March 2018

Research articles

1. 1. Neuroscience

   A transformation from temporal to ensemble coding in a model of piriform cortex

   Merav Stern, Kevin A Bolding ... Kevin M Franks

   A spiking network model that examines the transformation of odor information from olfactory bulb to piriform cortex demonstrates how intrinsic cortical circuitry preserves representations of odor identity across odorant concentrations.
2. 1. Developmental Biology

   Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb

   Carsten Wolff, Jean-Yves Tinevez ... Anastasios Pavlopoulos

   Quantitative analyses of multi-dimensional microscopy datasets with a new Fiji/ImageJ plugin for cell tracking reveal the lineage restrictions and morphogenetic cellular behaviors underlying embryonic limb outgrowth in the direct developing crustacean Parhyale hawaiensis.
3. 1. Cell Biology
   2. Computational and Systems Biology

   Size uniformity of animal cells is actively maintained by a p38 MAPK-dependent regulation of G1-length

   Shixuan Liu, Miriam Bracha Ginzberg ... Ran Kafri

   The p38 MAPK pathway functions downstream of a cell-size-sensing process to coordinate cell size/growth with G1 progression in animal cells.
4. 1. Neuroscience

   Oligodendrocytes control potassium accumulation in white matter and seizure susceptibility

   Valerie A Larson, Yevgeniya Mironova ... Dwight E Bergles

   Oligodendrocytes in white matter use Kir4.1 inwardly rectifying potassium channels to prevent extracellular potassium accumulation, enabling neurons to sustain repetitive firing and limiting the initiation of seizures.
5. 1. Structural Biology and Molecular Biophysics

   Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme

   Zhening Zhang, Wenguang G Liang ... Wei-Jen Tang

   Integrative structural analyses of human insulin degradingenzyme (IDE) reveal how IDE selectively degrades peptides that form toxicaggregates, which guides IDE-based therapeutic innovations to treat diabetesand Alzheimer's disease.
6. 1. Developmental Biology

   Mechanism and consequence of abnormal calcium homeostasis in Rett syndrome astrocytes

   Qiping Dong, Qing Liu ... Qiang Chang

   Increased spontaneous calcium activity in Rett syndrome astrocytes is a key cell-autonomous phenotype that affects synaptic function and network activity.
7. 1. Stem Cells and Regenerative Medicine

   Live cell-lineage tracing and machine learning reveal patterns of organ regeneration

   Oriol Viader-Llargués, Valerio Lupperger ... Hernán López-Schier

   A combination of live cell tracking, cell-lineage tracing and machine learning shows that injured sensory organs repair accurately regardless of the extent of damage.
8. 1. Biochemistry and Chemical Biology
   2. Structural Biology and Molecular Biophysics

   Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage

   Timothy J Wendorff, James M Berger

   The engagement of DNA crossings is shown to license ATP hydrolysis and DNA cleavage by topoisomerase VI, a finding with mechanistic ramifications for related GHKL ATPases and meiotic recombination machineries.
9. 1. Genetics and Genomics
   2. Microbiology and Infectious Disease

   Transmission genetics of drug-resistant hepatitis C virus

   Nicholas van Buuren, Timothy L Tellinghuisen ... Karla Kirkegaard

   Interactions between viral genomes within the same cells can impact the selection of drug-resistant variants and this has been finessed by hepatitis C virus.
10. 1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Mapping mutational effects along the evolutionary landscape of HIV envelope

    Hugh K Haddox, Adam S Dingens ... Jesse D Bloom

    Deep mutational scanning of Env proteins from two transmitted-founder strains of HIV shows how the accessible evolutionary space changes as the virus evolves.
11. 1. Neuroscience

    Comprehensive machine learning analysis of Hydra behavior reveals a stable basal behavioral repertoire

    Shuting Han, Ekaterina Taralova ... Rafael Yuste

    A novel automated behavior analysis method for Hydra identifies pre-defined and new behavior types, and reveals a stable behavior repertoire.
12. 1. Neuroscience

    Cellular tolerance at the µ-opioid receptor is phosphorylation dependent

    Seksiri Arttamangkul, Daniel A Heinz ... John T Williams

    The role of C-terminal phosphorylation is critical for the expression of acute desensitization, trafficking and long-term tolerance to morphine.
13. 1. Neuroscience

    Structural and functional properties of a probabilistic model of neuronal connectivity in a simple locomotor network

    Andrea Ferrario, Robert Merrison-Hort ... Roman Borisyuk

    A new probabilistic model of connectivity reveals the structural and functional properties of the neural networks controlling locomotion in many individual tadpoles.
14. 1. Microbiology and Infectious Disease

    The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

    Christoph M Deeg, Cheryl-Emiliane T Chow, Curtis A Suttle

    Bodo saltans virus defines the most abundant giant viruses in the ocean and highlights the genomic plasticity, rooted in evolutionary arms races, that gave rise to giant viruses.
15. 1. Neuroscience

    Endogenous opioids in the nucleus accumbens promote approach to high-fat food in the absence of caloric need

    Kevin Caref, Saleem M Nicola

    Activation of mu-opioid receptors in the nucleus accumbens by their endogenous ligands promotes consumption of high-fat food in sated but not hungry rats, via enhancement of a neural signal that promotes cued approach behavior.
16. 1. Cancer Biology
    2. Stem Cells and Regenerative Medicine

    The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells

    Lisa Landskron, Victoria Steinmann ... Jürgen A Knoblich

    Genetic analyses uncovered that the asymmetrically long non-coding RNA cherub is required for brain tumor growth.
17. 1. Chromosomes and Gene Expression

    High levels of histones promote whole-genome-duplications and trigger a Swe1^WEE1-dependent phosphorylation of Cdc28^CDK1

    Douglas Maya Miles, Xenia Peñate ... Vincent Geli

    Ploidy is stably maintained in Saccharomyces cerevisae by a tight coordination between histone levels and cell cycle events.
18. 1. Microbiology and Infectious Disease

    Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids

    Sara C Di Rienzi, Juliet Jacobson ... Ruth E Ley

    Comparisons between lactobacilli bacteria in the small intestine and those evolved in the lab reveal several modes of resistance to toxic fatty acids.
19. 1. Evolutionary Biology
    2. Plant Biology

    Origin and evolution of the nuclear auxin response system

    Sumanth K Mutte, Hirotaka Kato ... Dolf Weijers

    The system that controls gene expression by the plant signaling molecule auxin has deep evolutionary roots, and stepwise increases in system complexity shaped the highly diverse auxin response in land plants.
20. 1. Neuroscience

    Hypoexcitability precedes denervation in the large fast-contracting motor units in two unrelated mouse models of ALS

    María de Lourdes Martínez-Silva, Rebecca D Imhoff-Manuel ... Marin Manuel

    The most vulnerable motor units lose a fundamental firing property before the denervation of their muscle fibers in ALS mice, changing our view of the role of excitability in neurodegeneration.
21. 1. Neuroscience

    Occurrence of long-term depression in the cerebellar flocculus during adaptation of optokinetic response

    Takuma Inoshita, Tomoo Hirano

    Motor training decreased the unit synaptic response and suppressed induction of long-term depression at parallel fiber to Purkinje cell synapses in the cerebellum, supporting involvement of long-term depression in motor learning.
22. 1. Cell Biology

    Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites

    Adam J Reid, Arthur M Talman ... Mara KN Lawniczak

    Plasmodium parasite transcription shifts dramatically along asexual development, and transmission stages variably express important immune evasion genes, suggesting much interesting biology has until now been hidden by bulk analyses.
23. 1. Microbiology and Infectious Disease

    Spontaneous dormancy protects Trypanosoma cruzi during extended drug exposure

    Fernando J Sánchez-Valdéz, Angel Padilla ... Rick L Tarleton

    Intracellular amastigotes of the Chagas disease agent Trypanosoma cruzi can spontaneously enter an extended state of replicative dormancy, during which time they are resistant to drug treatment both in vitro and in vivo.
24. 1. Neuroscience

    Pauses in cholinergic interneuron firing exert an inhibitory control on striatal output in vivo

    Stefano Zucca, Aya Zucca ... Jeffery Wickens

    Optogenetics and in vivo recordings in mice reveal that pauses in cholinergic interneurons offer an alternative mechanism to inhibit subthreshold and suprathreshold events of spiny projection neurons.
25. 1. Medicine
    2. Neuroscience

    Neurovascular sequestration in paediatric P. falciparum malaria is visible clinically in the retina

    Valentina Barrera, Ian James Callum MacCormick ... Simon Peter Harding

    Clinical, clinicopathological and image data from Malawian children shows that sequestration in P. falciparum cerebral malaria is visible clinically in the eye as orange retinal vessels and is strongly associated with death.
26. 1. Neuroscience

    Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types

    Saša Jereb, Hun-Way Hwang ... Robert B Darnell

    Differential expression of 3'UTR isoforms expands regulatory and protein diversity in cerebellar Purkinje and granule cells and during granule cell development.
27. 1. Cell Biology
    2. Chromosomes and Gene Expression

    A conserved function for pericentromeric satellite DNA

    Madhav Jagannathan, Ryan Cummings, Yukiko M Yamashita

    Satellite DNA mediates clustering of multiple chromosomes via formation of chromocenter to encapsulate the full complement of the genome into a single nucleus.
28. 1. Cell Biology
    2. Developmental Biology

    Cytokine receptor-Eb1 interaction couples cell polarity and fate during asymmetric cell division

    Cuie Chen, Ryan Cummings ... Yukiko M Yamashita

    A separation-of-function mutation reveals that a niche ligand receptor Dome functions in spindle orientation during asymmetric stem cell division by directly binding to Eb1, independent of its role in downstream JAK-STAT signaling.
29. 1. Developmental Biology

    NOTCH activity differentially affects alternative cell fate acquisition and maintenance

    Leonard Cheung, Paul Le Tissier ... Karine Rizzoti

    Activation of NOTCH signalling in different cell lineages of the embryonic murine pituitary uncovers an unexpected differential sensitivity, and this consequently reveals new aspects of endocrine lineages development and plasticity.
30. 1. Neuroscience

    Dendritic spikes in hippocampal granule cells are necessary for long-term potentiation at the perforant path synapse

    Sooyun Kim, Yoonsub Kim ... Won-Kyung Ho

    A novel mechanism of local plasticity in the distal dendrites of hippocampal granule cells.
31. 1. Cell Biology

    The yeast H⁺-ATPase Pma1 promotes Rag/Gtr-dependent TORC1 activation in response to H⁺-coupled nutrient uptake

    Elie Saliba, Minoas Evangelinos ... Bruno André

    The H+ influx coupled to nutrient uptake and the plasma membrane H+-ATPase are central actors of the activation of target of rapamycin complex 1 (TORC1) in budding yeast Saccharomyces cerevisiae..
32. 1. Genetics and Genomics

    Normal mitochondrial function in Saccharomyces cerevisiae has become dependent on inefficient splicing

    Marina Rudan, Peter Bou Dib ... Anita Kriško

    Removal of mitochondrial introns (Saccharomyces cerevisiae) from their host genes leads to detrimental increase in their transcript levels.
33. 1. Neuroscience

    Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity

    Amy E Pohodich, Hari Yalamanchili ... Huda Y Zoghbi

    Forniceal deep brain stimulation is a promising treatment for several neuropsychiatric disorders as it upregulates synaptic and neurogenesis-associated genes, normalizes genes misregulated in Rett syndrome mice, and regulates genes altered in intellectual disability and major depression.
34. 1. Neuroscience

    Ventral pallidal encoding of reward-seeking behavior depends on the underlying associative structure

    Jocelyn M Richard, Nakura Stout ... Patricia H Janak

    Reward-related cues elicit phasic changes in activity in ventral pallidum neurons, which predict and functionally contribute to the speed of behaviors trained on the basis of act-outcome, but not stimulus-outcome, contingencies.
35. 1. Chromosomes and Gene Expression

    A gene-specific T2A-GAL4 library for Drosophila

    Pei-Tseng Lee, Jonathan Zirin ... Hugo J Bellen

    A library of a thousand gene-specific intronic GAL4 insertions was generated, which caused a severe loss of function, permitted the assessing of gene expression, allowed the rescue of mutated gene with UAS-cDNA constructs, and provided a tool for the reversion of mutant phenotypes in specific cells or tissues.
36. 1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p

    Elena Khazina, Oliver Weichenrieder

    Human LINE-1 retrotransposition is found to critically depend on the rapidly evolving N-terminal sequence of the LINE-1 ORF1 protein and on the metastability of its coiled coil domain, indicating uncharacterized steps in LINE-1 retrotransposition.
37. 1. Developmental Biology

    Specialized impulse conduction pathway in the alligator heart

    Bjarke Jensen, Bastiaan J Boukens ... Vincent M Christoffels

    A specialized conduction pathway for the electrical impulse in the heart, previously thought to be associated with the endothermic mammals and birds only, is also present in the ectothermic crocodiles.
38. 1. Neuroscience

    Capillary pericytes express α-smooth muscle actin, which requires prevention of filamentous-actin depolymerization for detection

    Luis Alarcon-Martinez, Sinem Yilmaz-Ozcan ... Turgay Dalkara

    Pericytes surrounding capillaries in the retina contain α-smooth muscle actin, demonstrating that pericytes have the necessary molecular machinery to change capillary diameter during neurovascular coupling.
39. 1. Neuroscience

    Stomach-brain synchrony reveals a novel, delayed-connectivity resting-state network in humans

    Ignacio Rebollo, Anne-Dominique Devauchelle ... Catherine Tallon-Baudry

    Coupling between the gastric rhythm and brain activity at rest reveals a novel resting-state network, characterized by delayed functional connectivity.
40. 1. Developmental Biology

    A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila

    Joana Torres, Remo Monti ... Renato Paro

    A previously unknown oncogenic feature of an embryonic transcription factor was uncovered from transcriptomic analysis of tumors that lack functional Polycomb silencing.
41. 1. Cancer Biology
    2. Cell Biology

    Transient external force induces phenotypic reversion of malignant epithelial structures via nitric oxide signaling

    Benjamin L Ricca, Gautham Venugopalan ... Daniel A Fletcher

    In a 3D culture model of breast epithelium, application of a short-timescale compression to single malignant cells promotes the long-timescale development of polarized, growth-arrested structures.
42. 1. Neuroscience

    The signaling lipid sphingosine 1-phosphate regulates mechanical pain

    Rose Z Hill, Benjamin U Hoffman ... Diana M Bautista

    Constitutive sphingosine 1-phosphate signaling via the G-protein coupled receptor S1PR3 in mechanonociceptive somatosensory neurons is required for normal behavioral responses to noxious mechanical stimuli.
43. 1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations

    Xiaochu Ma, Maolin Lu ... Walther Mothes

    The identification of a single-CD4 bound asymmetric HIV-1 Envelope trimer intermediate provides new mechanistic insights into the activation of Envelope for fusion, and highlights the importance of asymmetry in biology.
44. 1. Developmental Biology
    2. Neuroscience

    Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex

    Marta Florio, Michael Heide ... Michael Hiller

    Transcriptomic and genomic analysis provides a resource of 50 primate-specific genes preferentially expressed in neural progenitors of fetal human neocortex, 15 of which are specific to humans.
45. 1. Neuroscience

    A zebrafish and mouse model for selective pruritus via direct activation of TRPA1

    Kali Esancy, Logan Condon ... Ajay Dhaka

    A pain-relaying ion channel on a hypersensitive population of sensory neurons can instead elicit sensations of itch in both fish and mice when directly activated, providing a novel model of itch transduction.
46. 1. Cancer Biology
    2. Cell Biology

    Laminin signals initiate the reciprocal loop that informs breast-specific gene expression and homeostasis by activating NO, p53 and microRNAs

    Saori Furuta, Gang Ren ... Mina J Bissell

    Endogenous laminins are necessary to build a functional acinus via generating NO, activating p53, HOXD10 and other positive players, but tumor cells neither make laminin nor generate NO, unless they are reverted to an organized structure.
47. 1. Stem Cells and Regenerative Medicine

    Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

    Isabelle Bergiers, Tallulah Andrews ... Christophe Lancrin

    Single-cell transcriptomics analysis identifies the dynamic activity of transcription factors at the onset of hematopoeitic stem and progenitor cells formation during embryonic development.
48. 1. Microbiology and Infectious Disease

    Dengue viruses cleave STING in humans but not in nonhuman primates, their presumed natural reservoir

    Alex C Stabell, Nicholas R Meyerson ... Sara L Sawyer

    An analysis of innate immunity reveals why dengue viruses do not reach high titers in primate laboratory models, even though they emerged through zoonotic transmission from primate reservoirs.
49. 1. Computational and Systems Biology
    2. Neuroscience

    The periaqueductal gray and Bayesian integration in placebo analgesia

    Arvina Grahl, Selim Onat, Christian Büchel

    Bayesian integration is able to predict placebo treatment outcomes by focusing especially on the influence of the precision of expectations.
50. 1. Developmental Biology
    2. Microbiology and Infectious Disease

    Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in Schistosoma mansoni

    George R Wendt, Julie NR Collins ... James J Collins III

    The specification of tegumental progenitor cells in Schistosoma mansoni relies on a pair of flatworm-specific transcription factors that are related to genes regulating epidermal specification in free-living flatworms.
51. 1. Cancer Biology

    A polymorphism in the tumor suppressor p53 affects aging and longevity in mouse models

    Yuhan Zhao, Lihua Wu ... Wenwei Hu

    A mouse model reveals that a p53 SNP impacts longevity via modulating the balance of cancer risk and the self-renewal function of stem/progenitor cells, which supports a role of p53 in regulation of longevity.
52. 1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death

    Laurelle Jackson, Jessica Hunter ... Alex Sigal

    Under conditions where the force of HIV infection per cell is high, partial attenuation of infection with inhibitors can increase the number of live infected cells and may paradoxically be beneficial for viral spread.
53. 1. Neuroscience

    A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

    Pierre Yger, Giulia LB Spampinato ... Olivier Marre

    A spike sorting toolbox to quickly and reliably access the activity of thousands of neurons recorded with dense extracellular probes.
54. 1. Neuroscience

    Neurogliaform cortical interneurons derive from cells in the preoptic area

    Mathieu Niquille, Greta Limoni ... Alexandre Dayer

    In vivo genetic lineage-tracing reveals the developmental trajectory of neurogliaform cells, the main effectors of a powerful inhibitory motif in the neocortex.
55. 1. Neuroscience

    Auditory experience controls the maturation of song discrimination and sexual response in Drosophila

    Xiaodong Li, Hiroshi Ishimoto, Azusa Kamikouchi

    Auditory experience of a species-specific courtship song in developing Drosophila tunes adult song perception and resultant sexual behavior more selective.
56. 1. Cancer Biology

    Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy

    Simeon U Springer, Chung-Hsin Chen ... George J Netto

    The creation of a non-invasive assay for detecting urothelial cancer could have a profound impact on how we find and treat the disease.
57. 1. Developmental Biology
    2. Neuroscience

    A transcription factor collective defines the HSN serotonergic neuron regulatory landscape

    Carla Lloret-Fernández, Miren Maicas ... Nuria Flames

    The collective action of six transcription factors selects and activates the regulatory regions of the HSN serotonergic neuron effector genes constituting a signature that can be used for the novo identification of HSN expressed genes.
58. 1. Neuroscience

    Synapse maintenance and restoration in the retina by NGL2

    Florentina Soto, Lei Zhao, Daniel Kerschensteiner

    Single cell knockout and overexpression reveal that the synaptic cell adhesion molecule NGL2 maintains synapses and axons, and can restore lost connections in the developing and mature retina.
59. 1. Cell Biology

    Integrin-based diffusion barrier separates membrane domains enabling the formation of microbiostatic frustrated phagosomes

    Michelle E Maxson, Xenia Naj ... Sergio Grinstein

    The diffusional barrier formed between phagocyte integrin and fungal glucans preserves the microbiostatic phagocytic environment generated during the frustrated phagocytosis of Candida albicans hypha.
60. 1. Cell Biology

    Control of endothelial cell polarity and sprouting angiogenesis by non-centrosomal microtubules

    Maud Martin, Alexandra Veloso ... Anna Akhmanova

    Non-centrosomal microtubules are required for endothelial polarization and sprouting, while centrosomally anchored microtubule arrays are both dispensable and insufficient for these processes.
61. 1. Stem Cells and Regenerative Medicine

    Positional information specifies the site of organ regeneration and not tissue maintenance in planarians

    Eric M Hill, Christian P Petersen

    Homeostatic tissue maintenance can occur at locations distinct from the target sites of organ regeneration planarians.
62. 1. Neuroscience

    Drosophila mushroom bodies integrate hunger and satiety signals to control innate food-seeking behavior

    Chang-Hui Tsao, Chien-Chun Chen ... Suewei Lin

    Mushroom bodies are a hunger and satiety integrative center that controls food-seeking behavior in Drosophila..
63. 1. Genetics and Genomics

    Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

    Zhipeng Zhou, Yunkun Dang ... Yi Liu

    Genetic and bioinformatic analyses uncover an unexpected role for codon usage biases in regulating gene expression at the transcriptional level by suppressing premature transcription termination.
64. 1. Biochemistry and Chemical Biology
    2. Immunology and Inflammation

    Fine-tuning of substrate preferences of the Src-family kinase Lck revealed through a high-throughput specificity screen

    Neel H Shah, Mark Löbel ... John Kuriyan

    A high-throughput comparison of substrate specificities of the Src-family kinases Lck and c-Src against a library of proteome-derived phosphorylation sites reveals that Lck has evolved divergent electrostatic features reflecting its involvement in T-cell signaling.
65. 1. Cancer Biology

    SPIN1 promotes tumorigenesis by blocking the uL18 (universal large ribosomal subunit protein 18)-MDM2-p53 pathway in human cancer

    Ziling Fang, Bo Cao ... Hua Lu

    SPIN1, a nucleolar protein, plays an oncogenic role by suppressing the tumor suppressor p53's function via regulation of the uL18-MDM2-p53 pathway.
66. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Acyl chain asymmetry and polyunsaturation of brain phospholipids facilitate membrane vesiculation without leakage

    Marco M Manni, Marion L Tiberti ... Bruno Antonny

    The asymmetric combination of saturated and polyunsaturated acyl chains in phospholipids as typically observed in synapses makes membranes prone to deformation and fission without compromising their impermeability.
67. 1. Developmental Biology
    2. Chromosomes and Gene Expression

    A universal vector concept for a direct genotyping of transgenic organisms and a systematic creation of homozygous lines

    Frederic Strobl, Anita Anderl, Ernst HK Stelzer

    In transgenesis assays involving diploid model organisms, two clearly distinguishable transformation markers embedded in interweaved, but incompatible Lox site pairs allow the systematic creation of homozygous transgenic lines and minimize the number of wasted animals.
68. 1. Plant Biology

    The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors

    Byoung Il Je, Fang Xu ... David Jackson

    The maize CLAVATA receptor, FEA2, functions in the perception of two different ligands, and remarkably that signaling from these different inputs is differentiated by the receptor interacting with two different downstream components.
69. 1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease

    Codon choice directs constitutive mRNA levels in trypanosomes

    Janaina de Freitas Nascimento, Steven Kelly ... Mark Carrington

    The information for mRNAs expression level is set by codon choice in trypanosomes and requires translation to be interpreted into a turnover rate.
70. 1. Microbiology and Infectious Disease

    Codon usage bias controls mRNA and protein abundance in trypanosomatids

    Laura Jeacock, Joana Faria, David Horn

    Global relative mRNA and protein abundance in trypanosomatids can be effectively estimated at transcriptomic and proteomic scales based on protein-coding sequences alone.
71. 1. Neuroscience

    Encoding sensory and motor patterns as time-invariant trajectories in recurrent neural networks

    Vishwa Goudar, Dean V Buonomano

    A recurrent network model trained to transcribe temporally scaled spoken digits into handwritten digits proposes that the brain flexibly encodes time-varying stimuli as neural trajectories that can be traversed at different speeds.
72. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Modulation of Prdm9-controlled meiotic chromosome asynapsis overrides hybrid sterility in mice

    Sona Gregorova, Vaclav Gergelits ... Jiri Forejt

    Prdm9-generated meiotic asynapsis of homologous chromosomes in mouse subspecific hybrids causes hybrid sterility and can be reversed by introducing random stretches of consubspecific sequence (≥ 27Mb) on four chromosomes most sensitive to asynapsis.
73. 1. Developmental Biology
    2. Evolutionary Biology

    Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita

    Juan Jose Fraire-Zamora, Johannes Jaeger, Jérôme Solon

    Evolutionary reduction in tissue number involves the simplification of the seaming process but not signaling during epithelial fusion.
74. 1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival

    Matthew Tien, Aretha Fiebig, Sean Crosson

    A gene network analysis approach reveals a conserved small regulatory RNA that is crucial for bacterial cell survival across distinct stress conditions.
75. 1. Cell Biology
    2. Neuroscience

    Neurexin–Neuroligin 1 regulates synaptic morphology and functions via the WAVE regulatory complex in Drosophila neuromuscular junction

    Guanglin Xing, Moyi Li ... Wei Xie

    Neurexin–Neuroligin1 complex positively regulates F-actin assembly through direct interaction with WAVE complex to control normal synaptic growth and electrophysiological function in Drosophila neuromuscular junction.
76. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    IRF4 haploinsufficiency in a family with Whipple’s disease

    Antoine Guérin, Gaspard Kerner ... Jean-Laurent Casanova

    Autosomal dominant IRF4 deficiency is the first genetic etiology of Whipple's disease, a very rare chronic condition following a rather common infection by Tropheryma whipplei.
77. 1. Neuroscience

    Entorhinal cortex receptive fields are modulated by spatial attention, even without movement

    Niklas Wilming, Peter König ... Elizabeth A Buffalo

    Moving covert attention can activate spatial representations in the Entorhinal cortex.
78. 1. Cancer Biology

    Replication Study: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

    John Repass, Reproducibility Project: Cancer Biology

    Editors' Summary: This Replication Study did not reproduce those experiments in the original paper that it attempted to reproduce.
79. 1. Neuroscience

    Closed-loop neuromodulation restores network connectivity and motor control after spinal cord injury

    Patrick D Ganzer, Michael J Darrow ... Robert L Rennaker II

    Precisely-timed bursts of closed-loop vagus nerve stimulation during rehabilitation restore neural connectivity and substantially improve recovery of motor function after SCI.
80. 1. Developmental Biology
    2. Structural Biology and Molecular Biophysics

    Large, long range tensile forces drive convergence during Xenopus blastopore closure and body axis elongation

    David R Shook, Eric M Kasprowicz ... Raymond Keller

    Blastopore closure in Xenopus is driven by two morphogenic mechanisms that have strongly context dependent effects on tissue movement and that generate tensile force across tissues: convergent extension, as expected, and, unexpectedly, convergent thickening.
81. 1. Neuroscience

    Adult-born neurons facilitate olfactory bulb pattern separation during task engagement

    Wankun L Li, Monica W Chu ... Takaki Komiyama

    Adult-born neurons in the olfactory bulb allow state-dependent pattern separation of representations of similar odorants.
82. 1. Computational and Systems Biology
    2. Immunology and Inflammation

    Method for identification of condition-associated public antigen receptor sequences

    Mikhail V Pogorelyy, Anastasia A Minervina ... Aleksandra M Walczak

    Without using control cohorts, a statistical method identifies candidates for immune receptors associated with diseases from repertoire sequencing datasets.
83. 1. Neuroscience

    Covert shift of attention modulates the value encoding in the orbitofrontal cortex

    Yang Xie, Chechang Nie, Tianming Yang

    The orbitofrontal neurons only encode the value of one item, which may be selected by covert attention combining factors of value and visual salience, suggesting a sequential processing mechanism of value information in the brain.
84. 1. Chromosomes and Gene Expression

    NuRD and CAF-1-mediated silencing of the D4Z4 array is modulated by DUX4-induced MBD3L proteins

    Amy E Campbell, Sean C Shadle ... Stephen J Tapscott

    CRISPR/Cas9 engineered locus-specific proteomics leads to the identification of NuRD, CAF-1, and MBD3L2 as regulators of the early embryonic transcription factor DUX4.
85. 1. Neuroscience

    POMC neurons expressing leptin receptors coordinate metabolic responses to fasting via suppression of leptin levels

    Alexandre Caron, Heather M Dungan Lemko ... Joel K Elmquist

    A subset of hypothalamic POMC neurons that express leptin receptors control metabolic responses to changing energy availability including regulating blood glucose and leptin levels.
86. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    ICE1 promotes the link between splicing and nonsense-mediated mRNA decay

    Thomas D Baird, Ken Chih-Chien Cheng ... J Robert Hogg

    A whole-genome siRNA screen identifies ICE1 as a factor required for accurate sensing and quality control of mRNAs containing premature stop codons.
87. 1. Neuroscience

    Nociceptive interneurons control modular motor pathways to promote escape behavior in Drosophila

    Anita Burgos, Ken Honjo ... Wesley B Grueber

    A class of interneuron is identified that promotes escape behavior downstream of nociceptor inputs via connections to nociceptive integrator and premotor networks.
88. 1. Developmental Biology
    2. Neuroscience

    Movement maintains forebrain neurogenesis via peripheral neural feedback in larval zebrafish

    Zachary Jonas Hall, Vincent Tropepe

    Early postembryonic bodily movement sends neural feedback through dorsal root ganglia to the forebrain in order to regulate the rate of neurogenesis and subsequent brain growth.
89. 1. Cell Biology
    2. Developmental Biology

    Proteolytic processing of palmitoylated Hedgehog peptides specifies the 3-4 intervein region of the Drosophila wing

    Sabine Schürmann, Georg Steffes ... Kay Grobe

    Proteolysis of lipidated N-terminal peptides that tether Hedgehog morphogens to the surface of source cells is absolutely required for their coupled release and bioactivation in vivo in Drosophila melanogaster.
90. 1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

    Samuel T Coradetti, Dominic Pinel ... Jeffrey M Skerker

    Using barcoded mutagenesis and a high-throughput genetic screen results in the identification of 150 genes that affect lipid accumulation in a non-model yeast system.
91. 1. Ecology
    2. Evolutionary Biology

    CRISPR-based herd immunity can limit phage epidemics in bacterial populations

    Pavel Payne, Lukas Geyrhofer ... Jonathan P Bollback

    Bacteria can exhibit herd immunity protection against phages, which may play a significant role in their ecology and evolution.
92. 1. Cell Biology

    Myotubularin related protein-2 and its phospholipid substrate PIP₂ control Piezo2-mediated mechanotransduction in peripheral sensory neurons

    Pratibha Narayanan, Meike Hütte ... Manuela Schmidt

    Local Mtmr2 activity and PI(3,5)P2 abundance dynamically control Piezo2-dependent mechanotransduction in peripheral sensory neurons.
93. 1. Cell Biology
    2. Chromosomes and Gene Expression

    A compartmentalized signaling network mediates crossover control in meiosis

    Liangyu Zhang, Simone Köhler ... Abby F Dernburg

    A regulatory circuit that localizes to the synaptonemal complex, a liquid crystalline compartment between chromosomes, ensures crossing-over while limiting the number of crossovers between homologous chromosomes during meiosis.
94. 1. Immunology and Inflammation

    IgM and IgD B cell receptors differentially respond to endogenous antigens and control B cell fate

    Mark Noviski, James L Mueller ... Julie Zikherman

    Self-reactive B cells downregulate the IgM but not the IgD B cell receptor, and this serves as a critical tolerance mechanism because IgD is less sensitive to bona fide endogenous antigens than IgM.
95. 1. Neuroscience

    Temporal transitions of spontaneous brain activity

    Zhiwei Ma, Nanyin Zhang

    Analysis of resting-state fMRI data revealed nonrandom temporal transitions between spontaneous brain activity patterns in both awake rats and humans.
96. 1. Cell Biology

    Sumoylation promotes optimal APC/C activation and timely anaphase

    Christine C Lee, Bing Li ... Michael J Matunis

    The Anaphase Promoting Complex/Cyclosome is regulated by sumoylation to ensure timely mitotic exit in human cells.
97. 1. Neuroscience

    Single-exposure visual memory judgments are reflected in inferotemporal cortex

    Travis Meyer, Nicole C Rust

    In response to the question "Have you seen this image before?", remembering and forgetting can be accounted for by a weighted linear read-out of memory signals in monkey inferotemporal cortex.
98. 1. Neuroscience

    Drosophila Fezf coordinates laminar-specific connectivity through cell-intrinsic and cell-extrinsic mechanisms

    Jing Peng, Ivan J Santiago ... Matthew Y Pecot

    Transcriptional modules underlie the step-wise construction of neural circuits in the Drosophila visual system.
99. 1. Neuroscience

    Orbitofrontal neurons signal sensory associations underlying model-based inference in a sensory preconditioning task

    Brian F Sadacca, Heather M Wied ... Geoffrey Schoenbaum

    Neural activity in the orbitofrontal cortex (OFC) represents incidental stimulus-stimulus associations, providing additional evidence for OFC having a role in cognition beyond functions centered on processing value or biological significance.
100. 1. Cell Biology
     2. Structural Biology and Molecular Biophysics

     TANGO1 builds a machine for collagen export by recruiting and spatially organizing COPII, tethers and membranes

     Ishier Raote, Maria Ortega-Bellido ... Vivek Malhotra

     TANGO1 creates a sub-compartment at the endoplasmic reticulum, to segregate and export fully assembled bulky cargoes.
101. 1. Cell Biology

     Site-specific glycosylation regulates the form and function of the intermediate filament cytoskeleton

     Heather J Tarbet, Lee Dolat ... Michael Boyce

     The in vivo modification of the canonical intermediate filament protein vimentin with O-linked beta-N-acetylglucosamine affects its function in filament assembly, cell migration and host-pathogen interactions.
102. 1. Neuroscience

     Distinct contributions of functional and deep neural network features to representational similarity of scenes in human brain and behavior

     Iris IA Groen, Michelle R Greene ... Chris I Baker

     Deep network features exhibit a robust correlation with brain activity in scene-selective cortex, but are not sufficient to explain human scene categorization behavior, which is strongly shaped by information about the function (possibility for action) of the scene.
103. 1. Structural Biology and Molecular Biophysics

     cisTEM, user-friendly software for single-particle image processing

     Timothy Grant, Alexis Rohou, Nikolaus Grigorieff

     cisTEM enables fast processing of single-particle cryo-EM data on CPU-based workstations and is easily accessible to new users.
104. 1. Neuroscience

     Pupillometry reveals perceptual differences that are tightly linked to autistic traits in typical adults

     Marco Turi, David Charles Burr, Paola Binda

     Pupil difference during bistable perception of bright and dark elements predicts autistic traits.
105. 1. Biochemistry and Chemical Biology
     2. Microbiology and Infectious Disease

     Neutrophil-generated HOCl leads to non-specific thiol oxidation in phagocytized bacteria

     Adriana Degrossoli, Alexandra Müller ... Lars I Leichert

     The use of genetically encoded redox sensors in phagocytized bacteria reveals that, among the toxic cocktail of oxidants released into the neutrophil's phagolysosome, HOCl is the main component responsible for the oxidative modification of bacterial protein thiols.
106. 1. Computational and Systems Biology
     2. Structural Biology and Molecular Biophysics

     Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB

     Yasuhiro Matsunaga, Tsutomu Yamane ... Akinori Kidera

     High-performance computing simulations reveal how two remote sites in the multidrug transporter AcrB work together for drug extrusion using the proton-motive force.
107. 1. Computational and Systems Biology

     Antibiotic-induced population fluctuations and stochastic clearance of bacteria

     Jessica Coates, Bo Ryoung Park ... Minsu Kim

     The extinction of bacterial populations by antibiotics is stochastic and can be predicted only probabilistically, not deterministically.
108. 1. Computational and Systems Biology
     2. Ecology

     Individual crop loads provide local control for collective food intake in ant colonies

     Efrat Esther Greenwald, Lior Baltiansky, Ofer Feinerman

     Colony satiation level determines the unloading rate of laden foragers, which, in turn, rely on their own food load to adjust their foraging effort.
109. 1. Neuroscience

     Early structural and functional plasticity alterations in a susceptibility period of DYT1 dystonia mouse striatum

     Marta Maltese, Jennifer Stanic ... Antonio Pisani

     Structural and functional striatal synaptic plasticity abnormalities occur early in a sensitive developmental period, representing a potential unique endophenotypic traits that increase the risk of manifesting clinical symptoms in DYT1 mutation carriers.
110. 1. Biochemistry and Chemical Biology

     Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

     Madeline E Sherlock, Narasimhan Sudarsan ... Ronald R Breaker

     A riboswitch class has been discovered for phosphoribosyl pyrophosphate, the biochemical precursor of nucleotides, and this novel RNA sensor commonly operates in tandem with a guanine aptamer to function like a Boolean logic gate.
111. 1. Chromosomes and Gene Expression
     2. Genetics and Genomics

     Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance

     Dorine Jeanne Mariëtte du Mee, Maxim Ivanov ... Sebastian Marquardt

     RNA Polymerase II transcriptional termination of a nuclear long non-coding RNA is required to maintain the mitochondrial genome and hence promotes budding yeast growth.
112. 1. Biochemistry and Chemical Biology
     2. Structural Biology and Molecular Biophysics

     Mechanochemical coupling and bi-phasic force-velocity dependence in the ultra-fast ring ATPase SpoIIIE

     Ninning Liu, Gheorghe Chistol ... Carlos Bustamante

     Probing the DNA motor SpoIIIE at the single-molecule level has revealed its force-generating step, rich translocation dynamics during motor operation and a novel, bi-phasic mechanical response to opposing force.
113. 1. Neuroscience

     Neurexin and Neuroligin-based adhesion complexes drive axonal arborisation growth independent of synaptic activity

     William D Constance, Amrita Mukherjee ... Darren W Williams

     Axonal arborisation growth is regulated by dynamic, focal localisations of Neurexin and Neuroligin that provide stability for filopodia, enabling a 'stick and grow'-based mechanism, wholly independent of synapse formation.
114. 1. Cell Biology

     SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation

     Mohsen Sarikhani, Sneha Mishra ... Nagalingam R Sundaresan

     Mass spectroscopy, molecular modeling and/or molecular dynamics simulations reveal how acetylation regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation.