June 2019

Cover articles

    1. Developmental Biology
    2. Evolutionary Biology

    Limb evolution in cephalopods

    Oscar A Tarazona, Davys H Lopez ... Martin J Cohn
    1. Microbiology and Infectious Disease

    Insights into influenza A viruses

    Jason S Long, Alewo Idoko-Akoh ... Wendy Barclay
    1. Ecology
    2. Evolutionary Biology

    How wasps kill microbes with nitric oxide

    Erhard Strohm, Gudrun Herzner ... Tobias Engl
    1. Developmental Biology

    Misr2+ mesenchymal cells and infertility

    Hatice Duygu Saatcioglu, Motohiro Kano ... David Pépin

Highlights controls:

Research articles

    1. Neuroscience

    The manifold structure of limb coordination in walking Drosophila

    Brian D DeAngelis, Jacob A Zavatone-Veth, Damon A Clark
    During walking and turning, the fruit fly Drosophila uses variable limb coordination patterns, which exist on a low-dimensional, continuous manifold.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Cryo-EM structure of the rhodopsin-Gαi-βγ complex reveals binding of the rhodopsin C-terminal tail to the gβ subunit

    Ching-Ju Tsai, Jacopo Marino ... Gebhard Schertler
    The structure of a light-sensitive G protein-coupled receptor in complex with a Gi-protein heterotrimer provides a structural foundation for the role of the receptor C-terminal tail in scaffolding and signaling.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Interactions between a subset of substrate side chains and AAA+ motor pore loops determine grip during protein unfolding

    Tristan A Bell, Tania A Baker, Robert T Sauer
    The AAA+ protein unfolding motor ClpX grips substrates with the uppermost part of its substrate-binding pore, and requires interactions with hydrophobic amino acid side chains to operate with optimal efficiency.
    1. Computational and Systems Biology
    2. Neuroscience

    Front-end Weber-Fechner gain control enhances the fidelity of combinatorial odor coding

    Nirag Kadakia, Thierry Emonet
    In multi-channel sensory systems, gain adaptation can help maintain not only coding capacity across changes in signal intensity, but also combinatorial representations of odor identity.
    1. Cell Biology

    A two-step mechanism for the inactivation of microtubule organizing center function at the centrosome

    Jérémy Magescas, Jenny C Zonka, Jessica L Feldman
    The microtubule organizing potential of the centrosome is inactivated in a stepwise process through phosphatase activity and mechanical disruption to remove an aging matrix of proteins.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structural and mutational analysis of the ribosome-arresting human XBP1u

    Vivekanandan Shanmuganathan, Nina Schiller ... Roland Beckmann
    Two integrated approaches shed light on how XBP1 arrest peptide induces intermediate level of translational pausing and identify hotspot positions to make it stronger.
    1. Neuroscience

    Shared neural underpinnings of multisensory integration and trial-by-trial perceptual recalibration in humans

    Hame Park, Christoph Kayser
    Facing discrepancies in the sensory environment, multisensory information is combined in the medial superior parietal cortex to guide immediate judgements and to also adjust subsequent unisensory perception.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity

    Mohammed Jamshad, Timothy J Knowles ... Damon Huber
    The interaction of SecA with its substrate proteins is regulated by its evolutionarily conserved C-terminal tail, which autoinhibits SecA unless SecA binds to the ribosome.
    1. Microbiology and Infectious Disease

    Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production

    MengJie Hu, Keith E Schulze ... David A Jans
    RSV's unique ability to co-opt host cell mitochondria to facilitate viral infection reveals the RSV-mitochondrial interface as a viable target for therapeutic intervention.
    1. Cell Biology
    2. Developmental Biology

    Non-canonical Wnt signaling regulates junctional mechanocoupling during angiogenic collective cell migration

    Joana R Carvalho, Isabela C Fortunato ... Claudio A Franco
    Analysis of axial polarity distributions shows that Wnt5a regulates collective cell migration in vivo by stabilizing vinculin at adherens junctions and fine-tuning mechanocoupling between neighbouring cells.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Electrostatic lateral interactions drive ESCRT-III heteropolymer assembly

    Sudeep Banjade, Shaogeng Tang ... Scott D Emr
    ESCRT-III heteropolymers utilize non-specific lateral electrostatic interactions to recognize one another, which may enable the polymers to slide along one another and adapt to different curvatures.
    1. Immunology and Inflammation

    Response to comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'

    Christina Hertel, Dmytro Fishman ... Adrian Hayday
    We are writing to reply to the comment by Landegren et al., 2019 about our study (Meyer et al., 2016) on disease-ameliorating autoantibodies.
    1. Immunology and Inflammation

    Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'

    Nils Landegren, Lindsey B Rosen ... Olle Kämpe
    We are writing to comment on the study by Meyer et al., 2016 on disease-ameliorating autoantibodies.
    1. Cell Biology
    2. Physics of Living Systems

    Metabolic constraints drive self-organization of specialized cell groups

    Sriram Varahan, Adhish Walvekar ... Sunil Laxman
    In a developing yeast colony, cells go from homogeneous states to spatially organized, specialized metabolic states, and the new metabolic states depend on resources produced by the original state.
    1. Neuroscience

    Imaging neuropeptide release at synapses with a genetically engineered reporter

    Keke Ding, Yifu Han ... David J Anderson
    A series of genetically-encoded fluorescent reporters that allow imaging of neuropeptide release in vivo, with sub-second temporal and nerve terminal-level spatial resolution are developed.
    1. Developmental Biology

    Neural crest-specific deletion of Rbfox2 in mice leads to craniofacial abnormalities including cleft palate

    Dasan Mary Cibi, Masum M Mia ... Manvendra K Singh
    The identification of the splicing code and all the required components of alternative splicing will be crucial for a comprehensive understanding of this process in the neural crest cell biology.
    1. Developmental Biology

    Fetal and trophoblast PI3K p110α have distinct roles in regulating resource supply to the growing fetus in mice

    Jorge López-Tello, Vicente Pérez-García ... Amanda N Sferruzzi-Perri
    Fetus and trophoblast interplay to regulate fetal nutrient supply and, ultimately, affect healthy growth.
    1. Immunology and Inflammation

    Circulating T cell-monocyte complexes are markers of immune perturbations

    Julie G Burel, Mikhail Pomaznoy ... Bjoern Peters
    Human blood contains T cell-monocyte complexes which are not technical artefacts but reflect true in vivo immune cell interactions.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Unified single-cell analysis of testis gene regulation and pathology in five mouse strains

    Min Jung, Daniel Wells ... Donald F Conrad
    A statistical method for summarizing single-cell gene expression data identifies normal and disease-specific transcriptional programs from an atlas of 57,600 cells.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay

    Jirka Peschek, Peter Walter
    Interconnected RNA processing mechanisms ensure the fidelity of non-conventional mRNA splicing during the unfolded protein response.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA

    Sasha A Langley, Karen H Miga ... Charles H Langley
    Genomic polymorphism across centromeric regions of humans is organized into large-scale haplotypes with great diversity, including entire Neanderthal centromeres.
    1. Developmental Biology

    Hemodynamic-mediated endocardial signaling controls in vivo myocardial reprogramming

    Manuel Gálvez-Santisteban, Danni Chen ... Neil C Chi
    The heart is able to sense and adaptively respond to environmental changes due to cardiac injury through flow-mediated mechanisms that regulate cardiomyocyte reprogramming and regeneration.
    1. Evolutionary Biology
    2. Physics of Living Systems

    Elastic instability during branchial ectoderm development causes folding of the Chlamydosaurus erectile frill

    Sophie A Montandon, Anamarija Fofonjka, Michel C Milinkovitch
    Robust wrinkling pattern of the frilled dragon’s spectacular erectile ruff emerges from an elastic instability during homogeneous growth of the embryonic neck fold frustrated by its attachment to adjacent tissues.
    1. Cell Biology
    2. Neuroscience

    Frontotemporal dementia mutant Tau promotes aberrant Fyn nanoclustering in hippocampal dendritic spines

    Pranesh Padmanabhan, Ramón Martínez-Mármol ... Frédéric A Meunier
    Super-resolution imaging reveals that the microtubule-associated protein Tau regulates the Fyn kinase organisation in dendrites, and that the frontotemporal dementia mutant Tau promotes aberrant Fyn clustering, potentially leading to synaptic dysfunction.
    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Massive antibody discovery used to probe structure–function relationships of the essential outer membrane protein LptD

    Kelly M Storek, Joyce Chan ... Steven T Rutherford
    Dispensable loops shield the functionally-important extracellular loops of the essential Gram-negative bacterial outer membrane protein LptD from antibody interference.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Rhodoquinone biosynthesis in C. elegans requires precursors generated by the kynurenine pathway

    Samantha Del Borrello, Margot Lautens ... Andrew G Fraser
    Parasitic helminths infect over a billion humans and use unusual anaerobic metabolism that needs a rare electron carrier, Rhodoquinone (RQ), whose synthesis requires the kynurenine pathway of tryptophan degradation.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Improved CUT&RUN chromatin profiling tools

    Michael P Meers, Terri D Bryson ... Steven Henikoff
    Enhancements to the CUT&RUN antibody-targeted nuclease strategy for chromatin profiling include an improved affinity-cleavage fusion protein and digestion protocol, and a simplified calibration strategy.
    1. Neuroscience

    Active information maintenance in working memory by a sensory cortex

    Xiaoxing Zhang, Wenjun Yan ... Chengyu T Li
    Delay-period activity of anterior piriform cortex is important for working memory tasks requiring active maintenance and encodes the maintained information.
    1. Developmental Biology

    Glycosylphosphatidylinositol biosynthesis and remodeling are required for neural tube closure, heart development, and cranial neural crest cell survival

    Marshall Lukacs, Tia Roberts ... Rolf W Stottmann
    Anchoring of proteins to the cell membrane through the glycosylphosphatidylinositol (GPI) anchor is critical for the survival of the cells that will give rise to the brain and face.
    1. Structural Biology and Molecular Biophysics

    Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP

    Mufeng Li, Yao Wang ... Kenton Jon Swartz
    Structural, computational and functional approaches reveal the role of an extended acidic chamber near the nucleotide binding site in activation of P2X3 receptor channels by divalent-bound ATP.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    An elusive electron shuttle from a facultative anaerobe

    Emily Mevers, Lin Su ... Jon Clardy
    The identification of ACNQ as an extracellular electron shuttle solves a longstanding problem in bacterial physiology and provides new tool for bioenergy development.
    1. Ecology
    2. Microbiology and Infectious Disease

    Light-dependent single-cell heterogeneity in the chloroplast redox state regulates cell fate in a marine diatom

    Avia Mizrachi, Shiri Graff van Creveld ... Assaf Vardi
    Single-cell analysis of the chloroplast redox response to high light and oxidative stress revealed light-dependent heterogeneity, and was linked to cell fate determination within isogenic diatom populations.
    1. Neuroscience

    Impact of precisely-timed inhibition of gustatory cortex on taste behavior depends on single-trial ensemble dynamics

    Narendra Mukherjee, Joseph Wachutka, Donald B Katz
    Primary taste cortex does far more than code tastes by turning taste codes into motor commands via population dynamics.
    1. Neuroscience

    Exercise-induced enhancement of synaptic function triggered by the inverse BAR protein, Mtss1L

    Christina Chatzi, Yingyu Zhang ... Gary L Westbrook
    Single episodes of voluntary exercise induced a functional increase in hippocampal synapses mediated by activity-dependent expression of the BAR protein Mtss1L, acting as a novel early effector of synapse formation.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Monitoring site-specific conformational changes in real-time reveals a misfolding mechanism of the prion protein

    Ishita Sengupta, Jayant Udgaonkar
    Multi-site FRET measurements of moPrP oligomerization at low pH indicate that major conformational changes take place as monomers reversibly transform into large oligomers, which subsequently disassemble reversibly into small oligomers.
    1. Developmental Biology

    Single-cell sequencing of neonatal uterus reveals an Misr2+ endometrial progenitor indispensable for fertility

    Hatice Duygu Saatcioglu, Motohiro Kano ... David Pépin
    Single-cell RNA sequencing of neonatal uterus revealed an Misr2+ endometrial stromal progenitor whose inhibition by ectopic administration of MIS caused uterine hypoplasia and infertility in adulthood.
    1. Neuroscience

    optoPAD, a closed-loop optogenetics system to study the circuit basis of feeding behaviors

    José-Maria Moreira, Pavel M Itskov ... Carlos Ribeiro
    The optoPAD system combines real-time behavioral analysis with optogenetic manipulations to study how animals adapt to dynamic gustatory environments and to identify the circuit basis of feeding.
    1. Microbiology and Infectious Disease

    A dedicated diribonuclease resolves a key bottleneck for the terminal step of RNA degradation

    Soo-Kyoung Kim, Justin D Lormand ... Vincent T Lee
    RNA degradation is completed through specific intermediates, such as diribonucleotides, which must be removed from the cells by a specific enzyme.
    1. Immunology and Inflammation

    The quantity of CD40 signaling determines the differentiation of B cells into functionally distinct memory cell subsets

    Takuya Koike, Koshi Harada ... Daisuke Kitamura
    Unveiling a mechanism for the fate decision of B-cell differentiation into two functionally distinct memory B cell subsets.
    1. Chromosomes and Gene Expression

    Scc2 counteracts a Wapl-independent mechanism that releases cohesin from chromosomes during G1

    Madhusudhan Srinivasan, Naomi J Petela ... Kim A Nasmyth
    In G1 cells, Scc2 loads and maintains cohesin on chromosomes by counteracting a Wapl-independent releasing activity, which is neutralized in S phase by CDK1.
    1. Developmental Biology
    2. Neuroscience

    Functional divergence of Plexin B structural motifs in distinct steps of Drosophila olfactory circuit assembly

    Ricardo Guajardo, David J Luginbuhl ... Jiefu Li
    Systematic in vivo analysis reveals the divergent engagement of Plexin B structural motifs in distinct neurodevelopmental processes and a regulatory role of convertase cleavage in Plexin B signaling.
    1. Developmental Biology
    2. Neuroscience

    Molecular determinants in Frizzled, Reck, and Wnt7a for ligand-specific signaling in neurovascular development

    Chris Cho, Yanshu Wang ... Jeremy Nathans
    Molecular dissection of Frizzled, Reck, and Wnt7a provides critical insight into the long-standing question of ligand-receptor specificity in the field of Wnt signaling.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

    Jeehae Park, Javier Estrada ... Angela H DePace
    The sharp expression pattern driven by a classic, simple animal enhancer is determined by multiple molecular mechanisms, not only cooperative binding of the activating transcription factor as was previously thought.
    1. Neuroscience

    Voluntary and involuntary contributions to perceptually guided saccadic choices resolved with millisecond precision

    Emilio Salinas, Benjamin R Steinberg ... Terrence R Stanford
    Looking away from a salient visual stimulus pits the reflexive urge to look toward it against the voluntary intention not to, and this conflict is resolved within tens of milliseconds.
    1. Chromosomes and Gene Expression

    piRNA-guided co-transcriptional silencing coopts nuclear export factors

    Martin H Fabry, Filippo Ciabrelli ... Benjamin Czech
    A member of the Drosophila Nuclear Export Factor (Nxf) family, Nxf2, forms part of the piRNA-dependent co-transcriptional silencing complex and is essential for transposon repression in fly ovaries.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Krystel El Hage, Florent Hédin ... Martin Karplus
    We are writing to respond to the comment by Gapsys and de Groot, 2019 on our article about molecular dynamics simulations of human hemoglobin (El Hage et al., 2018).
    1. Genetics and Genomics

    The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay

    Karole N D'Orazio, Colin Chih-Chien Wu ... Rachel Green
    Cue2 is an endonuclease that cleaves mRNA in the A site of the lagging ribosome upon ribosome collision events.
    1. Structural Biology and Molecular Biophysics

    Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Vytautas Gapsys, Bert L de Groot
    We are writing to comment on the article by El Hage et al., 2018 about molecular dynamics simulations of human hemoglobin.
    1. Neuroscience

    A connectional hub in the rostral anterior cingulate cortex links areas of emotion and cognitive control

    Wei Tang, Saad Jbabdi ... Suzanne N Haber
    A hub in the rostral anterior cingulate cortex receives unusually high and functionally diverse inputs, providing a biological interface between motivation, incentive based learning, and decision making.
    1. Microbiology and Infectious Disease

    Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

    Emma J Gehrke, Xiafei Zhang ... Marie A Elliot
    In Streptomyces, the nucleoid-associated protein Lsr2 functions as a xenogenic silencer of foreign genes, and as a metabolic gatekeeper, repressing expression of both cryptic and well-studied specialized metabolic biosynthetic clusters.
    1. Neuroscience

    Inhibitory muscarinic acetylcholine receptors enhance aversive olfactory learning in adult Drosophila

    Noa Bielopolski, Hoger Amin ... Moshe Parnas
    Muscarinic acetylcholine receptor type A in adult Drosophila inhibits Kenyon cells, and is required for aversive olfactory learning and learning-associated synaptic depression between Kenyon cells and their output neurons.
    1. Cancer Biology

    Replication Study: Wnt activity defines colon cancer stem cells and is regulated by the microenvironment

    Anthony Essex, Javier Pineda ... Reproducibility Project: Cancer Biology
    Editors' Summary: This Replication Study has reproduced important parts of the original paper.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

    Evan T Saitta, Renxing Liang ... Tullis Onstott
    Subterranean fossil bone hosts a living microbiome different from the surrounding sediment without evidence of original protein preservation.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

    Jean Paul Armache, Nathan Gamarra ... Yifan Cheng
    Cryo-EM structures capture different conformational states of chromatin remodeler-nucleosome complexes.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    A FRET sensor of C-terminal movement reveals VRAC activation by plasma membrane DAG signaling rather than ionic strength

    Benjamin König, Yuchen Hao ... Tobias Stauber
    VRAC activation, observed with a FRET sensor of intracellular LRRC8-domains movement during gating and by fluorometry, requires plasma membrane localization and diacylglycerol signaling, but is independent of intracellular ionic strength.
    1. Ecology
    2. Evolutionary Biology

    Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation

    Anna-Liisa Laine, Benoit Barrès ... Jukka P Siren
    In natural pathogen populations opportunities for sexual outcrossing vary, leading to spatial variation in genetic diversity and between-season survival.
    1. Medicine
    2. Neuroscience

    Family history of Alzheimer’s disease alters cognition and is modified by medical and genetic factors

    Joshua S Talboom, Asta Håberg ... Matthew J Huentelman
    An internet-based cohort study of paired associate learning shows that a first-degree family history of dementia is associated with lowered performance, an effect modified by apolipoprotein E genotype and diabetes.
    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Structure of the Helicobacter pylori Cag type IV secretion system

    Jeong Min Chung, Michael J Sheedlo ... Melanie D Ohi
    The Helicobacter pylori Cag T4SS has unique structural features, including unexpected symmetry mismatch between sub-complexes, with implications for protein secretion.
    1. Developmental Biology
    2. Evolutionary Biology

    Evolution of limb development in cephalopod mollusks

    Oscar A Tarazona, Davys H Lopez ... Martin J Cohn
    Cuttlefish embryos reveal that cephalopod mollusks evolved specialized arms and tentacles by activating the same genetic circuits that control development of limbs in arthropods and vertebrates.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Absolute quantification of cohesin, CTCF and their regulators in human cells

    Johann Holzmann, Antonio Z Politi ... Jan-Michael Peters
    Absolute quantification of cohesin, CTCF, NIPBL, WAPL and sororin in HeLa cells implies that some genomic cohesin and CTCF enrichment sites are unoccupied at any one time.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research

    Franziska Mohring, Melissa Natalie Hart ... Robert William Moon
    Optimised genome editing in P. knowlesi enables transgenic expression of a lead P. vivax vaccine candidate, revealing roles in host cell tropisms and providing tools for scalable vaccine efficacy testing.
    1. Cell Biology
    2. Neuroscience

    Pregnancy-associated plasma protein-aa supports hair cell survival by regulating mitochondrial function

    Mroj Alassaf, Emily C Daykin ... Marc A Wolman
    Hair cell survival and mitochondrial function is supported by an extracellular stimulator of IGF1 signaling, the protease pregnancy-associated plasma protein-aa.
    1. Neuroscience

    Acetic acid activates distinct taste pathways in Drosophila to elicit opposing, state-dependent feeding responses

    Anita V Devineni, Bei Sun ... Richard Axel
    A single taste input, acetic acid, elicits opposing behavioral outputs depending on a fly's hunger state.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Conformational switches control early maturation of the eukaryotic small ribosomal subunit

    Mirjam Hunziker, Jonas Barandun ... Sebastian Klinge
    Mass spectrometry analysis of purified pre-ribosomal RNAs shows that stable ribosomal RNA domains independently recruit assembly factors, and the cryo-EM structure of the 5' ETS ribonucleoprotein reveals regulatory conformational switches.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Cas9+ conditionally-immortalized macrophages as a tool for bacterial pathogenesis and beyond

    Allison W Roberts, Lauren M Popov ... Jeffery S Cox
    Combination of stem cell engineering and CRISPR technologies created a facile method to genetically manipulate macrophages, a multifunctional cell type that plays critical roles in immunity, cancer, and tissue homeostasis.
    1. Structural Biology and Molecular Biophysics

    Cystic fibrosis drug ivacaftor stimulates CFTR channels at picomolar concentrations

    László Csanády, Beáta Töröcsik
    Aqueous solubility of cystic fibrosis drug ivacaftor is ~200-fold lower, whereas the potency of its stimulatory effect on the CFTR channel is >100-fold higher, than reported, and is fully reversible.
    1. Physics of Living Systems

    Liquid-crystal organization of liver tissue

    Hernán Morales-Navarrete, Hidenori Nonaka ... Marino Zerial
    Bidirectional communication between hepatocytes and sinusoids governs long-range liquid-crystal order of hepatocyte polarity.
    1. Neuroscience

    Anatomical and physiological foundations of cerebello-hippocampal interaction

    Thomas Charles Watson, Pauline Obiang ... Laure Rondi-Reig
    Anatomical tracing and physiological recordings reveal neuronal pathways through which the cerebellum may influence hippocampal activity.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Determining cellular CTCF and cohesin abundances to constrain 3D genome models

    Claudia Cattoglio, Iryna Pustova ... Anders S Hansen
    Absolute quantification of CTCF and cohesin reveals quantitative constraints on 3D genome organization and illuminates the molecular architecture of the cohesin complex.
    1. Neuroscience

    Coding strategies in the otolith system differ for translational head motion vs. static orientation relative to gravity

    Mohsen Jamali, Jerome Carriot ... Kathleen E Cullen
    Through different coding strategies, irregular and regular otolith afferents preferentially encode translational self-motion and changes in static head orientation relative to gravity.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Protein quality control in the nucleolus safeguards recovery of epigenetic regulators after heat shock

    Maria Azkanaz, Aida Rodríguez López ... Vincent van den Boom
    Heat shock induces relocalization of epigenetic modifiers to the nucleolus, which acts as a dedicated protein quality control center that is indispensable for recovery of epigenetic regulators and epigenetic modifications.
    1. Computational and Systems Biology

    Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

    David B Bernstein, Floyd E Dewhirst, Daniel Segrè
    A novel metabolic network analysis method enables large-scale computational predictions of biosynthetic capabilities across the human oral microbiome, revealing a unique cluster of fastidious microorganisms and potential metabolic interdependencies.
    1. Cell Biology
    2. Plant Biology

    The GluTR-binding protein is the heme-binding factor for feedback control of glutamyl-tRNA reductase

    Andreas S Richter, Claudia Banse, Bernhard Grimm
    Heme-dependent feedback inhibition of rate-limiting ALA-synthesis of plant tetrapyrrole biosynthesis depends on binding of heme to glutamyl-tRNA reductase-binding protein.
    1. Cell Biology
    2. Developmental Biology

    Vps8 overexpression inhibits HOPS-dependent trafficking routes by outcompeting Vps41/Lt

    Péter Lőrincz, Lili Anna Kenéz ... Gábor Juhász
    Recruitment of HOPS tethering complex to target membranes to promote vesicle fusions requires proper complex assembly and specific small GTPases, and HOPS is not transformed from the related miniCORVET complex.
    1. Structural Biology and Molecular Biophysics

    The structure of the yeast Ctf3 complex

    Stephen M Hinshaw, Andrew N Dates, Stephen C Harrison
    The cryo-EM structure of the yeast Ctf3 complex enables near-atomic modeling of most Ctf19c/CCAN factors and their interactions.
    1. Neuroscience

    Sonic hedgehog signaling in astrocytes mediates cell type-specific synaptic organization

    Steven A Hill, Andrew S Blaeser ... A Denise R Garcia
    Astrocytes modulate synaptic remodeling of developing circuits in a cell type-specific manner, with long lasting deficits in synaptic plasticity.
    1. Neuroscience

    The dorsomedial prefrontal cortex computes task-invariant relative subjective value for self and other

    Matthew Piva, Kayla Velnoskey ... Steve WC Chang
    Activity in the dorsomedial prefrontal cortex encodes relative subjective value in a common neural code across decision-making for self and other and across tasks with divergent cognitive requirements.
    1. Neuroscience

    Multiple mechanisms link prestimulus neural oscillations to sensory responses

    Luca Iemi, Niko A Busch ... Vadim V Nikulin
    Neural oscillations prior to a stimulus modulate the strength of early and late responses in opposite directions via distinct mechanisms.
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Epithelial geometry regulates spindle orientation and progenitor fate during formation of the mammalian epidermis

    Kimberly Box, Bradley W Joyce, Danelle Devenport
    Early in mammalian epidermal development, basal epidermal progenitor cells utilize packing and three-dimensional geometry, rather than cortical polarity cues, to inform division orientation and progenitor cell fate.
    1. Ecology

    Wind prevents cliff-breeding birds from accessing nests through loss of flight control

    Emily Shepard, Emma-Louise Cole ... Andrew Ross
    Even moderate winds cause auks to abort landing attempts at nest-sites, and as a result, wind characteristics may affect where these, and other seabirds, choose to breed.
    1. Developmental Biology
    2. Neuroscience

    A counter gradient of Activin A and follistatin instructs the timing of hair cell differentiation in the murine cochlea

    Meenakshi Prajapati-DiNubila, Ana Benito-Gonzalez ... Angelika Doetzlhofer
    Opposing gradients of activin A and follistatin within the spiral shaped mammalian cochlea instruct the graded pattern of mechano-sensory hair cell formation.
    1. Biochemistry and Chemical Biology
    2. Neuroscience

    Mouse TRPA1 function and membrane localization are modulated by direct interactions with cholesterol

    Justyna B Startek, Brett Boonen ... Karel Talavera
    The activation and membrane localization of the broadly-tuned noxious chemosensory cation channel TRPA1 are regulated by direct interactions with cholesterol via CRAC motifs in transmembane segments 2 and 4.
    1. Ecology
    2. Evolutionary Biology

    Nitric oxide radicals are emitted by wasp eggs to kill mold fungi

    Erhard Strohm, Gudrun Herzner ... Tobias Engl
    To protect their food and themselves against detrimental mould fungi, the eggs of a wasp species synthesize and emit remarkable amounts of gaseous nitrogen oxides that are highly effective antimicrobials.
    1. Cell Biology

    Pericentrin-mediated SAS-6 recruitment promotes centriole assembly

    Daisuke Ito, Sihem Zitouni ... Mónica Bettencourt-Dias
    Newly discovered interaction between fission yeast SPB and animal centriole components reveals that pericentrin not only functions as a microtubule-nucleator, but also promotes centriole assembly in animals.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases

    Han Han, James M Fulcher ... Christopher P Hill
    Structural and biochemical studies indicate that AAA+ ATPase employ a general mechanism to translocate a variety of substrates, including extended polypeptides, hairpins, crosslinked chains, and chains conjugated to other molecules.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs

    Leah Guthrie, Sarah Wolfson, Libusha Kelly
    A network of the gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs and supports the generation of mechanistic hypotheses of microbiome metabolic phenotypes that shape human biology.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Ion counting demonstrates a high electrostatic field generated by the nucleosome

    Magdalena Gebala, Stephanie L Johnson ... Dan Herschlag
    First experimental studies on the ion atmosphere around a nucleosome provide a quantitative analysis of the molecule's electrostatic properties.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    The interplay at the replisome mitigates the impact of oxidative damage on the genetic integrity of hyperthermophilic Archaea

    Tom Killelea, Adeline Palud ... Ghislaine Henneke
    An investigation into 8-oxodeoxguanosine bypass by archaeal DNA polymerases.
    1. Neuroscience

    Transitioning between preparatory and precisely sequenced neuronal activity in production of a skilled behavior

    Vamsi K Daliparthi, Ryosuke O Tachibana ... Todd F Roberts
    Precisely sequenced patterns of neuronal activity associated with the production of a skilled behavior begin and end as part of orchestrated activity across functionally diverse populations of cortical premotor neurons.
    1. Cell Biology

    Proinsulin misfolding is an early event in the progression to type 2 diabetes

    Anoop Arunagiri, Leena Haataja ... Peter Arvan
    Proinsulin misfolding, an established cause of diabetes in patients with INS gene mutations, is now observed in normal human pancreatic islets, and rodents with genetic predisposition to type 2 diabetes.
    1. Neuroscience

    Sweet neurons inhibit texture discrimination by signaling TMC-expressing mechanosensitive neurons in Drosophila

    Shun-Fan Wu, Ya-Long Ja ... Chung-Hui Yang
    Drosophila use distinct sensory mechanisms to detect and integrate the same tactile and taste information in two decision-making tasks that serve two different purposes.
    1. Cell Biology

    PDIA1/P4HB is required for efficient proinsulin maturation and ß cell health in response to diet induced obesity

    Insook Jang, Anita Pottekat ... Randal J Kaufman
    The major protein disulfide isomerase family member, PDIA1, is essential in beta cells of mice fed a high-fat diet to maintain glucose homeostasis, proinsulin maturation and organelle integrity.
    1. Developmental Biology
    2. Neuroscience

    Robo2 regulates synaptic oxytocin content by affecting actin dynamics

    Savani Anbalagan, Janna Blechman ... Gil Levkowitz
    Real-time monitoring of oxytocin-loaded vesicles and synaptic actin dynamics in zebrafish reveal that Slit3-Robo2-Cdc42 signalling maintains steady-state levels of mature oxytocin neuropeptide readily primed to be secreted upon physiological demand.
    1. Microbiology and Infectious Disease

    Heterogeneity in surface sensing suggests a division of labor in Pseudomonas aeruginosa populations

    Catherine R Armbruster, Calvin K Lee ... Matthew R Parsek
    Subpopulations of polysaccharide producer and surface explorer cells play specialized roles in early Pseudomonas aeruginosa biofilm formation.
    1. Neuroscience

    'Online' integration of sensory and fear memories in the rat medial temporal lobe

    Francesca S Wong, R Fred Westbrook, Nathan M Holmes
    Elements of a past sensory memory are incorporated into a new fear memory, and in this way, a stimulus never paired with danger becomes frightening.
    1. Neuroscience

    Short-term synaptic dynamics control the activity phase of neurons in an oscillatory network

    Diana Martinez, Haroon Anwar ... Farzan Nadim
    The phase of a neuron in an oscillatory network can remain independent of network frequency when synaptic input strength and peak phase are adjusted in a frequency-dependent manner.
    1. Neuroscience

    Maintenance of homeostatic plasticity at the Drosophila neuromuscular synapse requires continuous IP3-directed signaling

    Thomas D James, Danielle J Zwiefelhofer, C Andrew Frank
    Synapses employ distinct acute and chronic signaling processes in order to maintain physiologically appropriate levels of function.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Molecular organization and dynamics of the fusion protein Gc at the hantavirus surface

    Eduardo A Bignon, Amelina Albornoz ... Nicole D Tischler
    Hantavirus spikes are related laterally by 2-fold Gc contacts that can be disulfide-linked and display a temperature-dependent dynamic behavior at neutral pH, exposing and masking the Gc fusion loops.
    1. Developmental Biology
    2. Neuroscience

    Identification of compounds that rescue otic and myelination defects in the zebrafish adgrg6 (gpr126) mutant

    Elvira Diamantopoulou, Sarah Baxendale ... Tanya T Whitfield
    Results of a zebrafish whole-animal chemical screen for compounds that can rescue ear and myelination defects in an adhesion GPCR (Adgrg6/Gpr126) mutant.
    1. Neuroscience

    Glycolysis upregulation is neuroprotective as a compensatory mechanism in ALS

    Ernesto Manzo, Ileana Lorenzini ... Daniela C Zarnescu
    Degenerating motor neurons compensate for energetic deficits by upregulating glycolysis in flies and humans, with increased glucose availability improving locomotor function and lifespan in flies.
    1. Cell Biology

    Cooperation between tropomyosin and α-actinin inhibits fimbrin association with actin filament networks in fission yeast

    Jenna R Christensen, Kaitlin E Homa ... David R Kovar
    The contractile ring actin binding proteins tropomyosin Cdc8 and a-actinin Ain1 synergize to effectively compete with the endocytic actin patch protein fimbrin Fim1 for associating with F-actin networks.
    1. Physics of Living Systems
    2. Structural Biology and Molecular Biophysics

    Nanoresolution real-time 3D orbital tracking for studying mitochondrial trafficking in vertebrate axons in vivo

    Fabian Wehnekamp, Gabriela Plucińska ... Don C Lamb
    The ability to follow single objects in 3D in a living organism with high spatiotemporal resolution opens new possibilities for quantitative biophysical studies of complex systems in their physiological context.
    1. Biochemistry and Chemical Biology

    HDX-MS reveals structural determinants for RORγ hyperactivation by synthetic agonists

    Timothy S Strutzenberg, Ruben D Garcia-Ordonez ... Patrick R Griffin
    Unique methodology was used to generate a large HDX-MS dataset to inform ligand-mediated activation of RORγ, an approach that can be extended to other nuclear receptors with unresolved ligand-dependent activities.
    1. Neuroscience

    Ca2+ sensor synaptotagmin-1 mediates exocytosis in mammalian photoreceptors

    Justin J Grassmeyer, Asia L Cahill ... Wallace B Thoreson
    The vesicular Ca2+ sensor synaptotagmin-1 regulates both fast phasic and slow tonic glutamate release at ribbon synapses of rod and cone photoreceptor cells.
    1. Cell Biology

    Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins

    Verena Dederer, Anton Khmelinskii ... Marius K Lemberg
    The endoplasmic reticulum E3 ubiquitin ligase Doa10 and the mitochondrial AAA-ATPase Msp1 govern targeting fidelity of outer mitochondrial tail-anchored proteins by controlling cytoplasmic concentration and extracting mistargeted and orphan species.
    1. Cell Biology

    Reconstruction of Par-dependent polarity in apolar cells reveals a dynamic process of cortical polarization

    Kalyn Kono, Shigeki Yoshiura ... Fumio Matsuzaki
    Par-complex-dependent cell polarity can be cell-autonomously conferred to non-polar Drosophila S2 cells, unveiling temporal patterns toward the cortical localization of Par-complex aggregates that include a meshwork containing unit segments.
    1. Biochemistry and Chemical Biology

    The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation

    Mikael Holm, Chandra Sekhar Mandava ... Suparna Sanyal
    The antibiotic viomycin induces errors during initial codon selection by the ribosome by locking the monitoring bases in their active conformation.
    1. Microbiology and Infectious Disease

    CCL2 mobilizes ALIX to facilitate Gag-p6 mediated HIV-1 virion release

    David O Ajasin, Vasudev R Rao ... Vinayaka R Prasad
    Effect of CCL2 on HIV-1 replication is mediated by mobilization of ALIX from F-actin leading to enhanced virion release and improved fitness and this requires the Gag late motif, LYPX.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Conformational dynamics between transmembrane domains and allosteric modulation of a metabotropic glutamate receptor

    Vanessa A Gutzeit, Jordana Thibado ... Joshua Levitz
    Single molecule subunit counting, FRET and electrophysiology experiments reveal that metabotropic glutamate receptor subunits interact and rearrange at the level of the transmembrane domains in response to allosteric modulators.
    1. Biochemistry and Chemical Biology

    A toolkit for studying cell surface shedding of diverse transmembrane receptors

    Amanda N Hayward, Eric J Aird, Wendy R Gordon
    The modularity and unequivocal input/response of Notch signaling are harnessed to measure cell-surface shedding of diverse transmembrane receptors to identify new proteolytic switches and detect modulation of proteolysis by therapeutics.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Genome plasticity in Candida albicans is driven by long repeat sequences

    Robert T Todd, Tyler D Wikoff ... Anna Selmecki
    Previously uncharacterized long repeat sequences are associated with significant genome variation that can increase fitness and promote antifungal drug resistance in diverse isolates of Candida albicans.
    1. Computational and Systems Biology
    2. Developmental Biology

    Modularity, criticality, and evolvability of a developmental gene regulatory network

    Berta Verd, Nicholas AM Monk, Johannes Jaeger
    A new approach focusing on dynamic modularity helps overcome traditional challenges detecting modularity in complex adaptive systems.
    1. Developmental Biology
    2. Evolutionary Biology

    An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice

    João PL Castro, Michelle N Yancoskie ... Yingguang Frank Chan
    Genome sequencing of mice selected for longer limbs reveals that rapid selection response is due to both discrete loci and polygenic adaptation.
    1. Biochemistry and Chemical Biology

    GPIHBP1 expression in gliomas promotes utilization of lipoprotein-derived nutrients

    Xuchen Hu, Ken Matsumoto ... Haibo Jiang
    The expression of the lipoprotein lipase (LPL) transporter GPIHBP1 in glioma capillaries promotes the LPL-mediated processing of triglyceride-rich lipoproteins, thereby providing lipid nutrients for glioma cells.
    1. Neuroscience

    Post-decision processing in primate prefrontal cortex influences subsequent choices on an auditory decision-making task

    Joji Tsunada, Yale Cohen, Joshua I Gold
    A behavioral model, neuronal recordings, and electrical microstimulation reveal that the ventrolateral prefrontal cortex plays a causal role in evaluating prior decisions and biasing future decisions.
    1. Cancer Biology

    A four-DNA methylation biomarker is a superior predictor of survival of patients with cutaneous melanoma

    Wenna Guo, Liucun Zhu ... Jian-Qun Chen
    This four-DNA methylation signature demonstrates potential as a novel independent prognostic indicator for risk-stratifying patients with CM.
    1. Neuroscience

    Slow presynaptic mechanisms that mediate adaptation in the olfactory pathway of Drosophila

    Carlotta Martelli, André Fiala
    Slow presynaptic depression in olfactory receptor neurons rescales combinatorial odor representations in postsynaptic neurons and mediates the encoding of stimulus mean and variance.
    1. Neuroscience

    GABA neurons in the ventral tegmental area regulate non-rapid eye movement sleep in mice

    Srikanta Chowdhury, Takanori Matsubara ... Akihiro Yamanaka
    Functional identification of GABAergic neurons in the ventral tegmental area as a important neuronal subpopulation regulating non-rapid eye movement (NREM) sleep in mice.
    1. Microbiology and Infectious Disease

    Species specific differences in use of ANP32 proteins by influenza A virus

    Jason S Long, Alewo Idoko-Akoh ... Wendy Barclay
    Chicken ANP32A, and not chicken ANP32B, supports influenza polymerase activity and thus editing of this single gene may generate chickens that are resilient to influenza virus infection.
    1. Neuroscience

    Dissociating orexin-dependent and -independent functions of orexin neurons using novel Orexin-Flp knock-in mice

    Srikanta Chowdhury, Chi Jung Hung ... Akihiro Yamanaka
    Subtraction analysis using novel Orexin-Flp mice isolated physiological importance of orexin peptides.
    1. Developmental Biology

    Detailed analysis of chick optic fissure closure reveals Netrin-1 as an essential mediator of epithelial fusion

    Holly Hardy, James GD Prendergast ... Joe Rainger
    Chick optic fissure closure is a powerful new model system for epithelial fusion and has revealed Netrin-1 as a conserved and essential mediator of tissue fusion in multiple contexts.
    1. Ecology
    2. Evolutionary Biology

    Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community

    Samuel Frederick Mock Hart, Jose Mario Bello Pineda ... Wenying Shou
    Whereas partner-serving phenotype is intuitively quantified as benefit release rate, molecular genetics revealed an example where this thinking fails, motivating a more general metric.
    1. Cell Biology
    2. Evolutionary Biology

    Genetic diversity of CHC22 clathrin impacts its function in glucose metabolism

    Matteo Fumagalli, Stephane M Camus ... Frances M Brodsky
    Natural selection shaped CHC22 clathrin genetic variation in humans with different diets and potentially influenced the human insulin response.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Communication between distinct subunit interfaces of the cohesin complex promotes its topological entrapment of DNA

    Vincent Guacci, Fiona Chatterjee ... Douglas E Koshland
    The interface formed where Smc3p and Mcd1p bind each other regulates cohesin DNA binding and cohesion by a mechanism independently from its putative role as a DNA exit gate.
    1. Cell Biology
    2. Evolutionary Biology

    Sterol transfer by atypical cholesterol-binding NPC2 proteins in coral-algal symbiosis

    Elizabeth Ann Hambleton, Victor Arnold Shivas Jones ... Annika Guse
    Diversification of a conserved cholesterol binder drives functional replacement of cholesterol with symbiont-produced sterols in corals living in nutrient-poor environments.
    1. Evolutionary Biology

    Compound-V formations in shorebird flocks

    Aaron J Corcoran, Tyson L Hedrick
    Shorebird flocks fly in a formation that re-creates the neighbor positioning relationship of a V-formation in cluster flocks of more than 1000 birds.
    1. Neuroscience
    2. Stem Cells and Regenerative Medicine

    Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons

    Disi An, Ryosuke Fujiki ... Esteban Orlando Mazzoni
    Stem cell-derived motor neurons with differential ALS vulnerability identified proteasome activity as a possible mechanism that explains their differential sensitivity.
    1. Cell Biology

    Age-dependent deterioration of nuclear pore assembly in mitotic cells decreases transport dynamics

    Irina L Rempel, Matthew M Crane ... Liesbeth M Veenhoff
    In replicative ageing yeast cells, an age-dependent impediment in proper assembly of nuclear pore complexes is associated with altered nuclear transport.
    1. Cell Biology
    2. Immunology and Inflammation

    Arp2/3 complex-driven spatial patterning of the BCR enhances immune synapse formation, BCR signaling and B cell activation

    Madison Bolger-Munro, Kate Choi ... Michael R Gold
    Arp2/3 complex-mediated actin polymerization shapes how B lymphocytes probe the surface of antigen-presenting cells, promotes coalescence of B cell receptor (BCR) microclusters, amplifies BCR signaling, and enhances B cell activation.

Magazine

    1. Neuroscience

    Philosophy of Biology: Seizing an opportunity

    Perry Zurn, Danielle S Bassett