control of grip force

    Mor Farajian et al.
    Elucidating the contribution of augmented artificial skin-stretch stimulation to the fingertips to the immediate illusion of a higher stiffness and to an increased predictive grip force control.
    1. Cell Biology

    STK25 suppresses Hippo signaling by regulating SAV1-STRIPAK antagonism

    Sung Jun Bae et al.
    Phosphorylation-dependent regulation of SAV1-STRIPAK antagonism by STK25.
    1. Cell Biology
    2. Neuroscience

    Cortical anchoring of the microtubule cytoskeleton is essential for neuron polarity

    Liu He et al.
    UNC119 complexes the microtubule binding CRMP to the cortical Ankyrin to immobilize the microtubule cytoskeleton in Caenorhabditis elegans neurons.
    1. Cell Biology

    Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment

    Leilei Zhong et al.
    A newly identified adipose lineage cell population, MALP, regulates marrow vasculature and osteogenesis in bone.
    1. Computational and Systems Biology
    2. Neuroscience

    The natverse, a versatile toolbox for combining and analysing neuroanatomical data

    Alexander Shakeel Bates et al.
    Open source software enables neuroscientists to integrate single neuron or synaptic-resolution datasets from different imaging modalities to analyse morphology and connectivity at the scale of whole brains and connectomes.
    1. Neuroscience

    Cre-assisted fine-mapping of neural circuits using orthogonal split inteins

    Haojiang Luan et al.
    A genetic method allows neurons to be individually identified and characterized by combining information about both their developmental origins and their mature patterns of gene expression.
    1. Neuroscience

    The sifting of visual information in the superior colliculus

    Kyu Hyun Lee et al.
    The superior colliculus reveals hallmarks of sophisticated visual computation, including selectivity, invariance, and stimulus-specific habituation to behaviorally relevant stimuli.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital

    Daniel R Evans et al.
    Mobile genetic elements were identified and tracked as they exchanged between multidrug-resistant bacteria causing infections at a single hospital.
    1. Structural Biology and Molecular Biophysics

    Cryo-EM structure in situ reveals a molecular switch that safeguards virus against genome loss

    Oliver W Bayfield et al.
    Structure of the portal protein of a thermostable virus, determined in its capsid-bound state, reveals a molecular mechanism that prevents DNA slippage during genome packaging.
    1. Neuroscience

    Reinforcement biases subsequent perceptual decisions when confidence is low, a widespread behavioral phenomenon

    Armin Lak et al.
    Confidence-dependent reinforcement learning is active and produces trial-to-trial choice updating even in well-learned perceptual decisions without explicit reward biases, across species and sensory modalities.
    1. Developmental Biology

    Chloride channels regulate differentiation and barrier functions of the mammalian airway

    Mu He et al.
    The chloride channel Ano1/Tmem16a plays an essential and non-redundant role in the developing airway by inhibiting mucus cell hyperplasia and promoting proper immune function of the airway mucosal barrier.
    1. Structural Biology and Molecular Biophysics

    A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate

    Ritam Neupane et al.
    The ribosome bound structure of a new IRES reveals novel architecture features used by viruses to hijack cellular translation.
    1. Structural Biology and Molecular Biophysics

    Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family

    Stefan Brückner et al.
    Structural, biophysical and physiological analysis reveals how yeast cell surface adhesins evolved to confer self-nonself discrimination in single cells and whole populations.
    1. Cell Biology
    2. Neuroscience

    Retromer subunit, VPS29, regulates synaptic transmission and is required for endolysosomal function in the aging brain

    Hui Ye et al.
    Vps29 promotes retromer localization in the adult Drosophila brain, engaging Rab7 and TBC1D5, and its loss triggers age-dependent neuronal impairments in endolysosomal trafficking and synaptic transmission.
    1. Structural Biology and Molecular Biophysics

    Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs

    Michelle S Reid et al.
    The structure of the potassium-chloride cotransporter KCC4 provides insight into the basis of ion specificity, transport stoichiometry, and activity regulation for a broadly physiologically and clinically important transporter family.
    1. Human Biology and Medicine

    High-phytate/low-calcium diet is a risk factor for crystal nephropathies, renal phosphate wasting, and bone loss

    Ok-Hee Kim et al.
    A high-phytate-low Ca2+ diet causes crystal nephropathies, renal phosphate wasting, and bone disease in rats, whereas high Ca2+ intake ameliorates the detrimental effects of a high-phytate diet.
    1. Cancer Biology
    2. Genetics and Genomics

    Differential expression of MAGEA6 toggles autophagy to promote pancreatic cancer progression

    Yiu Huen Tsang et al.
    An unrecognized regulation on MAGEA protein stability promotes pancreatic cancer progression via manipulating autophagy and may impact the clinical utility of MAGEA-targeted immunotherapy.
    1. Ecology
    2. Neuroscience

    The social life of Norway rats (Rattus norvegicus)

    Manon K Schweinfurth
    Rats are highly social animals that show complex social skills, which has not been acknowledged enough when controlling them in the wild and conducting research in the laboratory.
    1. Biochemistry and Chemical Biology

    Cooperative enzymatic control of N-acyl amino acids by PM20D1 and FAAH

    Joon T Kim et al.
    Enzymatic division of labor is identified as an enabling biochemical strategy for regulating a family of structurally diverse bioactive lipids.
    1. Evolutionary Biology
    2. Neuroscience

    CNGA3 acts as a cold sensor in hypothalamic neurons

    Viktor V Feketa et al.
    CNGA3 is a cold-potentiated ion channel that confers cold sensitivity to mouse hypothalamic neurons, whereas CNGA3 from hibernating ground squirrels is cold-insensitive.
    1. Structural Biology and Molecular Biophysics

    Structural basis for ion selectivity in TMEM175 K+ channels

    Janine D Brunner et al.
    Structural and functional analysis of a recently discovered non-canonical potassium channel family reveals a unique selectivity filter that is exposed to permeating ions only in the conductive state.
    1. Physics of Living Systems
    2. Cell Biology

    The axonal actin-spectrin lattice acts as a tension buffering shock absorber

    Sushil Dubey et al.
    A linear array of spectrin tetramers imparts mechanical stability to axons by allowing spectrin domains to unfold reversibly when an axon is stretched, thereby acting as tension buffers.
    1. Biochemistry and Chemical Biology

    Single-molecule functional anatomy of endogenous HER2-HER3 heterodimers

    Byoungsan Choi et al.
    Single-molecule immunoprecipitation method reveals that the high catalytic rate and multi-tasking capability make a concerted contribution to the strong signaling potency of the HER2-HER3 heterodimers.
    1. Structural Biology and Molecular Biophysics

    Top-down machine learning approach for high-throughput single-molecule analysis

    David S White et al.
    A new analysis algorithm (DISC) enables accurate analysis of data from high-throughput single-molecule paradigms and reveals a non-cooperative binding mechanism of cyclic nucleotide-binding domains from HCN ion channels.
    1. Developmental Biology
    2. Plant Biology

    Direct ETTIN-auxin interaction controls chromatin states in gynoecium development

    André Kuhn et al.
    Auxin binding to the ETTIN transcription factor disrupts the interaction between ETT and a TPL/TPR co-repressor and subsequently affects chromatin dynamics to ensure proper gynoecium development.
    1. Biochemistry and Chemical Biology

    Lipid polarity gradient formed by ω-hydroxy lipids in tear film prevents dry eye disease

    Masatoshi Miyamoto et al.
    (O-Acyl)-ω-hydroxy fatty acids and their derivatives, produced by the fatty acid ω-hydroxylase Cyp4f39, form a lipid polarity gradient in the lipid layer of the tear film and prevent dry eye.
    1. Neuroscience

    Preparation for upcoming attentional states in the hippocampus and medial prefrontal cortex

    Eren Günseli, Mariam Aly
    Memory guides attention by enabling preparation for upcoming states in the hippocampus and medial prefrontal cortex.
    1. Evolutionary Biology
    2. Plant Biology

    Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)

    Tobias Züst et al.
    A gain-of-function in a new chemical defense resulted in no trade-offs and and independent evolution between novel and ancestral defenses, suggesting low redundancy among different defensive chemicals.
    1. Developmental Biology

    Conservation and divergence of related neuronal lineages in the Drosophila central brain

    Ying-Jou Lee et al.
    Comprehensive, high-resolution lineage mapping of the fly brain reveals straightforward rules that drive neuronal complexity and probable evidence of brain evolution.
    1. Neuroscience

    A muscle-epidermis-glia signaling axis sustains synaptic specificity during allometric growth in Caenorhabditis elegans

    Jiale Fan et al.
    The work uncovers a muscle-epidermis-glia signaling axis, modulated by protease mig-17 and the basement membrane, that regulates synaptic allometry during growth in Caenorhabditis elegans.
    1. Neuroscience

    Separable gain control of ongoing and evoked activity in the visual cortex by serotonergic input

    Zohre Azimi et al.
    Serotonergic input to visual cortex controls ongoing and evoked activity in a separable manner via distinct receptor pathways.
    1. Cancer Biology
    2. Genetics and Genomics

    A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes

    Mohammad KaramiNejadRanjbar et al.
    A robust library preparation and variant calling strategy (DigiPico/MutLX) eliminates false positive single nucleotide variants from picogram quantities of DNA following whole genome amplification.
    1. Developmental Biology

    Condensin I subunit Cap-G is essential for proper gene expression during the maturation of post-mitotic neurons

    Amira Hassan et al.
    The condensin I subunit Cap-G is expressed in post-mitotic neurons and its removal, especially from less mature neurons, results in gene expression changes, reduced survival and behavioural defects in Drosophila.
    1. Biochemistry and Chemical Biology
    2. Neuroscience

    Post-translational regulation of retinal IMPDH1 in vivo to adjust GTP synthesis to illumination conditions

    Anna Plana-Bonamaisó et al.
    The nucleotide sensing ability of IMPDH1 at the Bateman domain is regulated by light-dependent phosphorylation in the retina, to adjust GTP synthesis to illumination conditions.
    1. Cell Biology
    2. Immunology and Inflammation

    Endogenous itaconate is not required for particulate matter-induced NRF2 expression or inflammatory response

    Kaitlyn A Sun et al.
    Aconitate decarboxylase 1-derived itaconate reduces mitochondrial respiration via inhibition of succinate dehydrogenase but does not regulate inflammatory response or NRF2 expression in response to particulate matter.
    1. Evolutionary Biology

    Structural color in Junonia butterflies evolves by tuning scale lamina thickness

    Rachel C Thayer et al.
    Artificial selection on wing color and CRISPR/Cas9 knockout of the optix gene both alter scale lamina thickness in Junonia coenia, which shifts structural color wavelength and mimics macroevolutionary butterfly diversity.
    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9

    Joseph L Harman et al.
    In the ancestor of mammals, a multifunctional innate immune protein evolved when a mutation enhanced the protein’s pro-inflammatory activity and proteolytic regulation without disrupting the protein’s antimicrobial activity.
    1. Cell Biology

    Stress-mediated exit to quiescence restricted by increasing persistence in CDK4/6 activation

    Hee Won Yang et al.
    Application of a live-cell reporter for CDK4/6 activity reveals rapid activity changes and reversibility in the cell-cycle entry signaling program.
    1. Human Biology and Medicine

    Germline burden of rare damaging variants negatively affects human healthspan and lifespan

    Anastasia V Shindyapina et al.
    Rare highly damaging mutations that are present in most human genomes decrease lifespan and are associated with an earlier onset of chronic diseases.
    1. Evolutionary Biology

    The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts

    Patric M Vaelli et al.
    Skin-associated bacteria underlie the production of a potent defensive neurotoxin in newts, impacting host physiology, molecular evolution, and predator-prey interactions in a coevolutionary arms race.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Cell and molecular transitions during efficient dedifferentiation

    John ME Nichols et al.
    Efficient dedifferentiation is characterized by robustness to mutation, flexibility in ordering of cellular events and reversal of developmental changes along a single gene expression trajectory.
    1. Neuroscience

    Diminished responses to bodily threat and blunted interoception in suicide attempters

    Danielle C DeVille et al.
    People who have attempted suicide exhibit blunted sensory processing during breathing and pain perturbations, as well as lower heartbeat perception accuracy and reduced mid/posterior insula activity during interoceptive attention.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Zebrafish embryonic explants undergo genetically encoded self-assembly

    Alexandra Schauer et al.
    Blastoderm tissue organization and patterning in zebrafish explants is driven by a genetically encoded and controlled self-assembly mechanism, rather than a bonafide self-organization mechanism.
    1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    Chromosome organization by one-sided and two-sided loop extrusion

    Edward J Banigan et al.
    Seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization are reconciled by computationally investigating mechanisms of loop extrusion that are consistent with both.
    1. Physics of Living Systems

    Dynamics of pattern formation and emergence of swarming in Caenorhabditis elegans

    Esin Demir et al.
    Collective responses of animals are generally controlled by complex biological mechanisms and in Caenorhabditis eleganscollective dynamics are purely controlled by physical parameters such as oxygen penetration and bacterial diffusion.
    1. Biochemistry and Chemical Biology

    Nicotinamide mononucleotide adenylyltransferase uses its NAD+ substrate-binding site to chaperone phosphorylated Tau

    Xiaojuan Ma et al.
    Mechanistic insight into the chaperone-like activity of NMNAT to phosphorylated Tau reveals a connection between NAD+metabolism and Tau homeostasis.
    1. Human Biology and Medicine

    Potential harmful effects of discontinuing ACE-inhibitors and ARBs in COVID-19 patients

    Gian Paolo Rossi et al.
    Current evidence does not suggest adverse effects of ACE inhibitors or ARBs in COVID-19 patients and, to the contrary, discontinuing these drugs in these patients may potentially be harmful.
    1. Cell Biology
    2. Developmental Biology

    Super-resolution microscopy reveals coupling between mammalian centriole subdistal appendages and distal appendages

    Weng Man Chong et al.
    Super-resolved architectural framework of subdistal appendages surprisingly reveals coupling between distal appendages and subdistal appendages.
    1. Neuroscience

    KIT ligand protects against both light-induced and genetic photoreceptor degeneration

    Huirong Li et al.
    A combination of in vitro and in vivo experiments demonstrate a cell-autonomous role of the KIT ligand/KIT signaling pathway in protecting retinal photoreceptor cells from environmentally or genetically caused degeneration.
    1. Genetics and Genomics
    2. Stem Cells and Regenerative Medicine

    Cell-type diversity and regionalized gene expression in the planarian intestine

    David J Forsthoefel et al.
    Application of laser-capture microdissection to planarian intestinal tissue provides a new tool for analysis of tissue-specific gene expression in flatworms, and a new resource to advance investigations of gastrointestinal regeneration.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    Identifying the immune interactions underlying HLA class I disease associations

    Bisrat J Debebe et al.
    HLA class I-disease associations have been studied for decades; a new approach for investigating the underlying mechanism can overcome past problems with interpretation and help to understand the etiology of human diseases.
    1. Developmental Biology
    2. Neuroscience

    Intermediate progenitors support migration of neural stem cells into dentate gyrus outer neurogenic niches

    Branden R Nelson et al.
    Multiphoton live-imaging illuminates the dynamic underpinnings of how different types of progenitor cells migrate and interact to robustly build the mammalian Dentate Gyrus neural circuitry and new outer neurogenic niche.
    1. Neuroscience

    Proteome dynamics during homeostatic scaling in cultured neurons

    Aline Ricarda Dörrbaum et al.
    Dynamic SILAC labeling in combination with mass spectrometry revealed substantial regulation of protein synthesis, degradation, turnover, and abundance during homeostatic scaling in neurons.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    Deep evolutionary analysis reveals the design principles of fold A glycosyltransferases

    Rahil Taujale et al.
    Deep mining of GT-A fold sequences provides an evolutionary framework for investigating complex relationships connecting GT-A fold sequence, structure, function and regulation.
    1. Immunology and Inflammation
    2. Neuroscience

    CSF1R blockade induces macrophage ablation and results in mouse choroidal vascular atrophy and RPE disorganization

    Xiao Yang et al.
    Vascular degeneration of the choroid and RPE disorganization were associated with pharmacological macrophage ablation, indicating that insufficiency of macrophage function may be a mechanism underlying age- and AMD-associated pathology.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Delta glutamate receptor conductance drives excitation of mouse dorsal raphe neurons

    Stephanie C Gantz et al.
    In mouse brain slices, native delta glutamate receptors carry ionic current and underlie the α1-adrenergic receptor-mediated depolarization of dorsal raphe neurons that drives action potential firing in vivo.
    1. Developmental Biology
    2. Human Biology and Medicine

    Mutations associated with human neural tube defects display disrupted planar cell polarity in Drosophila

    Ashley C Humphries et al.
    Human neural tube closure defects associated mutations in planar cell polarity (PCP) genes are causative of the disease, as revealed in the intricate Drosophila PCP model.
    1. Human Biology and Medicine
    2. Stem Cells and Regenerative Medicine

    Functionally heterogeneous human satellite cells identified by single cell RNA sequencing

    Emilie Barruet et al.
    Single cell RNA sequencing leads to identification and separation of transcriptionally and functionally heterogeneous, natural human satellite cells, including a subpopulation marked by CAV1 harboring quiescence phenotypes and engraftment potential.
    1. Cell Biology

    Calcium-stimulated disassembly of focal adhesions mediated by an ORP3/IQSec1 complex

    Ryan S D'Souza et al.
    Calcium influx stimulates formation of ER/plasma membrane contacts adjacent to focal adhesions, and lipid transfer at these sites is required for adhesion disassembly during cell migration.

Magazine

    1. Neuroscience

    Imaging: The many facets of brain aging

    Lars Nyberg, Anders Wåhlin