February 2024

Research articles

1. 1. Ecology

   Linking root-associated fungal and bacterial functions to root economics

   Ran Wu, Xiaoyue Zeng ... Weile Chen
2. 1. Neuroscience

   The spatial extent of anatomical connections within the thalamus varies across the cortical hierarchy in humans and macaques

   Amber M. Howell, Shaun Warrington ... Alan Anticevic
3. 1. Computational and Systems Biology
   2. Neuroscience

   Endotaxis: A neuromorphic algorithm for mapping, goal-learning, navigation, and patrolling

   Tony Zhang, Matthew Rosenberg ... Markus Meister

   A neural circuit model reveals how biological brains may implement rapid learning and navigation in complex spaces.
4. 1. Medicine

   Sperm motility in mice with Oligo-astheno-teratozoospermia restored by in vivo injection and electroporation of naked mRNA

   Charline Vilpreux, Guillaume Martinez ... Jessica Escoffier
5. 1. Neuroscience

   The asymmetric transfers of visual perceptual learning determined by the stability of geometrical invariants

   Yan Yang, Yan Zhuo ... Lin Chen
6. 1. Genetics and Genomics
   2. Cancer Biology

   Combinatorial CRISPR screen reveals FYN and KDM4 as targets for synergistic drug combination for treating triple negative breast cancer

   Tackhoon Kim, Byung-Sun Park ... Timothy K. Lu
7. 1. Developmental Biology
   2. Neuroscience

   Volumetric trans-scale imaging of massive quantity of heterogeneous cell populations in centimeter-wide tissue and embryo

   Taro Ichimura, Taishi Kakizuka ... Takeharu Nagai
8. 1. Epidemiology and Global Health

   Effect of an enhanced public health contact tracing intervention on the secondary transmission of SARS-CoV-2 in educational settings: The four-way decomposition analysis

   Olivera Djuric, Elisabetta Larosa ... The Reggio Emilia Covid-19 Working Group

   Prompt contact tracing (testing at the beginning instead of at the end of isolation period) of individuals with COVID-19 in the community reduces delays in contact tracing, increases identification of source of infection, and reduces transmission rates in educational settings.
9. 1. Structural Biology and Molecular Biophysics

   Binding to nucleosome poises human SIRT6 for histone H3 deacetylation

   Ekaterina Smirnova, Emmanuelle Bignon ... Adam Ben Shem

   The dynamics of Sirtuin 6 binding to the nucleosome shed light on how it is able to deacetylate histone H3 lysines close to the core, including K27.
10. 1. Microbiology and Infectious Disease

    Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster

    Julia R Port, Dylan H Morris ... Vincent J Munster

    An experimental animal model provides further insights into the host and viral mechanisms underlying airborne transmission of SARS-CoV-2.
11. 1. Developmental Biology
    2. Neuroscience

    Temporal transcriptomic dynamics in developing macaque neocortex

    Longjiang Xu, Zan Yuan ... Xiaozhong Peng

    A useful single-cell resource provides the prenatal macaque different cell types’ gene expression profiles in the parietal cerebral cortex lobe.
12. 1. Evolutionary Biology

    Evolutionary rate covariation is a reliable predictor of co-functional interactions but not necessarily physical interactions

    Jordan Little, Maria Chikina, Nathan L Clark

    Physical interactions are a minor contributor to the correlations in evolutionary rate over time that are observed between co-functional proteins.
13. 1. Cell Biology
    2. Genetics and Genomics

    A seven-sex species recognizes self and non-self mating-type via a novel protein complex

    Guanxiong Yan, Yang Ma ... Wei Miao

    A giant multifunctional protein complex mediates mating-type recognition through a non-ligand–receptor mechanism in a multisexual species.
14. 1. Neuroscience

    Uncertainty-modulated prediction errors in cortical microcircuits

    Katharina A Wilmes, Mihai A Petrovici ... Walter Senn
15. 1. Genetics and Genomics
    2. Neuroscience

    Plasticity of gene expression in the nervous system by exposure to environmental odorants that inhibit HDACs

    Sachiko Haga-Yamanaka, Rogelio Nunez-Flores ... Anandasankar Ray

    Volatile compounds from microbes and food alter epigenetic states by inhibiting histone deacetylases and alter gene expression, slow degeneration in Huntington’s model flies, and slow proliferation of a neuroblastoma cell line.
16. 1. Neuroscience

    The mTOR pathway genes MTOR, Rheb, Depdc5, Pten, and Tsc1 have convergent and divergent impacts on cortical neuron development and function

    Lena H Nguyen, Youfen Xu ... Angelique Bordey

    Expression of mTORC1 pathway gene variants in mouse medial prefrontal cortex leads to shared alterations in pyramidal neuron morphology, positioning, and membrane excitability but different changes in excitatory synaptic transmission.
17. 1. Cell Biology
    2. Neuroscience

    SNAP25 disease mutations change the energy landscape for synaptic exocytosis due to aberrant SNARE interactions

    Anna Kádková, Jacqueline Murach ... Jakob Balslev Sørensen

    SNAP25 disease mutations within the synaptotagmin interface impair vesicle priming and cause uncontrolled spontaneous release due to enhanced SNARE:SNARE interactions, whereas a mutation within the SNARE-bundle increases the fusion energy barrier.
18. 1. Immunology and Inflammation
    2. Medicine

    Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice

    Yufang Ding, Karin Yanagi ... Arul Jayaraman

    A microbiome metabolite alleviates liver steatosis and inflammation, and shows its potential as a therapeutic modality for non-alcoholic fatty liver disease.
19. 1. Genetics and Genomics

    The genomic landscape of transposable elements in yeast hybrids is shaped by structural variation and genotype-specific modulation of transposition rate

    Mathieu Hénault, Souhir Marsit ... Christian R Landry

    The gain of transposable elements in yeast hybrids does not scale with genetic divergence levels and is most impacted by structural variations and multiple aspects of individual hybrid genetic backgrounds.
20. 1. Plant Biology

    The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies

    Daniel S Yu, Megan A Outram ... Simon J Williams

    Computational and experimental structural biology reveals the structural repertoire of effector proteins produced by Fusarium oxysporum f. sp. lycopersici during infection of tomato.
21. 1. Chromosomes and Gene Expression

    Control of meiotic entry by dual inhibition of a key mitotic transcription factor

    Amanda J Su, Siri C Yendluri, Elçin Ünal

    Investigation of how cells rewire their transcriptional programs during transition from mitotic to meiotic cell fate reveals a two-pronged mechanism for inactivating a key mitotic transcription factor.
22. 1. Neuroscience

    An Information-Theoretic Approach to Reward Rate Optimization in the Tradeoff Between Controlled and Automatic Processing in Neural Network Architectures

    Giovanni Petri, Sebastian Musslick, Jonathan D. Cohen
23. 1. Neuroscience

    Molecular identification of wide-field amacrine cells in mouse retina that encode stimulus orientation

    Silvia J. Park, Wanyu Lei ... Jonathan B. Demb
24. 1. Evolutionary Biology

    Coenzyme-Protein Interactions since Early Life

    Alma Carolina Sanchez-Rocha, Mikhail Makarov ... Klára Hlouchová
25. 1. Genetics and Genomics
    2. Neuroscience

    Rapid and Inducible Mislocalization of Endogenous TDP43 in a Novel Human Model of Amyotrophic Lateral Sclerosis

    Johanna Ganssauge, Sophie Hawkins ... Akshay Bhinge
26. 1. Cell Biology

    The ubiquitin-conjugating enzyme UBE2D/eff maintains a youthful proteome and ensures protein quality control during aging

    Liam C Hunt, Kudzai Nyamkondiwa ... Fabio Demontis
27. 1. Developmental Biology

    Mouse SAS-6 is required for centriole formation in embryos and integrity in embryonic stem cells

    Marta Grzonka, Hisham Bazzi

    Unlike mouse embryos, mouse embryonic stem cells are able to use a SAS-6-independent pathway for imperfect centriole biogenesis that is associated with a rich centrosomal milieu and robust PLK4 activity.
28. 1. Cancer Biology

    Molecular classification and tumor microenvironment characteristics in pheochromocytomas

    Sen Qin, Yawei Xu ... Zheng Zhang

    ScRNA-seq of diverse pheochromocytoma patients reveals distinct microenvironment characteristics and supports an informative molecular classification system.
29. 1. Immunology and Inflammation

    RBP-J regulates homeostasis and function of circulating Ly6C^lo monocytes

    Tiantian Kou, Lan Kang ... Xiaoyu Hu

    Experiments including cell and animal models investigate the molecular mechanisms underlying the regulation of homeostasis and function of monocytes.
30. 1. Neuroscience

    Causal role of the angular gyrus in insight-driven memory reconfiguration

    Anna-Maria Grob, Hendrik Heinbockel ... Lars Schwabe

    Behavioral and neural analyses unravel the angular gyrus’ key role in the prioritization of integrated narratives in memory and the orchestration of theta-frequency reconfigurations underpinning the process of memory integration.
31. 1. Computational and Systems Biology

    What fraction of cellular DNA turnover becomes cfDNA?

    Ron Sender, Elad Noor ... Yuval Dor

    Comparing tissue-specific plasma cfDNA concentration with cellular turnover rates reveals that less than 10% of dying cells' DNA reaches plasma, highlighting significant local clearance mechanisms and suggesitng approaches to enhance liquid biopsy sensitivity.
32. 1. Neuroscience

    Mechanical activation of TWIK-related potassium channel by nanoscopic movement and rapid second messenger signaling

    E Nicholas Petersen, Mahmud Arif Pavel ... Scott B Hansen

    Cells utilize a membrane-mediated mechanism for mechanosensation, which involves the disruption of lipid rafts and a signal relayed to an ion channel.
33. 1. Chromosomes and Gene Expression

    DNA methylation-environment interactions in the human genome

    Rachel A Johnston, Katherine A Aracena ... Jenny Tung

    A massively parallel reporter assay, mSTARR-seq, reveals widespread DNA methylation-environment interactions across the genome, prioritizing CpG sites identified in epigenome-wide association studies that may be most relevant to biological embedding.
34. 1. Developmental Biology
    2. Neuroscience

    A new look at the architecture and dynamics of the Hydra nerve net

    Athina Keramidioti, Sandra Schneid ... Charles N David

    A novel pan-neuronal antibody has revealed the organization of the nerve net controlling all behavior in the simple cnidarian Hydra.
35. 1. Computational and Systems Biology
    2. Neuroscience

    Dissecting muscle synergies in the task space

    David O'Reilly, Ioannis Delis

    A novel network information framework quantifies muscle interactions, characterises their task-relevance, and identifies networks of muscles with similar and complementary functional roles.
36. 1. Ecology

    Small deviations in kinematics and body form dictate muscle performances in the finely tuned avian downstroke

    Marc E Deetjen, Diana D Chin ... David Lentink

    Doves improve their wingbeat efficacy without elevating maximum pectoralis power by angling their wings mid-downstroke to efficiently generate aerodynamic force while simultaneously tensioning the supracoracoideus tendon to assist the upstroke.
37. 1. Cancer Biology

    Large pan-cancer cell screen coupled to (phospho-)proteomics underscores high-dose vitamin C as a potent anti-cancer agent

    Andrea Vallés-Martí, Franziska Böttger ... Connie R Jiménez
38. 1. Medicine
    2. Computational and Systems Biology

    Clinical phenotypes in acute and chronic infarction explained through human ventricular electromechanical modelling and simulations

    Xin Zhou, Zhinuo Jenny Wang ... Blanca Rodriguez
39. 1. Neuroscience

    High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling

    Peibo Xu, Jian Peng ... Yuejun Chen

    A multiplexed retrograde virus tracing method captures single-neuron projectome and transcriptome simultaneously.
40. 1. Biochemistry and Chemical Biology

    Noncanonical usage of stop codons in ciliates expands proteins with structurally flexible Q-rich motifs

    Chi-Ning Chuang, Hou-Cheng Liu ... Ting-Fang Wang

    Noncanonical usage of stop codons in ciliates expands structurally flexible Q-rich domains and coevolves with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
41. 1. Cell Biology
    2. Chromosomes and Gene Expression

    A TOPBP1 allele causing male infertility uncouples XY silencing dynamics from sex body formation

    Carolline Ascenção, Jennie R Sims ... Marcus B Smolka

    A Topbp1 mutant mouse reveals a non-canonical role for the ATR-TOPBP1 signaling axis in meiosis, separating ATR signaling and meiotic sex chromosome inactivation from sex body formation.
42. 1. Developmental Biology

    Delta-dependent Notch activation closes the early neuroblast temporal program to promote lineage progression and neurogenesis termination in Drosophila

    Chhavi Sood, Md Ausrafuggaman Nahid ... Sarah E Siegrist

    Notch signaling regulates the neuroblast intrinsic temporal program to determine when neuroblasts terminate their cell divisions during development.
43. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    An engineered biosensor enables dynamic aspartate measurements in living cells

    Kristian Davidsen, Jonathan S Marvin ... Lucas B Sullivan

    A genetically encoded fluorescent biosensor reveals temporally resolved changes to aspartate concentration during genetic, pharmacological, and nutritional manipulations.
44. 1. Cell Biology
    2. Immunology and Inflammation

    Piezo1 mechanosensing regulates integrin-dependent chemotactic migration in human T cells

    Chinky Shiu Chen Liu, Tithi Mandal ... Dipyaman Ganguly

    A hitherto unknown role of Piezo1 mechanosensors in chemotactic migration of human T cells is identified, linking focal adhesion formation to integrin recruitment.
45. 1. Microbiology and Infectious Disease

    The intricate relationship of G-Quadruplexes and bacterial pathogenicity islands

    Bo Lyu, Qisheng Song

    Unveiling the intricate web of interactions between G4 structures and pathogenicity islands in 89 bacterial genomes significantly advances our understanding of bacterial virulence mechanisms.
46. 1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

    Hisato Kobayashi, Tatsushi Igaki ... Kazuki Kurimoto
47. 1. Neuroscience

    The Neural Correlates of Ambiguity and Risk in Human Decision-Making under an Active Inference Framework

    Shuo Zhang, Yan Tian ... Haiyan Wu
48. 1. Neuroscience

    Towards biologically plausible phosphene simulation for the differentiable optimization of visual cortical prostheses

    Maureen van der Grinten, Jaap de Ruyter van Steveninck ... Yağmur Güçlütürk

    The provided framework based on biological models and clinical literature can aid in the optimization of visual cortical prostheses through computational or behavioral simulation experiments, serving as a flexible tool for computational, clinical, and behavioral neuroscientists working on visual neuroprosthetics.
49. 1. Cell Biology

    Rapid binding to protofilament edge sites facilitates tip tracking of EB1 at growing microtubule plus-ends

    Samuel J Gonzalez, Julia M Heckel ... Melissa K Gardner

    Computational modeling combined with biophysical and cellular experiments reveal that rapid binding to incomplete, partial microtubule binding sites facilitates tracking of the end-binding protein EB1 with growing microtubule plus-ends.
50. 1. Neuroscience

    Optogenetic stimulation of the locus coeruleus enhances appetitive extinction in rats

    Simon Lui, Ashleigh K Brink, Laura H Corbit

    The long-term retention of extinction is enhanced by ontogenetic stimulation of locus coeruleus neurons applied during extinction of a reward-seeking response, further implicating noradrenaline in appetitive extinction.
51. 1. Developmental Biology
    2. Neuroscience

    Touch receptor end-organ innervation and function require sensory neuron expression of the transcription factor Meis2

    Simon Desiderio, Frederick Schwaller ... Frederic Marmigere

    Combining mouse genetic, behavioral, and electrophysiological approaches revealed that a transcription factor is required to shape touch neurons' distal projections in the skin while dispensable for their survival and specification.
52. 1. Immunology and Inflammation

    Tailoring T_fh profiles enhances antibody persistence to a clade C HIV-1 vaccine in rhesus macaques

    Anil Verma, Chase E Hawes ... Smita S Iyer

    Strategies to enhance Tfh cells for HIV-vaccine antibody persistence and protection is pivotal for vaccine success.
53. 1. Ecology
    2. Plant Biology

    High-resolution kinetics of herbivore-induced plant volatile transfer reveal clocked response patterns in neighboring plants

    Jamie Mitchel Waterman, Tristan Michael Cofer ... Matthias Erb

    Real-time volatile emission kinetics reveal stress volatiles emitted from herbivore-damaged plants can sequentially prime and induce defense responses in undamaged plants following distinct temporal patterns.
54. 1. Cell Biology
    2. Plant Biology

    Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery

    Maciek Adamowski, Ivana Matijević, Jiří Friml

    The plant developmental regulator GNOM performs its unique function from the cell periphery, through sequence features present in all its domains, and not by the control of endocytosis.
55. 1. Computational and Systems Biology

    Metabolic model-based ecological modeling for probiotic design

    James D Brunner, Nicholas Chia

    Genome-scale metabolic models can be used to predict the engraftment of probiotics.
56. 1. Computational and Systems Biology
    2. Evolutionary Biology

    Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes

    Roee Ben Nissan, Eliya Milshtein ... Ron Milo

    Achieving autotrophy in E. coli by introducing a small number of genetic changes crosses a milestone in engineering major metabolic transitions and paves a way for sustainable bio-production from CO₂.
57. 1. Evolutionary Biology
    2. Genetics and Genomics

    Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice

    Thomas A Sasani, Aaron R Quinlan, Kelley Harris

    Germline mutation rates in mice are shaped by two mutator alleles that interact epistatically, showing that DNA repair defects that map to different loci can have snowballing effects.
58. 1. Neuroscience

    Sexual coordination in a whole-brain map of prairie vole pair bonding

    Morgan L Gustison, Rodrigo Muñoz-Castañeda ... Steven M Phelps

    A brain-wide map of neural activation reveals how sexual experience becomes a pair bond in the monogamous prairie vole.
59. 1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    Energetics of the microsporidian polar tube invasion machinery

    Ray Chang, Ari Davydov ... Manu Prakash

    Unraveling the ultrafast polar tube ejection in microsporidia reveals extreme cellular hydraulics, providing a data-driven model for infectious cargo transport, with implications for physical approaches to understanding microsporidia transmission.
60. 1. Structural Biology and Molecular Biophysics

    Mobile barrier mechanisms for Na⁺-coupled symport in an MFS sugar transporter

    Parameswaran Hariharan, Yuqi Shi ... Lan Guan

    The use of a conformation-selective inhibitory nanobody provides critical information on MelB at a low-sugar affinity inward-facing Na⁺-bound state for establishing the mobile barrier and substrate-releasing mechanisms.
61. 1. Genetics and Genomics
    2. Immunology and Inflammation

    Paradoxical dominant negative activity of an immunodeficiency-associated activating PIK3R1 variant

    Patsy R. Tomlinson, Rachel Knox ... Robert K. Semple
62. 1. Microbiology and Infectious Disease

    Transcriptional regulation of SARS-CoV-2 receptor ACE2 by SP1

    Hui Han, Rong-Hua Luo ... Cheng-Gang Zou

    SP1 serves as an important transcription factor in the regulation of ACE2 expression.
63. 1. Structural Biology and Molecular Biophysics

    Disordered regions and folded modules in CAF-1 promote histone deposition in Schizosaccharomyces pombe

    Fouad Ouasti, Maxime Audin ... Francoise Ochsenbein

    Histone, PCNA, and DNA binding are essential for CAF-1 functions in preventing DNA damage during DNA replication in Schizosaccharomyces pombe, while its C-terminal domain specifies distinct cellular processes.
64. 1. Computational and Systems Biology
    2. Physics of Living Systems

    How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution

    Nicholas M Boffi, Yipei Guo ... Ariel Amir

    High-resolution simulations of evolving microbial populations reveal that microscopic epistasis slows the rate of adaptation, while clonal interference can either speed it up or leave it fixed.
65. 1. Physics of Living Systems

    Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores

    Nils Klughammer, Anders Barth ... Cees Dekker

    Nuclear pore complex mimics based on solid-state nanopores show significant selectivity below a diameter of 55 nm, which decreases gradually for larger pore diameters.
66. 1. Computational and Systems Biology

    Spatial–temporal order–disorder transition in angiogenic NOTCH signaling controls cell fate specification

    Tae-Yun Kang, Federico Bocci ... Andre Levchenko

    The transition from a restrictive patterning mechanism to one sensitive to a variety of environmental cues in NOTCH-mediated angiogenesis offers crucial insights into vascularization in damaged organs and cancer therapy.
67. 1. Neuroscience

    Reward contingency gates selective cholinergic suppression of amygdala neurons

    Eyal Y Kimchi, Anthony Burgos-Robles ... Kay M Tye

    Electrophysiological recordings and optogenetic manipulations revealed the distinct roles that acetylcholine can have on the amygdala and prefrontal cortex in a Window of Opportunity Task.
68. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    β-catenin inhibition disrupts the homeostasis of osteogenic/adipogenic differentiation leading to the development of glucocorticoid-induced osteonecrosis of the femoral head

    Chenjie Xia, Huihui Xu ... Hongting Jin

    Deletion of β-catenin in Col2⁺ progenitor cells shifts their commitment from osteoblasts to adipocytes, leading to a full spectrum of disease phenotype of glucocorticoid-induced osteonecrosis of the femoral head in adult mice.
69. 1. Physics of Living Systems

    Energy conservation by collective movement in schooling fish

    Yangfan Zhang, George V Lauder

    Fish schools showed an U-shaped metabolism-speed curve and reduced the energy use per tail beat up to 56% at high swimming speeds compared to solitary fish.
70. 1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    How did UGA codon translation as tryptophan evolve in certain ciliates? A critique of Kachale et al. 2023 Nature

    Estienne Carl Swart, Christiane Emmerich ... Aditi Singh
71. 1. Genetics and Genomics
    2. Cancer Biology

    Functional characterization of all CDKN2A missense variants and comparison to in silico models of pathogenicity

    Hirokazu Kimura, Kamel Lahouel ... Nicholas J Roberts
72. 1. Cell Biology

    Genetic screen identified PRMT5 as a neuroprotection target against cerebral ischemia

    Haoyang Wu, Peiyuan Lv ... Jiaji Lin

    An RNAi screen in mouse hippocampal neuronal cell line targeting epigenetic regulators revealed a novel neuroprotection of Prmt5 and uncovered its nucleus translocation feature and epigenetic mechanism in cerebral ischemia.
73. 1. Cell Biology
    2. Immunology and Inflammation

    NAD⁺ prevents septic shock-induced death by non-canonical inflammasome blockade and IL-10 cytokine production in macrophages

    Jasper Iske, Rachid El Fatimy ... Abdallah Elkhal

    NAD⁺ exhibits profound therapeutic effects in experimental septic shock models by dampening the systemic inflammatory response and leading to improved survival.
74. 1. Biochemistry and Chemical Biology
    2. Plant Biology

    A translation proofreader of archaeal origin imparts multi-aldehyde stress tolerance to land plants

    Pradeep Kumar, Ankit Roy ... Rajan Sankaranarayanan

    Genetic, biochemical, and bioinformatic analyses reveal how expanding metabolic repertoire interferes with fundamental processes like protein synthesis inside cells and the role of D-aminoacyl-tRNA deacylase2 in protecting these processes during terrestrialisation.
75. 1. Microbiology and Infectious Disease

    Quantity of SARS-CoV-2 RNA copies exhaled per minute during natural breathing over the course of COVID-19 infection

    Gregory Lane, Guangyu Zhou ... Christina Zelano
76. 1. Neuroscience

    Functionally refined encoding of threat memory by distinct populations of basal forebrain cholinergic projection neurons

    Prithviraj Rajebhosale, Mala R Ananth ... David A Talmage

    Functionally refined organization of learned and innate threat encoding in the cholinergic basal forebrain.
77. 1. Microbiology and Infectious Disease

    Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes

    Sabrina Tetzlaff, Arne Hillebrand ... Christian Schmitz-Linneweber

    Sequences at mitochondrial genome recombination sites are dually used as mRNAs and as rRNAs in actively translating mitoribosomes of T. gondii.
78. 1. Computational and Systems Biology

    Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria

    Roswitha Dolcemascolo, María Heras-Hernández ... Guillermo Rodrigo

    A mammalian protein with RNA recognition motifs can be used in bacteria to engineer post-transcriptional regulation.
79. 1. Neuroscience

    Parahippocampal neurons encode task-relevant information for goal-directed navigation

    Alexander Gonzalez, Lisa M Giocomo

    Parahippocampal neurons increase their activity rates following navigational errors, and the error signal magnitude is related with overall task performance.
80. 1. Epidemiology and Global Health

    Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of antimalarial drug resistance

    Qixin He, John K Chaillet, Frédéric Labbé

    A novel compartment model identifies the impact of malaria strain diversity on biogeographic drug resistance patterns, supported by empirical evidence.
81. 1. Neuroscience

    Human Exploration Strategically Balances Approaching and Avoiding Uncertainty

    Yaniv Abir, Michael N. Shadlen, Daphna Shohamy
82. 1. Computational and Systems Biology

    AI-driven Automated Discovery Tools Reveal Diverse Behavioral Competencies of Biological Networks

    Mayalen Etcheverry, Clément Moulin-Frier ... Michael Levin
83. 1. Medicine

    Metabolomics identifies and validates serum androstenedione as novel biomarker for diagnosing primary angle closure glaucoma and predicting the visual field progression

    Shengjie Li, Jun Ren ... Wenjun Cao

    Metabolomic analyses have developed and validated serum androstenedione as a reliable and effective diagnostic and predictive biomarker for primary angle closure glaucoma in clinical routines.
84. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle

    Greg J Dodge, Alyssa J Anderson ... Barbara Imperiali

    Structural, functional, and bioinformatics analyses further understanding of the initial steps of prokaryotic glycoconjugate biosynthesis catalyzed by the large class of membrane-embedded monotopic phosphoglycosyl transferase superfamily.
85. 1. Evolutionary Biology
    2. Genetics and Genomics

    Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells

    Ban Wang, Alexander L Starr, Hunter B Fraser

    Exploring tissue-specific regulation of gene expression with human-chimpanzee hybrid cells helps us understand how life evolves and what makes us human.
86. 1. Neuroscience

    Regulation of hippocampal mossy fiber-CA3 synapse function by a Bcl11b/C1ql2/Nrxn3(25b+) pathway

    Artemis Koumoundourou, Märt Rannap ... Stefan Britsch

    Molecular genetic, cell culture as well as electrophysiological analyses reveal a C1ql2/Neurexin3(25b+)-dependent molecular pathway through which Bcl11b controls critical functions of adult hippocampal mossy fiber synapses.
87. 1. Microbiology and Infectious Disease

    The acetylase activity of Cdu1 regulates bacterial exit from infected cells by protecting Chlamydia effectors from degradation

    Robert J Bastidas, Mateusz Kędzior ... Raphael H Valdivia

    Genetic and biochemical analyses show that Chlamydia protects secreted effectors necessary for its exit from infected cells, preventing them from undergoing ubiquitination and degradation.
88. 1. Neuroscience

    Overnight fasting facilitates safety learning by changing the neurophysiological response to relief from threat omission

    Silvia Papalini, Tom Beckers ... Bram Vervliet
89. 1. Neuroscience

    A Myelin Map of Trunk Folds in the Elephant Trigeminal Nucleus

    Noémie Reveyaz, Undine Schneeweiß ... Michael Brecht
90. 1. Microbiology and Infectious Disease

    Fast Evolution of SOS-Independent Multi-Drug Resistance in Bacteria

    Le Zhang, Yunpeng Guan ... Dayong Jin
91. 1. Computational and Systems Biology
    2. Neuroscience

    A dynamical computational model of theta generation in hippocampal circuits to study theta-gamma oscillations during neurostimulation

    Nikolaos Vardalakis, Amélie Aussel ... Fabien B Wagner

    Combining biophysically realistic hippocampal neurons with coupled phase oscillators that represent theta inputs enables probing the phase-dependent effects of neurostimulation on theta-nested gamma oscillations in normal and pathological states.
92. 1. Evolutionary Biology
    2. Plant Biology

    Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant

    Lei Zhao, Wei Zhou ... Hong-Tao Li

    Computational analyses, for the first time in plants, reveal how male-biased genes evolve faster than female-biased and unbiased genes.
93. 1. Microbiology and Infectious Disease

    Detecting, mapping, and suppressing the spread of a decade-long Pseudomonas aeruginosa nosocomial outbreak with genomics

    William Stribling, Lindsey R. Hall ... Francois Lebreton
94. 1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure

    KM Rifat Faysal, James C Walsh ... Till Böcking

    The anti-HIV drug lenacapavir breaks the HIV capsid by stabilising regions of low curvature at the expense of maintaining a closed shell, leading to loss of viral DNA synthesis and inhibition of infection.
95. 1. Genetics and Genomics

    Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans

    Kurt Warnhoff, Sushila Bhattacharya ... Gary Ruvkun

    Cysteine dioxygenase, a conserved and critical enzyme in sulfur amino acid metabolism, is activated by the hypoxia-inducible transcription factor.
96. 1. Structural Biology and Molecular Biophysics

    Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter

    Michael J Currie, James S Davies ... Rachel A North

    Structure of the dimeric Haemophilus influenzae TRAP transporter (SiaQM) reveals two Na⁺ sites, the substrate-binding site and lipid-binding sites, and weak but promiscuous binding of SiaP to SiaQM.
97. 1. Cell Biology

    Human dynein-dynactin is a fast processive motor in living cells

    Vikash Verma, Patricia Wadsworth, Thomas J. Maresca
98. 1. Biochemistry and Chemical Biology
    2. Cancer Biology

    A methylation-phosphorylation switch controls EZH2 stability and hematopoiesis

    Pengfei Guo, Rebecca C Lim ... Hui Zhang

    EZH2 is regulated by a K20-methylation dependent proteolysis and this proteolysis process is negatively controlled by AKT-mediated S21 phosphorylation to establish a methylation-phosphorylation switch to control the PRC2 activity and hematopoiesis.
99. 1. Medicine

    Correlated signatures of social behavior in cerebellum and anterior cingulate cortex

    Sung Won Hur, Karen Safaryan ... Peyman Golshani

    Development of a novel open-source device, 'E-Scope,' to simultaneously record electrophysiology and calcium imaging in freely behaving animals, discovering co-modulation of the cerebellum, and anterior cingulate cortex during social interaction.
100. 1. Neuroscience
     2. Structural Biology and Molecular Biophysics

     CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism

     Mengyuan Xu, Torben Neelands ... Merritt Maduke

     A combination of high-resolution structure determination, electrophysiology, and MD simulations reveal fundamental insight into the molecular function of voltage-gated chloride channels.
101. 1. Neuroscience

     Hippocampome.org 2.0 is a knowledge base enabling data-driven spiking neural network simulations of rodent hippocampal circuits

     Diek W Wheeler, Jeffrey D Kopsick ... Giorgio A Ascoli

     Hippocampome.org v1.0, a foundational classification system of hippocampal neuron types, has evolved into 2.0, which recenters the focus on new functionality to build real-scale, biologically detailed, data-driven computational simulations.
102. 1. Neuroscience

     Circuit-based intervention corrects excessive dentate gyrus output in the fragile X mouse model

     Pan-Yue Deng, Ajeet Kumar ... Vitaly A Klyachko

     Circuit-based intervention corrects irreconcilable excitability defects between dentate granule cells and mossy cells in Fmr1 knockout mice, representing a promising strategy to restore the dentate excitation/inhibition balance and circuit computations.
103. 1. Structural Biology and Molecular Biophysics
     2. Computational and Systems Biology

     Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

     Ameya Harmalkar, Sergey Lyskov, Jeffrey J. Gray
104. 1. Cell Biology
     2. Neuroscience

     O-GlcNAc signaling increases neuron regeneration through one-carbon metabolism in Caenorhabditis elegans

     Dilip Kumar Yadav, Andrew C Chang ... Christopher V Gabel

     The specific metabolic pathways that increase neuron regeneration in ogt-1 mutant C. elegans following in vivo laser axotomy, highlighting the potential power for such metabolic targets in the treatment of neuronal injury.
105. 1. Neuroscience

     RatInABox, a toolkit for modelling locomotion and neuronal activity in continuous environments

     Tom M George, Mehul Rastogi ... Caswell Barry

     A new python package standardises and simplifies how spatial behaviour and neural representations are modelled in continuous environments.
106. 1. Genetics and Genomics

     Characterization of caffeine response regulatory variants in vascular endothelial cells

     Carly Boye, Cynthia A Kalita ... Francesca Luca

     Caffeine modulates the genetic risk for cardiovascular disease through changes in target gene expression, likely due to regulation of transcription factor binding.
107. 1. Neuroscience

     Altered hierarchical auditory predictive processing after lesions to the orbitofrontal cortex

     Olgerta Asko, Alejandro Omar Blenkmann ... Anne-Kristin Solbakk

     Orbitofrontal cortex lesions impact the neural correlates of detection of auditory regularity violation at two hierarchical levels of rule abstraction, providing a novel perspective on the role of the orbitofrontal cortex in auditory predictive processing.
108. 1. Ecology

     Species and habitat specific changes in bird activity in an urban environment during Covid 19 lockdown

     Congnan Sun, Yoel Hassin ... Yossi Yovel

     Bird activity during Covid 19 lockdown changed depending on species and site, as well as on environmental parameters and heterospecific (e.g., human) activity, revealing a complex and dynamic urban ecological system.
109. 1. Computational and Systems Biology
     2. Medicine

     A computational model predicts sex-specific responses to calcium channel blockers in mammalian mesenteric vascular smooth muscle

     Gonzalo Hernandez-Hernandez, Samantha C O'Dwyer ... Colleen E Clancy

     A computer model predicts different mechanisms of blood pressure regulation and effective hypertensive therapy for males and females, thereby serving as a foundational tool for improved treatment precision.
110. 1. Neuroscience

     A spatial-attentional mechanism underlies action-related distortions of time judgment

     Liyu Cao

     The distribution of visuospatial attention shapes the timing report results obtained with the Libet clock method, thus explaining the temporal binding effect in this context.
111. 1. Cell Biology
     2. Medicine

     PCBP2 as an intrinsic aging factor regulates the senescence of hBMSCs through the ROS-FGF2 signaling axis

     Pengbo Chen, Bo Li ... Xinfeng Zheng
112. 1. Structural Biology and Molecular Biophysics
     2. Evolutionary Biology

     Coevolution with toxic prey produces functional trade-offs in sodium channels of predatory snakes

     Robert E. del Carlo, Jessica S. Reimche ... Chris R. Feldman
113. 1. Neuroscience

     Driver lines for studying associative learning in Drosophila

     Yichun Shuai, Megan Sammons ... Yoshinori Aso
114. 1. Epidemiology and Global Health

     Modeling resource allocation strategies for insecticide-treated bed nets to achieve malaria eradication

     Nora Schmit, Hillary M Topazian ... Azra C Ghani

     The optimal allocation strategy prioritizes funding to high-transmission settings in sub-Saharan Africa, but highlights a trade-off between reducing clinical malaria burden and reducing the global population at risk of malaria.
115. 1. Structural Biology and Molecular Biophysics

     Novel sterol binding domains in bacteria

     Liting Zhai, Amber C Bonds ... Laura MK Dassama

     A combination of bioinformatics, protein biochemistry, and X-ray crystal structures reveals new bacterial proteins that are capable of binding to sterols.
116. 1. Neuroscience

     RIM-BP2 regulates Ca²⁺ channel abundance and neurotransmitter release at hippocampal mossy fiber terminals

     Rinako Miyano, Hirokazu Sakamoto ... Takeshi Sakaba

     By combining direct presynaptic patch-clamp electrophysiology and super-resolution microscopy, it was found that KO of RIM-BP2 reduced calcium channel abundance in hippocampal mossy terminals.
117. 1. Computational and Systems Biology

     The genetic and dietary landscape of the muscle insulin signalling network

     Julian van Gerwen, Stewart WC Masson ... David E James

     Genetic background and dietary environment interact to reshape metabolic signalling networks, and the resulting signalling diversity can illuminate regulatory mechanisms of complex traits.
118. 1. Neuroscience

     Sensitization of meningeal afferents to locomotion-related meningeal deformations in a migraine model

     Andrew S Blaeser, Jun Zhao ... Dan Levy

     Functional imaging of individual sensory afferents that innervate the cranial meninges in a mouse migraine model reveals heightened responsiveness to movement-related meningeal deformations that may underlie headache.
119. 1. Neuroscience

     Mediodorsal thalamic nucleus mediates resistance to ethanol through Cav3.1 T-type Ca²⁺ regulation of neural activity

     Charles-Francois V Latchoumane, Joon-Hyuk Lee ... Hee-Sup Shin
120. 1. Computational and Systems Biology
     2. Physics of Living Systems

     Overflow metabolism originates from growth optimization and cellheterogeneity

     Xin Wang
121. 1. Developmental Biology
     2. Evolutionary Biology

     Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator

     Paul Knabl, Alexandra Schauer ... Grigory Genikhovich

     ChIP-seq analysis reveals BMP signaling targets in a cnidarian and identifies ZSWIM4-6 as a dampener of the pSMAD1/5 gradient and a potential conveyor of the BMP-mediated gene repression.
122. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     Comment on 'The clinical pharmacology of tafenoquine in the radical cure of Plasmodium vivax malaria: An individual patient data meta-analysis'

     Raman Sharma, Chao Chen ... Panayota Bird

     We are writing to comment on the article by Watson et al., 2022 about the antimalarial drug tafenoquine.
123. 1. Epidemiology and Global Health
     2. Microbiology and Infectious Disease

     Response to comment on 'The clinical pharmacology of tafenoquine in the radical cure of Plasmodium vivax malaria: An individual patient data meta-analysis'

     James A Watson, Robert J Commons ... Nicholas J White

     We are writing to respond to comment by Sharma et al, 2024 on our article about the antimalarial drug tafenoquine.
124. 1. Genetics and Genomics
     2. Neuroscience

     Transcriptional cartography integrates multiscale biology of the human cortex

     Konrad Wagstyl, Sophie Adler ... Armin Raznahan

     An atlas of cortical expression for 20,781 genes in the adult human brain, validated against multiscale datasets, from neuroimaging measures of structure and function to molecular cell and layer markers.
125. 1. Cell Biology

     Liver regeneration by a population of midzone-located mesenchymal-hepatocyte hybrid cells

     Guo Yu, Shaoyang Zhang ... Jing Li
126. 1. Cell Biology
     2. Developmental Biology

     Pial collaterals develop through mosaic colonization of capillaries by arterial and microvascular endothelial cells

     Tijana Perovic, Irene Hollfinger ... Holger Gerhardt
127. 1. Cell Biology

     The Molecular Logic of Gtr1/2 and Pib2 Dependent TORC1 Regulation in Budding Yeast

     Jacob H. Cecil, Cristina M. Padilla ... Andrew P. Capaldi
128. 1. Neuroscience

     Neural Evidence of Functional Compensation for Fluid Intelligence in Healthy Ageing

     Ethan Knights, Richard N Henson ... Kamen A Tsvetanov
129. 1. Chromosomes and Gene Expression
     2. Neuroscience

     Inhibition of Cpeb3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs and enhances object location memory

     Claire C Chen, Joseph Han ... Andrej Luptak

     The mammalian CPEB3 self-cleaving ribozyme modulates expression of the CPEB3 mRNA and protein, altering translation of plasticity-related proteins and hippocampus-dependent memory.
130. 1. Chromosomes and Gene Expression
     2. Structural Biology and Molecular Biophysics

     Nucleosome conformation dictates the histone code

     Matthew R Marunde, Harrison A Fuchs ... Catherine A Musselman

     NMR spectroscopy, dCypher assays, and CUT&RUN demonstrate that occlusion of the histone tails in the nucleosome context alters histone PTM specificity for a tandem of reader domains.
131. 1. Neuroscience

     A prefrontal network model operating near steady and oscillatory states links spike desynchronization and synaptic deficits in schizophrenia

     David A Crowe, Andrew Willow ... Bagrat Amirikian

     Cortical network model suggests a mechanism explaining the link between NMDAR synaptic and spike synchrony deficits observed in a pharmacological monkey model of prefrontal network failure in schizophrenia.
132. 1. Epidemiology and Global Health
     2. Medicine

     Primaquine in glucose-6-phosphate dehydrogenase deficiency: an adaptive pharmacometric assessment of ascending dose regimens in healthy volunteers

     Sasithon Pukrittayakamee, Podjanee Jittamala ... Nicholas J White

     A full radical curative dose of primaquine can be given to fully glucose-6-phosphate dehydrogenase-deficient males safely using an ascending dose regimen.
133. 1. Immunology and Inflammation
     2. Medicine

     β-Carotene accelerates the resolution of atherosclerosis in mice

     Ivan Pinos, Johana Coronel ... Jaume Amengual

     Vitamin A formation from β-carotene promotes an anti-inflammatory environment and remodeling of atherosclerotic lesions during the healing of atherosclerosis.
134. 1. Neuroscience

     Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing

     Aixin Zhang, Lei Jin ... Xiaoyin Chen

     Barcoded rabies virus tracing combined with single-cell RNAseq and in situ sequencing achieves high-throughput retrograde projection mapping and synaptic connectivity mapping at cellular resolution.
135. 1. Medicine
     2. Neuroscience

     Depletion of SMN protein in mesenchymal progenitors impairs the development of bone and neuromuscular junction in spinal muscular atrophy

     Sang-Hyeon Hann, Seon-Yong Kim ... Young-Yun Kong

     Fibro-adipogenic progenitors in skeletal muscle contribute to the neuromuscular pathogenesis of spinal muscular atrophy, and depletion of SMN in chondrocytes reduces local IGF sigaling in growth plate.
136. 1. Cell Biology

     Cell Adhesion-Dependent Biphasic Axon Outgrowth Elucidated by Femtosecond Laser Impulse

     Sohei Yamada, Kentarou Baba ... Yoichiroh Hosokawa
137. 1. Genetics and Genomics
     2. Immunology and Inflammation

     Inhibition of the UFD-1-NPL-4 complex triggers an inflammation-like response in Caenorhabditis elegans

     Rajneesh Rao, Alejandro Aballay, Jogender Singh
138. 1. Neuroscience

     Visual homogeneity computations in the brain enable solving property-based visual tasks

     Georgin Jacob, Raghavendrarao T Pramod, Arun SP
139. 1. Medicine

     PSTPIP2 ameliorates aristolochic acid nephropathy by suppressing interleukin-19-mediated neutrophil extracellular trap formation

     Changlin Du, Chuanting Xu ... Taotao Ma

     PSTPIP2 reduced IL-19 secretion by inhibiting activation of the NF-κB pathway in renal tubular epithelial cells (RTECs), reducing the generation of neutrophil extracellular trap, which can participate in both aristolochic acid I-induced renal injury and apoptosis in RTECs.
140. 1. Biochemistry and Chemical Biology
     2. Developmental Biology

     The differential regulation of placenta trophoblast bisphosphoglycerate mutase in fetal growth restriction: preclinical study in mice and observational histological study of human placenta

     Sima Stroganov, Talia Harris ... Michal Neeman

     Expression of Bisphosphoglycerate mutase, a key enzyme affecting the release of oxygen from hemoglobin, is augmented in the murine placenta challenged by gestational hypoxia in mice while its expression is attenuated in placenta of human FGR.
141. 1. Chromosomes and Gene Expression
     2. Genetics and Genomics

     Identification of 1600 replication origins in S. cerevisiae

     Eric J Foss, Carmina Lichauco ... Antonio Bedalov

     Replication origins in yeast are more widespread than previously believed.
142. 1. Chromosomes and Gene Expression
     2. Genetics and Genomics

     Activity of MukBEF for chromosome management in E. coli and its inhibition by MatP

     Mohammed Seba, Frederic Boccard, Stéphane Duigou

     MukBEF selectively loads onto newly replicated DNA, and MatP prevents MukBEF activity, correlating with matS sites, likely due to MatP-mediated unloading.
143. 1. Developmental Biology

     Rtf1-dependent transcriptional pausing regulates cardiogenesis

     Adam D. Langenbacher, Fei Lu ... Jau-Nian Chen
144. 1. Neuroscience

     Mesoscale functional organization and connectivity of color, disparity, and naturalistic texture in human second visual area

     Hailin Ai, Weiru Lin ... Peng Zhang
145. 1. Biochemistry and Chemical Biology

     Daptomycin forms a stable complex with phosphatidylglycerol for selective uptake to bacterial membrane

     Pragyansree Machhua, Vignesh Gopalakrishnan Unnithan ... Zhihong Guo
146. 1. Developmental Biology

     ESCRT-III-dependent adhesive and mechanical changes are triggered by a mechanism detecting alteration of septate junction integrity in Drosophila epithelial cells

     Thomas Esmangart de Bournonville, Mariusz K Jaglarz ... Roland Le Borgne

     In response to disruption of barrier functions mediated by septate junctions, Drosophila epithelial cells restrict endosomal degradation of transmembrane cell adhesion proteins to promote their recycling in order to maintain tissue integrity.
147. 1. Computational and Systems Biology
     2. Immunology and Inflammation

     A kinase to cytokine explorer to identify molecular regulators and potential therapeutic opportunities

     Marina Chan, Yuqi Kang ... Taranjit S Gujral

     KinCytE is a web-based platform that explores kinase-cytokine-driven signaling and its relevance to understanding and treating diseases linked to disruptions in these pathways.
148. 1. Immunology and Inflammation

     Itaconate stabilizes CPT1a to enhance lipid utilization during inflammation

     Rabina Mainali, Nancy Buechler ... Matthew A Quinn

     Proteomic-based discovery of a novel mechanism of action affording anti-steatotic properties of itaconate through stabilization of fatty acid oxidation enzyme protein abundance.
149. 1. Neuroscience

     Chemo- and optogenetic activation of hypothalamic Foxb1-expressing neurons and their terminal endings in the rostral-dorsolateral PAG leads to tachypnea, bradycardia, and immobility

     Reto B Cola, Diana M Roccaro-Waldmeyer ... Marco R Celio

     Foxb1-expressing hypothalamic neurons in the parvafox nucleus and the dorsal premammillary nucleus both contribute to behavioral and physiological components associated with defensive behavior.
150. 1. Immunology and Inflammation

     Activation of the P2RX7/IL-18 pathway in immune cells attenuates lung fibrosis

     Serena Janho dit Hreich, Thierry Juhel ... Valerie Vouret-Craviari

     The use of a small activator of P2RX7 highlights the importance of the P2RX7 pathway to enhance the antifibrotic properties of lung immune cells.