February 2023

Cover articles

    1. Evolutionary Biology
    2. Genetics and Genomics

    Genetics and severe COVID-19

    Evelyn Jagoda, Davide Marnetto ... Terence D Capellini

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Research articles

    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Structural features stabilized by divalent cation coordination within hepatitis E virus ORF1 are critical for viral replication

    Robert LeDesma, Brigitte Heller ... Alexander Ploss
    A combined computational, genetic, and biochemical analysis of the hepatitis E virus open reading frame 1 (ORF1) protein identifies a novel domain-domain interaction that is vital for fitness and supports a proposed structural model of the ORF1 polyprotein.
    1. Microbiology and Infectious Disease

    Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions

    Ekansh Mittal, Andrew T Roth ... Jennifer A Philips
    The experimental methods that are routinely used to disperse mycobacterial aggregates markedly impact macrophage infection outcomes, which should be taken into account to appropriately interpret host-pathogen interactions studies.
    1. Genetics and Genomics

    An oligogenic architecture underlying ecological and reproductive divergence in sympatric populations

    Dušica Briševac, Carolina M Peralta, Tobias S Kaiser
    In the marine midge Clunio marinus, sympatric ecological population divergence with gene flow is based on at least four genetic loci, which partially overlap with large chromosomal inversions.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Polygenic adaptation from standing genetic variation allows rapid ecotype formation

    Nico Fuhrmann, Celine Prakash, Tobias S Kaiser
    Baltic and Arctic ecotypes of the marine midge Clunio emerged from a recent adaptive radiation, which is based on standing genetic variation at many loci involved in time-keeping and nervous system development.
    1. Ecology
    2. Computational and Systems Biology

    Competitive interactions between culturable bacteria are highly non-additive

    Amichai Baichman-Kass, Tingting Song, Jonathan Friedman
    High-throughput measurements of simplified bacterial communities find that when multiple species jointly inhibit a focal species of interest, their individual effects do not add up, but are dominated by the strongest single-species effect.
    1. Neuroscience

    Prolonged partner separation erodes nucleus accumbens transcriptional signatures of pair bonding in male prairie voles

    Julie M Sadino, Xander G Bradeen ... Zoe R Donaldson
    Pair bond induced transcriptional changes in the nucleus accumbens erode after long-term partner separation.
    1. Medicine

    Tracing the path of 37,050 studies into practice across 18 specialties of the 2.4 million published between 2011 and 2020

    Moustafa Abdalla, Salwa Abdalla, Mohamed Abdalla
    Comprehensive decade-long analysis of point-of-care resources reveals insights into how clinical research makes its way into practice across different medical specialties and through time to enable us to identify potential translational bottlenecks in the pathway from research to practice.
    1. Biochemistry and Chemical Biology
    2. Ecology

    A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

    Mingming Chen, Naoyoshi Kumakura ... Shintaro Iwasaki
    Secondary metabolites rocaglates produced by plants lead to a plant‒fungus tug-of-war, utilizing unique amino acid substitutions in eIF4A, a target of the compounds.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Chloride ions evoke taste sensations by binding to the extracellular ligand-binding domain of sweet/umami taste receptors

    Nanako Atsumi, Keiko Yasumatsu ... Atsuko Yamashita
    Sweet and umami taste receptors are capable of sensing chloride ions, a component of table salt other than the salty taste-inducing component, sodium ions, and induce preferable taste sensations such as sweet taste.
    1. Neuroscience

    Sensory input-dependent gain modulation of the optokinetic nystagmus by mid-infrared stimulation in pigeons

    Tong Xiao, Kaijie Wu ... Yan Yang
    Simultaneous stimulation and recording in awake-behaving pigeons showed that mid-infrared stimulation, as a promising neuromodulation approach, could facilitate or suppress neuronal firing activity depending on its ongoing sensory responsiveness levels, and cause reversible and gain modulation on sensorimotor behavior.
    1. Computational and Systems Biology

    ProteInfer, deep neural networks for protein functional inference

    Theo Sanderson, Maxwell L Bileschi ... Lucy J Colwell
    A machine learning model predicts the properties of proteins from their amino acid sequences and can run in a user's web browser.
    1. Genetics and Genomics
    2. Physics of Living Systems

    Coarsening dynamics can explain meiotic crossover patterning in both the presence and absence of the synaptonemal complex

    John A Fozard, Chris Morgan, Martin Howard
    Mathematical modelling, together with super-resolution imaging in Arabidopsis, demonstrates that a recently proposed coarsening model for meiotic crossover interference can explain the dynamic patterning of crossovers in many contexts, including in zyp1 and pch2 chromosome structure mutants.
    1. Neuroscience

    THINGS-data, a multimodal collection of large-scale datasets for investigating object representations in human brain and behavior

    Martin N Hebart, Oliver Contier ... Chris I Baker
    THINGS-data reflects three large-scale neuroimaging and behavioral datasets of object processing in humans, comprising densely sampled functional MRI and magnetoencephalographic recordings, as well as 4.70 million similarity judgments in response to thousands of photographic images for up to 1854 objects.
    1. Microbiology and Infectious Disease

    Intravital imaging-based genetic screen reveals the transcriptional network governing Candida albicans filamentation during mammalian infection

    Rohan S Wakade, Laura C Ristow ... Damian J Krysan
    An intravital screen identifies the transcription factors that govern gene expression of the human fungal pathogen Candida albicans during filamentation in a mammalian host.
    1. Cell Biology

    Bacillus thuringiensis toxins divert progenitor cells toward enteroendocrine fate by decreasing cell adhesion with intestinal stem cells in Drosophila

    Rouba Jneid, Rihab Loudhaief ... Armel Gallet
    Bacillus thuringiensis crystalline toxins used as microbial pesticides disrupt the homeostasis of intestinal cells of the non-target Drosophila melanogaster.
    1. Neuroscience

    MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function

    Sameer S Bajikar, Ashley G Anderson ... Huda Y Zoghbi
    Integrated analysis of transcriptional profiles from mice carrying distinct Mecp2 mutant alleles revealed that MeCP2 regulates Gdf11 expression in the brain, and that Gdf11 is a dosage-sensitive gene whose levels impact neuronal function and animal behavior.
    1. Cell Biology

    Specific targeting of inflammatory osteoclastogenesis by the probiotic yeast S. boulardii CNCM I-745 reduces bone loss in osteoporosis

    Maria-Bernadette Madel, Julia Halper ... Claudine Blin-Wakkach
    Transcriptomic comparison of inflammatory and steady-state osteoclasts reveals differences in their ability to sense their environment, which makes it possible to selectively inhibit inflammatory osteoclastogenesis and reduce bone loss in osteoporosis.
    1. Cell Biology
    2. Microbiology and Infectious Disease

    Myosin II regulatory light chain phosphorylation and formin availability modulate cytokinesis upon changes in carbohydrate metabolism

    Francisco Prieto-Ruiz, Elisa Gómez-Gil ... José Cansado
    A highly sophisticated and adaptive interplay between modulation of myosin II function by light chain phosphorylation and environmentally controlled formin availability, is critical for a successful cytokinesis during respiratory carbohydrate metabolism in the fission yeast Schizosaccharomyces pombe.
    1. Neuroscience

    BDNF/TrkB signaling endosomes in axons coordinate CREB/mTOR activation and protein synthesis in the cell body to induce dendritic growth in cortical neurons

    Guillermo Moya-Alvarado, Reynaldo Tiburcio-Felix ... Francisca C Bronfman
    BDNF axonal signaling regulates protein synthesis in neuronal cell bodies leading to dendritic arborization through dynein-dependent transport of signaling endosomes.
    1. Physics of Living Systems
    2. Structural Biology and Molecular Biophysics

    Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

    Zhuoran Zhao, Xiayu Shen ... Shozeb Haider
    Extremely significant interactions between α3-β7 and β12-α5 loops in the tetrameric L1 metallo-β-lactamase play an important role in the structural remodeling of the active site and offer insights into the potential for novel drug development by exploiting these interactions.
    1. Neuroscience

    A searchable image resource of Drosophila GAL4 driver expression patterns with single neuron resolution

    Geoffrey W Meissner, Aljoscha Nern ... FlyLight Project Team
    Single neuron images of Drosophila driver lines reveal neuron shape and are searchable, enabling comparisons to electron microscopy and prediction of intersectional neuron targeting strategies.
    1. Neuroscience

    Neural population dynamics of computing with synaptic modulations

    Kyle Aitken, Stefan Mihalas
    Synaptic modulations alone imbue networks with computational capabilities comparable to recurrent connections on several neuroscience-relevant tasks, which manifest in fundamentally different neuronal dynamics.
    1. Developmental Biology

    Generation of a transparent killifish line through multiplex CRISPR/Cas9mediated gene inactivation

    Johannes Krug, Birgit Perner ... Christoph Englert
    Using the short-lived turquoise killifish, a transparent in vivo reporter line named klara is established that will be a valuable tool to explore development, senescence, aging, and regeneration.
    1. Medicine

    Cardiac electrophysiological remodeling associated with enhanced arrhythmia susceptibility in a canine model of elite exercise

    Alexandra Polyák, Leila Topal ... András Varró
    Vigorous endurance training results in prolongation of cardiac repolarization and increased repolarization instability, mild ventricular fibrosis associated with decrease of the transient outward potassium current, and enhanced arrhythmia susceptibility in canine model.
    1. Neuroscience

    CaV1 and CaV2 calcium channels mediate the release of distinct pools of synaptic vesicles

    Brian D Mueller, Sean A Merrill ... Erik M Jorgensen
    The Caenorhabditis elegans presynapse contains two pools of synaptic vesicles at the active zone, coupled to either neuronal-type or muscle-type calcium channels, and to different docking machinery.
    1. Evolutionary Biology
    2. Structural Biology and Molecular Biophysics

    Peripheral and central employment of acid-sensing ion channels during early bilaterian evolution

    Josep Martí-Solans, Aina Børve ... Timothy Lynagh
    Expression patterns and biophysical properties of acid-sensing ion channels in numerous bilaterian animals offer insight into the deployment of ion channels by the evolving nervous system in complex animals.
    1. Neuroscience

    Enteroendocrine cell lineages that differentially control feeding and gut motility

    Marito Hayashi, Judith A Kaye ... Stephen D Liberles
    Intersectional genetic tools are used for selective control of enteroendocrine cell subtypes in vivo, revealing their differential roles in gut physiology and feeding behavior.
    1. Microbiology and Infectious Disease

    Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis

    Andrew I Wong, Tiago Beites ... Jeremy Rock
    The ubiquitous second messenger cyclic AMP, produced by Rv3645/MacE, controls long-chain fatty acid metabolism and intrinsic multidrug resistance in M. tuberculosis.
    1. Neuroscience

    The aperiodic exponent of subthalamic field potentials reflects excitation/inhibition balance in Parkinsonism

    Christoph Wiest, Flavie Torrecillos ... Huiling Tan
    The slope of the power spectrum of subthalamic local field potentials tracks pathological states in Parkinson’s disease and likely complements beta activity as a feedback marker for adaptive deep brain stimulation.
    1. Physics of Living Systems
    2. Neuroscience

    How human runners regulate footsteps on uneven terrain

    Nihav Dhawale, Madhusudhan Venkadesan
    When running on uneven terrain, humans mostly rely on the body's mechanical response for stability instead of planning their footsteps to seek out level ground.
    1. Computational and Systems Biology
    2. Medicine

    Development and evaluation of a live birth prediction model for evaluating human blastocysts from a retrospective study

    Hang Liu, Zhuoran Zhang ... Yu Sun
    The inclusion of the patient couple's clinical features along with blastocyst images increases live birth prediction accuracy.
    1. Neuroscience
    2. Developmental Biology

    Intraparietal stimulation disrupts negative distractor effects in human multi-alternative decision-making

    Carmen Kohl, Michelle XM Wong ... Bolton KH Chau
    Divisive normalisation effects on decision making caused by distractor options can be reduced by stimulating the parietal cortex using transcranial magnetic stimulation.
    1. Epidemiology and Global Health

    Direct and indirect mortality impacts of the COVID-19 pandemic in the United States, March 1, 2020 to January 1, 2022

    Wha-Eum Lee, Sang Woo Park ... Cécile Viboud
    The overall mortality consequences of the COVID-19 pandemic in the United States are predominantly attributable to the direct impact of SARS-CoV-2 infection but there are substantial indirect effects among children and young adults, and in mortality from accidents, homicides, and overdoses.
    1. Cancer Biology
    2. Immunology and Inflammation

    Proliferative exhausted CD8+ T cells exacerbate long-lasting anti-tumor effects in human papillomavirus-positive head and neck squamous cell carcinoma

    Danni Cheng, Ke Qiu ... Jianjun Ren
    Multi-omic profiling of tumor-infiltrating T cells provides new insights into the differences in the effectiveness of CDK4 inhibitor between human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma patients.
    1. Stem Cells and Regenerative Medicine

    Skeletal dysplasia-causing TRPV4 mutations suppress the hypertrophic differentiation of human iPSC-derived chondrocytes

    Amanda R Dicks, Grigory I Maksaev ... Farshid Guilak
    Chondrocytes derived from induced pluripotent stem cells with the dysplasia-causing TRPV4 mutations, V620I and T89I mutation, were resistant to BMP4-induced hypertrophy, suggesting a mechanism underlying the effects of TRPV4 dysfunction on the severity of skeletal dysplasia.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Directed differentiation of human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression

    Merrick D Pierson Smela, Christian C Kramme ... George M Church
    Making human stem cells express certain transcription factors can convert them into cells that are similar to ovarian granulosa cells, and perform several important functions of the ovary.
    1. Cell Biology

    Cryo-plasma FIB/SEM volume imaging of biological specimens

    Maud Dumoux, Thomas Glen ... Michael Grange
    Implementation and characterisation of plasma-focused ion beams for volumetric imaging of cryogenically preserved cells and tissues for ultrastructural examination in their native state.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Orai3 and Orai1 mediate CRAC channel function and metabolic reprogramming in B cells

    Scott M Emrich, Ryan E Yoast ... Mohamed Trebak
    Gene knockout in cell lines and mice reveal that store-operated calcium entry is synergistically mediated by Orai1 and Orai3 channel proteins in B cells and is important for signaling to the nucleus and metabolic activity in response to antigenic stimulation.
    1. Neuroscience

    Cerebrospinal fluid-contacting neuron tracing reveals structural and functional connectivity for locomotion in the mouse spinal cord

    Yuka Nakamura, Miyuki Kurabe ... Masaki Ueno
    Newly developed methods to genetically target cerebrospinal fluid-contacting neurons reveal unique caudorostrally extended projections and recurrent connections in the spinal motor circuitry to control locomotion in mice.
    1. Medicine

    Pharmacometrics of high-dose ivermectin in early COVID-19 from an open label, randomized, controlled adaptive platform trial (PLATCOV)

    William HK Schilling, Podjanee Jittamala ... Nicholas J White
    Pharmacometric evaluation of viral clearance rates based on frequent oropharyngeal sampling is a highly efficient and well-tolerated method of assessing and comparing SARS-CoV-2 antiviral therapeutics in vivo.
    1. Physics of Living Systems

    Nuclear export inhibition jumbles epithelial–mesenchymal states and gives rise to migratory disorder in healthy epithelia

    Carly M Krull, Haiyi Li, Amit Pathak
    Nuclear export inhibition reveals concurrent epithelial and mesenchymal phenotypes that cause mechanosensitive disorder in collectively migrating epithelia.
    1. Cancer Biology

    The role of macrophages in non-small cell lung cancer and advancements in 3D co-cultures

    Katarína Balážová, Hans Clevers, Antonella FM Dost
    As macrophages are involved in various aspects of non-small cell lung cancer development and progression it is crucial to develop appropriate 3D co-culture platforms for modeling immune cell-tumor cell interactions, leading to more efficacious macrophage-focused immunotherapies.
    1. Evolutionary Biology

    The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

    Alief Moulana, Thomas Dupic ... Michael M Desai
    The study of the interactions between 65,356 variants of the SARS-CoV-2 receptor binding domain and a panel of monoclonal antibodies shows that Omicron’s escape is driven by a small number of large effect mutations.
    1. Cell Biology

    Functional hierarchy among different Rab27 effectors involved in secretory granule exocytosis

    Kunli Zhao, Kohichi Matsunaga ... Tetsuro Izumi
    TIRF microscopy in living pancreatic beta cells lacking one or two of Rab27 effectors and the exocyst components reveals how each molecule functions in sequence or in parallel in multiple redundant paths and rate-limiting processes in granule exocytosis.
    1. Cell Biology
    2. Computational and Systems Biology

    Information transfer in mammalian glycan-based communication

    Felix F Fuchsberger, Dongyoon Kim ... Christoph Rademacher
    The information stored in glycans is interpreted and read by cell surface-exposed lectin receptors, and with information theory, the formal framework is set for how to analyze such complex single-cell data.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Structural screens identify candidate human homologs of insect chemoreceptors and cryptic Drosophila gustatory receptor-like proteins

    Richard Benton, Nathaniel J Himmel
    A new screening strategy for divergent homologs of insect odorant and gustatory receptors, based upon predicted three-dimensional structural similarity, unexpectedly identifies candidates in humans.
    1. Cancer Biology
    2. Chromosomes and Gene Expression

    eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways

    Ibrahim Ahmed, Shen-Hsi Yang ... Andrew D Sharrocks
    eRNAs detected in patient-derived transcriptomic data can delineate potential active enhancer regions in oesophageal adenocarcinoma and uncover genes associated with the cancer phenotype.
    1. Neuroscience

    Mechanisms and functions of respiration-driven gamma oscillations in the primary olfactory cortex

    Joaquin Gonzalez, Pablo Torterolo, Adriano BL Tort
    Computational analyses of in-vivo cerebral activity show that gamma oscillations in the olfactory cortex originate from local feedback inhibition following each sniff and serve to segregate competing odor representations through a winner-take-all process, providing an optimal window to decode odor.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Sweepstakes reproductive success via pervasive and recurrent selective sweeps

    Einar Árnason, Jere Koskela ... Bjarki Eldon
    Selective sweepstakes from pervasive positive selection, rather than demographic changes or random sweepstakes reproduction, is the primary determinant of reproductive skew and genetic diversity in the highly prolific Atlantic cod.
    1. Neuroscience

    Inhibition of noradrenergic signalling in rodent orbitofrontal cortex impairs the updating of goal-directed actions

    Juan Carlos Cerpa, Alessandro Piccin ... Etienne Coutureau
    Silencing noradrenergic projections from the locus coeruleus to the ventral and lateral regions of the orbitofrontal cortex prevents the updating of previously established goal-directed actions.
    1. Neuroscience
    2. Cell Biology

    Redox regulation of KV7 channels through EF3 hand of calmodulin

    Eider Nuñez, Frederick Jones ... Alvaro Villarroel
    Calmodulin mediates in the protective augmentation of KV7-currents in response to oxidative stress in a calcium-dependent manner by an unconventional signaling mechanism.
    1. Structural Biology and Molecular Biophysics
    2. Biochemistry and Chemical Biology

    A pathogenic human Orai1 mutation unmasks STIM1-independent rapid inactivation of Orai1 channels

    Priscilla S-W Yeung, Megumi Yamashita, Murali Prakriya
    A human Orai1 mutation linked to tubular myopathy activates Orai1 channels independently of STIM1 and unmasks calcium-dependent inactivation of Orai1 channels.
    1. Biochemistry and Chemical Biology
    2. Medicine

    Iron status influences mitochondrial disease progression in Complex I-deficient mice

    CJ Kelly, Reid K Couch ... Anthony S Grillo
    In vivo studies reveal that mitochondrial Complex I deficiencies induce iron misregulation and liver iron overload that may contribute to neurodegeneration in mitochondrial disease mice, and that iron restriction is effective in reducing disease progression.
    1. Cell Biology

    Synergistic stabilization of microtubules by BUB-1, HCP-1, and CLS-2 controls microtubule pausing and meiotic spindle assembly

    Nicolas Macaisne, Laura Bellutti ... Julien Dumont
    Promotion of microtubule pausing by a kinetochore module controls meiotic spindle assembly in Caenorhabditis elegans oocytes.
    1. Computational and Systems Biology

    Dynamics of co-substrate pools can constrain and regulate metabolic fluxes

    Robert West, Hadrien Delattre ... Orkun S Soyer
    Mathematical analyses explore the impact of co-substrate cycling on the dynamics of cellular metabolism, and demonstrate that these dynamics can limit cellular fluxes and that co-substrate pool dynamics can be regulated to regulate fluxes.
    1. Immunology and Inflammation

    The anti-caspase 1 inhibitor VX-765 reduces immune activation, CD4+ T cell depletion, viral load, and total HIV-1 DNA in HIV-1 infected humanized mice

    Mathieu Amand, Philipp Adams ... Carole Seguin-Devaux
    Inflamasomme inhibition prevents immune activation, HIV-1 pathogenesis and the splenic content of HIV-1 total DNA in humanized mice when administrated early after HIV-1 infection.
    1. Genetics and Genomics

    The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging

    Monica Sanchez-Contreras, Mariya T Sweetwyne ... Scott R Kennedy
    The accumulation of somatic mutations during aging is not uniform across tissue types and, in addition, shows significant variability in the source of mutation that can be modified by small molecule interventions.
    1. Neuroscience

    Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules

    Yufeng Zhou, John H Lewis, Zhe Lu
    The present fluorescence polarization microscopy method enables the determination of the spatial orientations and lifetimes of a transporter protein in individual conformational states required for understanding the complex conformational mechanism underlying its function, applicable to investigation of other membrane proteins.
    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Structure of Dunaliella photosystem II reveals conformational flexibility of stacked and unstacked supercomplexes

    Ido Caspy, Maria Fadeeva ... Nathan Nelson
    Photosystem II, the pigment-protein complex responsible for water oxidation in photosynthesis, was found to exist in two different core conformations with altered antennae connectivity.
    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology

    Coevolution-based prediction of key allosteric residues for protein function regulation

    Juan Xie, Weilin Zhang ... Luhua Lai
    Key allosteric residues are predicted based on sequence coevolution analysis, which serves as guidelines for allosteric drug design and optimization.
    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Nitrogenase resurrection and the evolution of a singular enzymatic mechanism

    Amanda K Garcia, Derek F Harris ... Betül Kaçar
    Life is constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions.
    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection

    Flora Mikaeloff, Marco Gelpi ... Ujjwal Neogi
    Multi-omics-driven patient stratification identify at-risk profile of metabolic complications in people living with HIV on suppressive therapy that need clinical attention.
    1. Neuroscience

    SUMOylation of NaV1.2 channels regulates the velocity of backpropagating action potentials in cortical pyramidal neurons

    Oron Kotler, Yana Khrapunsky ... Ilya Fleidervish
    In cortical pyramidal neurons, subtype-specific SUMOylation of Na+ channels regulates input-output relationships, synaptic boosting, and action potential propagation from the axonal trigger zone back into the dendrites.
    1. Computational and Systems Biology
    2. Developmental Biology

    MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy

    Valentyna Zinchenko, Johannes Hugger ... Anna Kreshuk
    Unsupervised machine learning on the ultrastructure and shape of cells in volume electron microscopy yields a compact representation of cellular morphology that complements genetics-based cell type characterisation.
    1. Neuroscience

    The tetraspanin TSPAN5 regulates AMPAR exocytosis by interacting with the AP4 complex

    Edoardo Moretto, Federico Miozzo ... Maria Passafaro
    In mature neurons, TSPAN5 assembles into a complex with AP4 and Stargazin to promote the exocytosis of AMPA receptors.
    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes

    Amelie A Raz, Gabriela S Vida ... Margaret T Fuller
    Single nucleus and single cell RNA-seq data uncover novel transcriptomic perspectives in Drosophila testis biology and provide access to user-friendly tools for further scientific discovery in the field.
    1. Ecology
    2. Evolutionary Biology

    Multiple preferred escape trajectories are explained by a geometric model incorporating prey’s turn and predator attack endpoint

    Yuuki Kawabata, Hideyuki Akada ... Paolo Domenici
    The mathematical model incorporating new parameters explains multimodal distributions in escape direction (i.e., multiple preferred escape trajectories), which are previously observed in various animal taxa.
    1. Developmental Biology
    2. Genetics and Genomics

    A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions

    Uri Seroussi, Andrew Lugowski ... Julie M Claycomb
    Systematically studying the expression, small RNA-binding partners, and loss-of-function phenotypes of all 19 Argonautes uncovers how small RNA regulatory pathways function and interact in Caenorhabditis elegans, a long-standing model for small RNA biology and RNAi.
    1. Stem Cells and Regenerative Medicine

    NFATc1 marks articular cartilage progenitors and negatively determines articular chondrocyte differentiation

    Fan Zhang, Yuanyuan Wang ... Xianpeng Ge
    NFATc1 is identified as a molecular marker of articular cartilage progenitor cells and a transcriptional repressor of chondrocyte differentiation, providing fundamental insights into the origin and differentiation mechanism of articular chondrocytes.
    1. Developmental Biology

    Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis

    Emma A Hall, Dhivya Kumar ... Pleasantine Mill
    Centriolar satellites facilitate efficient trafficking of proteins to and from centrioles and are required for early steps of cilia formation and timely ciliogenesis in vivo, where mice lacking satellites display perinatal lethality, hydrocephalus, oligospermia, and cerebellar hypoplasia.
    1. Neuroscience

    Circuit mechanisms underlying embryonic retinal waves

    Christiane Voufo, Andy Quaen Chen ... Alexandre Tiriac
    Calcium imaging reveals spatiotemporal properties of correlated spontaneous activity in the embryonic retina and implicates a role for electrical and chemical synapses in generating the activity.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections

    Madhura Raghavan, Katrina L Kalantar ... Joseph L DeRisi
    The dominant targets of host immune response to malaria are repeat elements, which are short stretches of amino acids repeated within Plasmodium falciparum proteins, and these are associated with short-lived and exposure-dependent antibody responses.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structural insights into actin isoforms

    Amandeep S Arora, Hsiang-Ling Huang ... Krishna Chinthalapudi
    The functional differences between actin isoforms have been explored through structural studies.
    1. Immunology and Inflammation
    2. Medicine

    Targeted multi-omic analysis of human skin tissue identifies alterations of conventional and unconventional T cells associated with burn injury

    Daniel R Labuz, Giavonni Lewis ... Daniel T Leung
    Compared to non-burn tissue, T cells in burn tissue have a pro-inflammatory rather than a homeostatic tissue-resident phenotype, and unconventional T cells in burn tissue have a higher cytotoxic capacity.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes

    Christopher H Bohrer, Daniel R Larson
    The physical distance between genes in individual cells is the major factor driving co-transcriptional bursts, showing a significant degree of correlation for distances below 400 nm.
    1. Evolutionary Biology
    2. Neuroscience

    Mice and primates use distinct strategies for visual segmentation

    Francisco J Luongo, Lu Liu ... Doris Y Tsao
    The behavioral ability of mice and treeshrews to detect visual figures is highly texture dependent, unlike that of primates including macaques and mouse lemurs, and neural responses to figures in mouse visual cortex are similarly texture dependent.
    1. Ecology
    2. Epidemiology and Global Health

    Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes

    Léa Pradier, Stéphanie Bedhomme
    Mobility across ecological contexts and continents is more important to describe the worldwide spread of bacterial resistance to aminoglycosides (a family of antibiotics), than the consumption of aminoglycosides itself.
    1. Neuroscience

    Strategically managing learning during perceptual decision making

    Javier Masís, Travis Chapman ... Andrew M Saxe
    During perceptual decision making, maximizing total reward in the long term requires trading reward in the short term for a faster improvement in perceptual representations.
    1. Genetics and Genomics

    Associations of genetic and infectious risk factors with coronary heart disease

    Flavia Hodel, Zhi Ming Xu ... Jacques Fellay
    In a prospective, population-based cohort, high polygenic risk and infection with Fusobacterium nucleatum have a small, yet independent impact on coronary heart disease risk.
    1. Neuroscience

    Representational integration and differentiation in the human hippocampus following goal-directed navigation

    Corey Fernandez, Jiefeng Jiang ... Anthony D Wagner
    Mnemonic mechanisms of differentiation and integration within the medial temporal lobe occur concurrently during the learning of local and global environmental knowledge.
    1. Plant Biology

    Arabidopsis transcriptome responses to low water potential using high throughput plate assays

    Stephen Gonzalez, Joseph Swift ... Joseph R. Ecker
    1. Stem Cells and Regenerative Medicine
    2. Cancer Biology

    Mesenchymal stem cell suppresses the efficacy of CAR-T toward killing lymphoma cells by modulating the microenvironment through stanniocalcin-1

    Rui Zhang, Qingxi Liu ... Wenjian Ma
    The stanniocalcin-1-dependent immunosuppressive roles of mesenchymal stem cell on chimeric antigen receptor modified T cell therapy.
    1. Computational and Systems Biology
    2. Neuroscience

    Optimization of energy and time predicts dynamic speeds for human walking

    Rebecca Elizabeth Carlisle, Arthur D Kuo
    Humans often walk in relatively brief bouts whose speed and duration vary dynamically and satisfy an optimal trade-off between effort and time.
    1. Neuroscience

    Single spikes drive sequential propagation and routing of activity in a cortical network

    Juan Luis Riquelme, Mike Hemberger ... Julijana Gjorgjieva
    Single-neuron spikes in a network model of the turtle cortex trigger reliable, yet flexible sequences of activity through a sparse backbone of strong synaptic connections.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Limited role of generation time changes in driving the evolution of the mutation spectrum in humans

    Ziyue Gao, Yulin Zhang ... Priya Moorjani
    A new framework for mutation spectrum analysis reveals multiple independent changes in the germline mutation patterns of human populations, which cannot be explained by shifts in average ages at reproduction.
    1. Medicine
    2. Immunology and Inflammation

    Bone marrow Adipoq-lineage progenitors are a major cellular source of M-CSF that dominates bone marrow macrophage development, osteoclastogenesis, and bone mass

    Kazuki Inoue, Yongli Qin ... Baohong Zhao
    Identification of bone marrow Adipoq-lineage progenitors as a novel and major cellular source of M-CSF in mice and humans, which controls bone marrow macrophage development, osteoclastogenesis, and bone mass in physiological and pathological conditions.
    1. Cell Biology
    2. Medicine

    Csf1 from marrow adipogenic precursors is required for osteoclast formation and hematopoiesis in bone

    Leilei Zhong, Jiawei Lu ... Ling Qin
    Bone marrow adipogenic precursors synthesize Csf1 to control bone remodeling and hematopoiesis.
    1. Developmental Biology
    2. Neuroscience

    Oligodendrocyte-lineage cell exocytosis and L-type prostaglandin D synthase promote oligodendrocyte development and myelination

    Lin Pan, Amelia Trimarco ... Ye Zhang
    Oligodendrocyte-lineage cells secrete L-type prostaglandin synthase in an autocrine loop to promote oligodendrocyte development and myelination.
    1. Neuroscience

    Multiphasic value biases in fast-paced decisions

    Elaine A Corbett, L Alexandra Martinez-Rodriguez ... Simon P Kelly
    Neurophysiological signatures of motor preparation reveal countervailing value biasing mechanisms that evolve across consecutive phases of anticipation, detection, and discrimination in sensorimotor decision making.
    1. Neuroscience

    NPAS4 in the medial prefrontal cortex mediates chronic social defeat stress-induced anhedonia-like behavior and reductions in excitatory synapses

    Brandon W Hughes, Benjamin M Siemsen ... Makoto Taniguchi
    Social defeat stress induces transcription factor Npas4 expression in the medial prefrontal cortex and its chronic stress-induced changes in excitatory synaptic transmission, reduction of dendritic spine density, and anhedonia-like behaviors.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation

    Wenfei Pan, Vladimir A Meshcheryakov ... Vivien Ya-Fan Wang
    Structural and biophysical characterization of NF-κB p52 in complex with closely related DNAs reveals the dynamic states of central base pair(s) have a strong influence on transcriptional activity of p52.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals

    Evelyn Jagoda, Davide Marnetto ... Terence D Capellini
    Key functional variants, discovered using Massively Parallel Reporter Assay (MPRA) and reporter assays in the context of SARS-CoV-2 infection, support the importance of two critical chemokine receptor genes CCR1 and CCR5 in severe Covid-19 illness.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Expansion and loss of sperm nuclear basic protein genes in Drosophila correspond with genetic conflicts between sex chromosomes

    Ching-Ho Chang, Isabel Mejia Natividad, Harmit S Malik
    Genetic conflicts between sex chromosomes during spermatogenesis may drive the rapid evolution, function, and turnover of some sperm nuclear basic proteins in Drosophila species.
    1. Cell Biology

    Nucleotide binding is the critical regulator of ABCG2 conformational transitions

    Zsuzsanna Gyöngy, Gábor Mocsár ... Katalin Goda
    The conformational switch of ABCG2 from the high substrate affinity inward-facing to a low substrate affinity outward-facing state is induced by nucleotide binding and accelerated by transported substrates.
    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics

    Activity-based CRISPR scanning uncovers allostery in DNA methylation maintenance machinery

    Kevin Chun-Ho Ngan, Samuel M Hoenig ... Brian B Liau
    Activity-based inhibitors, in conjunction with new experimental and computational tools, enable the discovery of mechanisms involved in DNMT1 autoinhibition.
    1. Computational and Systems Biology
    2. Epidemiology and Global Health

    National Institutes of Health research project grant inflation 1998 to 2021

    Michael S Lauer, Joy Wang, Deepshikha Roychowdhury
    National Institutes of Health (NIH) grants have evolved over time, with a greater proportion of funds going to solicited projects, but inflation-adjusted costs have remained relatively stable following a brief increase during the NIH-doubling (1998-2003).
    1. Neuroscience

    Neural activity tracking identity and confidence in social information

    Nadescha Trudel, Patricia L Lockwood ... Marco K Wittmann
    People's confidence in information and their neural correlates in key regions of the social brain are more stable when tracking social advice compared to non-social information.
    1. Microbiology and Infectious Disease

    Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota

    Daniel Hoces, Giorgia Greter ... Emma Slack
    Neutral tagging and detailed analysis of bacterial growth kinetics can quantify the mechanisms of colonization resistance in differently colonized animals.
    1. Ecology
    2. Evolutionary Biology

    The deep-rooted origin of disulfide-rich spider venom toxins

    Naeem Yusuf Shaikh, Kartik Sunagar
    A remarkable case of the common evolutionary origin of a prominent spider venom component.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The forgotten people: Hepatitis B virus (HBV) infection as a priority for the inclusion health agenda

    Emily Martyn, Sarah Eisen ... Philippa C Matthews
    Hepatitis B virus infection is a neglected challenge among communities who are under-served by conventional models of healthcare, requiring enhanced interventions to reduce inequity.
    1. Ecology
    2. Evolutionary Biology

    Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome

    Naïma Madi, Daisy Chen ... Nandita R Garud
    Longstanding eco-evolutionary theories are tested using shotgun metagenomic data from the human gut microbiome, showing links between community diversity and the evolutionary trajectory of a focal species within the community.
    1. Developmental Biology

    Absence of CEP78 causes photoreceptor and sperm flagella impairments in mice and a human individual

    Tianyu Zhu, Yuxin Zhang ... Chen Zhao
    Study of human, knockout mice, and in-vitro models revealed CEP78 absence is the genetical cause of cone-rod dystrophy and male infertility with multiple morphological abnormalities of sperm flagella, CEP78 interacted with IFT20 and TTC21A to modulate cilliogenesis and centriole length.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress

    Adwait A Godbole, Sneha Gopalan ... Amy K Walker
    Histone methylation patterns may differ depending on the enzymatic source of the methyl donor S-adenosylmethionine, suggesting the biological effects of low SAM may affect methylation targets in different ways, depending on the synthase producing it.
    1. Neuroscience

    Loss of aquaporin-4 results in glymphatic system dysfunction via brain-wide interstitial fluid stagnation

    Ryszard Stefan Gomolka, Lauren M Hablitz ... Yuki Mori
    Mice with aquaporin-4 channel deletion exhibit larger interstitial spaces, brain volume and water content, alongside reduced CSF space volume, which may increased resistance towards brain fluid efflux and suppress glymphatic flow.
    1. Physics of Living Systems

    Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies

    Rachel A Banks, Vahe Galstyan ... Rob Phillips
    Mesoscopic properties of motor-microtubule assemblies, such as contractile rates and length scales, can be quantitatively connected to single-motor properties of kinesin motors.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Coordinated evolution at amino acid sites of SARS-CoV-2 spike

    Alexey Dmitrievich Neverov, Gennady Fedonin ... Georgii Bazykin
    Analysis of population diversity of SARS-CoV-2 revealed positive epistasis between sites carrying mutations characterizing rapidly expanding lineages.
    1. Neuroscience

    A unified neural account of contextual and individual differences in altruism

    Jie Hu, Arkady Konovalov, Christian C Ruff
    Individual and situational differences in altruistic behavior do not reflect use of fundamentally different decision mechanisms, but instead differences in early perceptual or attentional processing of the choice-relevant information.
    1. Microbiology and Infectious Disease
    2. Immunology and Inflammation

    IL-4 and helminth infection downregulate MINCLE-dependent macrophage response to mycobacteria and Th17 adjuvanticity

    Judith Schick, Meltem Altunay ... Roland Lang
    The expression of DECTIN-2 family C-type lectin receptors on macrophages and monocytes is inhibited by the Th2 cytokine IL-4, which suggests a mechanism for inhibition of Th17 responses to MINCLE-dependent vaccination responses by underlying helminth infection.
    1. Computational and Systems Biology
    2. Epidemiology and Global Health

    CriSNPr, a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

    Asgar H Ansari, Manoj Kumar ... Debojyoti Chakraborty
    The web-server CriSNPr overcomes difficulties associated with the different CRISPR diagnostic platforms that stem from Cas-specific single guide RNA design parameters, thereby minimizing the time and effort required for individual assay design.
    1. Neuroscience

    Targeted anatomical and functional identification of antinociceptive and pronociceptive serotonergic neurons that project to the spinal dorsal horn

    Robert Philip Ganley, Marilia Magalhaes de Sousa ... Hanns Ulrich Zeilhofer
    Two populations of serotonergic neurons are present in the medial and lateral hindbrain, which are shown to project to distinct spinal cord regions and have opposing effects on nociception in mice.
    1. Developmental Biology

    miRNA-27a is essential for bone remodeling by modulating p62-mediated osteoclast signaling

    Shumin Wang, Eri O Maruyama ... Takamitsu Maruyama
    The loss of miRNA-27a stimulates osteoclast-mediated bone resorption but does not affect osteoblast-mediated bone formation, leading to the development of osteoporosis in mice.
    1. Microbiology and Infectious Disease

    Human influenza virus infection elicits distinct patterns of monocyte and dendritic cell mobilization in blood and the nasopharynx

    Sindhu Vangeti, Sara Falck-Jones ... Anna Smed-Sörensen
    Patterns of monocyte and dendritic cell mobilization and function during human respiratory viral infections are tissue-specific and pathogen-specific, and future studies must perform comparative investigations in blood and the site of infection for a comprehensive assessment of immune responses.
    1. Neuroscience
    2. Physics of Living Systems

    Granger causality analysis for calcium transients in neuronal networks, challenges and improvements

    Xiaowen Chen, Faustine Ginoux ... Claire Wyart
    A practical toolbox for application of Granger causality inference to calcium imaging data identifies strong driver neurons in the locus of the mesencephalic locomoter region in larval zebrafish.
    1. Neuroscience

    A transcriptional constraint mechanism limits the homeostatic response to activity deprivation in mammalian neocortex

    Vera Valakh, Derek Wise ... Sacha B Nelson
    For the first time, the strength of homeostatic plasticity has been shown to be negatively regulated and the transcription factors responsible for this regulation have been identified.
    1. Cell Biology

    Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast

    Rahul Bhattacharjee, Aaron R Hall ... Kathleen L Gould
    Biochemical studies and molecular dynamics simulations indicate that dephosphroylation of F-BAR protein Cdc15 promotes cytokinesis ring assembly in yeast via conformation change of intrinsically disorder regions and condensate formation.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation

    Marco Caligaris, Raffaele Nicastro ... Claudio De Virgilio
    Discovery of new Snf1/AMPK targets in the TORC1 pathway highlights the complex, multilayered crosstalk between major signaling pathways in the regulation of nutrient deprivation sensing.
    1. Neuroscience

    Microglial motility is modulated by neuronal activity and correlates with dendritic spine plasticity in the hippocampus of awake mice

    Felix Christopher Nebeling, Stefanie Poll ... Martin Fuhrmann
    Microglia that presumably sense neuronal activity via detection of glutamate at synapses in the hippocampus show higher fine process motility and increased contact rates associated with formation and elimination of dendritic spines under conditions of elevated neuronal activity.
    1. Cancer Biology
    2. Medicine

    Long COVID in cancer patients: preponderance of symptoms in majority of patients over long time period

    Hiba Dagher, Anne-Marie Chaftari ... Issam I Raad
    Long COVID occurred in the majority of cancer patients diagnosed with acute COVID-19 with a preponderance of symptoms (such as fatigue, sleep disturbances, and gastrointestinal symptoms) over a long time period.
    1. Physics of Living Systems

    In-line swimming dynamics revealed by fish interacting with a robotic mechanism

    Robin Thandiackal, George Lauder
    Fish in the thrust wake of a flapping foil reduce tail-beat frequencies, synchronize with oncoming vortices, and swim energetically more efficiently.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

    Krithika Venkataraman, Nadav Shai ... Leslie B Vosshall
    Two novel, tightly linked, and rapidly evolving genes encoding small secreted proteins are necessary for female mosquitoes to protect their retained eggs during extended periods of drought.
    1. Chromosomes and Gene Expression
    2. Neuroscience

    A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location

    Tooba Abbassi-Daloii, Salma el Abdellaoui ... Vered Raz
    Molecular atlas of Human leg muscles molecular atlas reveals muscle-specific signatures that discriminate between muscle groups.
    1. Developmental Biology
    2. Neuroscience

    Transcription factors underlying photoreceptor diversity

    Juan M Angueyra, Vincent P Kunze ... Wei Li
    Tools and resources to identify transcriptional regulators that create and maintain differences between photoreceptor subtypes.
    1. Neuroscience

    Activity in developing prefrontal cortex is shaped by sleep and sensory experience

    Lex J Gómez, James C Dooley, Mark S Blumberg
    Behavioral and neurophysiological recordings in infant rats reveal that sleep and sensory experience influence neural activity in prefrontal cortex, mirroring similar findings in developing sensorimotor cortex.
    1. Medicine

    Efficacy and safety of endocrine therapy after mastectomy in patients with hormone receptor positive breast ductal carcinoma in situ: Retrospective cohort study

    Nan Niu, Yinan Zhang ... Caigang Liu
    Endocrine therapy after mastectomy may not be recommended for patients with hormone receptor positive ductal carcinoma in situ, even for those with high-risk factors.
    1. Cancer Biology
    2. Developmental Biology

    Bilateral JNK activation is a hallmark of interface surveillance and promotes elimination of aberrant cells

    Deepti Prasad, Katharina Illek ... Anne-Kathrin Classen
    Deregulated cell fate specification pathways, including oncogenic Ras, cause activation of JNK-signaling at contact sites with wild type cells, which drives apoptosis and aberrant cell elimination in a contact-dependent manner.
    1. Developmental Biology

    Molecular characterization of the intact mouse muscle spindle using a multi-omics approach

    Bavat Bornstein, Lia Heinemann-Yerushalmi ... Elazar Zelzer
    Transcriptomic and proteomic analyses of the murine intact muscle spindle provide comprehensive datasets of its different tissues and identify new tools to study its development and function.
    1. Computational and Systems Biology

    Generative power of a protein language model trained on multiple sequence alignments

    Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
    An iterative procedure using language models allows the generation of sequences from protein families, which score similarly to natural and experimentally validated sequences, with particular promise for small families.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    Evolved bacterial resistance to the chemotherapy gemcitabine modulates its efficacy in co-cultured cancer cells

    Serkan Sayin, Brittany Rosener ... Amir Mitchell
    Mutations conferring resistance to Escherichia coli against the chemotherapy drug gemcitabine can have opposite effects on bacterial drug degradation and therefore can increase or decrease the chemotherapy load on neighboring cancer cells.
    1. Epidemiology and Global Health

    The impact of the COVID-19 pandemic on Italian population-based cancer screening activities and test coverage: Results from national cross-sectional repeated surveys in 2020

    Paolo Giorgi Rossi, Giuliano Carrozzi ... Paola Mantellini
    The COVID-19 pandemic caused an important delay in screening activities at the national level and increased the pre-existing individual and geographical inequalities in access.
    1. Immunology and Inflammation

    B cell receptor-induced IL-10 production from neonatal mouse CD19+CD43- cells depends on STAT5-mediated IL-6 secretion

    Jiro Sakai, Jiyeon Yang ... Mustafa Akkoyunlu
    A novel B cell receptor induced interleukin 10 (IL-10) production from B10 cells involves signal transducer and activator of transcription 5 (STAT5) mediated IL-6 production which induces IL-10 in an autocrine and paracrine fashion from B10 cells.
    1. Computational and Systems Biology
    2. Neuroscience

    Cellular composition and circuit organization of the locus coeruleus of adult mice

    Andrew McKinney, Ming Hu ... Xiaolong Jiang
    Interrogating mouse locus coeruleus via large-scale multipatch whole-cell recordings uncovers its cellular heterogeneity and cell-type-specific wiring logic.
    1. Cell Biology

    The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5

    Ryota Miyashita, Atsuya Nishiyama ... Makoto Nakanishi
    The cooperative action of PAF15 deubiquitylation by USP7 and its dissociation from chromatin by ATAD5 regulates proper PAF15Ub2 signaling termination, which is important for replication and maintenance of DNA methylation.
    1. Cell Biology
    2. Developmental Biology

    Peroxiredoxin 5 regulates osteogenic differentiation through interaction with hnRNPK during bone regeneration

    Eunjin Cho, Xiangguo Che ... Tae-Hoon Lee
    Peroxiredoxin 5 contributes to the maintenance of bone homeostasis by regulating osteoblast differentiation.
    1. Epidemiology and Global Health
    2. Genetics and Genomics

    Smoking, alcohol consumption, and 24 gastrointestinal diseases: Mendelian randomization analysis

    Shuai Yuan, Jie Chen ... Susanna C Larsson
    Smoking is a risk factor for a broad range of gastrointestinal diseases independent of alcohol consumption.
    1. Neuroscience

    Pallidal neuromodulation of the explore/exploit trade-off in decision-making

    Ana Luisa de A Marcelino, Owen Gray ... Tom Gilbertson
    Deep brain stimulation (DBS) exhibit that the excitability of the basal ganglia can govern the trade off between exploiting available resources or exploring alternative courses of action.
    1. Cell Biology
    2. Neuroscience

    Synaptic vesicle proteins are selectively delivered to axons in mammalian neurons

    Emma T Watson, Michaela M Pauers ... Edwin R Chapman
    Using carefully controlled expression levels and a variety of optical pulse-chase assays in mammalian neurons, an updated model for the polarized transport of synaptic vesicle proteins, and the first steps of synaptic vesicle biogenesis, were uncovered.
    1. Neuroscience

    Successor-like representation guides the prediction of future events in human visual cortex and hippocampus

    Matthias Ekman, Sarah Kusch, Floris P de Lange
    Early visual cortex (V1) and hippocampal cortex represent a predictive map of the visual world akin to the successor representation.
    1. Cancer Biology

    Arginase 1 is a key driver of immune suppression in pancreatic cancer

    Rosa E Menjivar, Zeribe C Nwosu ... Marina Pasca di Magliano
    Deletion of Arginase 1 in myeloid cells delays tumor formation in pancreatic cancer.
    1. Chromosomes and Gene Expression
    2. Plant Biology

    Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes

    Myeongjune Jeon, Goowon Jeong ... Ilha Lee
    CBFs, the central regulators of low-temperature signaling, have a function to directly activate the expression of COOLAIR, an antisense RNA of FLC, during vernalization process, but COOLAIR is not required for the vernalization response.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    N-terminal domain on dystroglycan enables LARGE1 to extend matriglycan on α-dystroglycan and prevents muscular dystrophy

    Hidehiko Okuma, Jeffrey M Hord ... Kevin P Campbell
    N-terminal domain of dystroglycan enables like-acetylglucosaminyl transferase to elongate matriglycan on α-dystroglycan and prevent skeletal muscle pathophysiology.
    1. Immunology and Inflammation

    Endo-lysosomal assembly variations among human leukocyte antigen class I (HLA class I) allotypes

    Eli Olson, Theadora Ceccarelli, Malini Raghavan
    Human leukocyte antigen class I (HLA class I) polymorphisms dictate the degree of endo-lysosomal assembly, which can supplement endoplasmic reticulum assembly for constitutive HLA class I expression and increase the efficiency of cross-presentation.
    1. Cell Biology

    A mouse model of human mitofusin-2-related lipodystrophy exhibits adipose-specific mitochondrial stress and reduced leptin secretion

    Jake P Mann, Xiaowen Duan ... David B Savage
    The p.Arg707Trp mutation in Mfn2 causes adipose-specific activation of the integrated stress response, which lowers secretion of adipokines.
    1. Cell Biology

    Neutral amino acid transporter SLC38A2 protects renal medulla from hyperosmolarity-induced ferroptosis

    Chunxiu Du, Hu Xu ... Xiaoyan Zhang
    The neutral amino acid transporter SLC38A2 is an essential protective factor for renal medulla during urine concentration.
    1. Genetics and Genomics

    Recognition of galactose by a scaffold protein recruits a transcriptional activator for the GAL regulon induction in Candida albicans

    Xun Sun, Jing Yu ... Yang Lu
    The transcriptional network for the GAL regulon induction in the pathogenic fungus Candida albicans represents an important advance in the evolution of the regulatory circuits, and would make a nice addition to the textbook version of eukaryotic gene regulation.
    1. Cell Biology
    2. Microbiology and Infectious Disease

    Creating an atlas of the bone microenvironment during oral inflammatory-related bone disease using single-cell profiling

    Yi Fan, Ping Lyu ... Chenchen Zhou
    Single-cell sequencing of the alveolar bone marrow of apical periodontitis reveals the cellular and molecular composition of the microenvironment and highlights an osteogenic potential within mesenchymal stem cells of inflammatory-related bone diseases.
    1. Structural Biology and Molecular Biophysics

    Muscle calcium stress cleaves junctophilin1, unleashing a gene regulatory program predicted to correct glucose dysregulation

    Eshwar R Tammineni, Lourdes Figueroa ... Eduardo Rios
    Novel components in the pathway from malignant hyperthermia to diabetes include promotion of a kinase that impedes glycogen synthesis, increased lysis of junctophilin1 and gene regulatory actions by a junctophilin fragment, surprisingly predicted to oppose the effects of elevated calcium.
    1. Genetics and Genomics
    2. Neuroscience

    Single-cell transcriptome profiles of Drosophila fruitless-expressing neurons from both sexes

    Colleen M Palmateer, Catherina Artikis ... Michelle N Arbeitman
    A single-cell RNA-seq study examining gene expression profiles in neurons that underlie Drosophila reproductive behaviors shows males and females build sex-specific behaviors at the molecular-genetic level by overlaying sex-specific information on core gene expression networks.
    1. Neuroscience

    Evidence for dopaminergic involvement in endogenous modulation of pain relief

    Simon Desch, Petra Schweinhardt ... Susanne Becker
    Endogenous modulation of pain relief perception is based on its motivational content and enhanced by increased dopamine availability with no significant effects of a pharmacological opioidergic manipulation in healthy volunteers.