March 2017

Research articles

1. 1. Biochemistry and Chemical Biology
   2. Chromosomes and Gene Expression

   Frequent exchange of the DNA polymerase during bacterial chromosome replication

   Thomas R Beattie, Nitin Kapadia ... Rodrigo Reyes-Lamothe

   DnaB Helicase is the only stable component of the bacterial replisome as the replicative DNA polymerase frequently exchanges in both leading and lagging strands.
2. 1. Immunology and Inflammation

   A type I IFN-dependent DNA damage response regulates the genetic program and inflammasome activation in macrophages

   Abigail J Morales, Javier A Carrero ... Barry P Sleckman

   Activated macrophages initiate a robust DNA damage response that depends on type I IFN and regulates their genetic program and inflammasome activation, establishing a mechanistic link between DNA damage responses and innate immunity.
3. 1. Biochemistry and Chemical Biology
   2. Genetics and Genomics

   Evolution of substrate specificity in a retained enzyme driven by gene loss

   Ana Lilia Juárez-Vázquez, Janaka N Edirisinghe ... Francisco Barona-Gómez

   An integrated biochemical and evolutionary analysis shows how enzyme specificity evolves after gene loss during genome decay, implicating relaxation of purifying selection as a driving force for functional divergence.
4. 1. Biochemistry and Chemical Biology
   2. Structural Biology and Molecular Biophysics

   Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS

   Komal Ishwar Pawar, Katta Suma ... Rajan Sankaranarayanan

   Along with preventing D-amino acids from being incorporated into proteins, D-aminoacyl-tRNA deacylase clears achiral glycine that is incorrectly attached to tRNA^Ala.
5. 1. Cancer Biology
   2. Computational and Systems Biology

   Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

   Malene Juul, Johanna Bertl ... Jakob Skou Pedersen

   A new statistical approach identifies non-coding regulatory regions of genes as driver candidates with recurrent mutations across cancer samples that associate with gene expression, patient survival or mutational phenotype.
6. 1. Biochemistry and Chemical Biology
   2. Cell Biology

   A CDC25 family protein phosphatase gates cargo recognition by the Vps26 retromer subunit

   Tie-Zhong Cui, Tabitha A Peterson, Christopher G Burd

   The CDC25 family protein phosphatase Mih1 promotes downregulation of cell surface proteins in budding yeast by dephosphorylating a subunit of the retromer complex, which mediates plasma membrane recycling.
7. 1. Immunology and Inflammation
   2. Microbiology and Infectious Disease

   Ribonuclease L mediates the cell-lethal phenotype of double-stranded RNA editing enzyme ADAR1 deficiency in a human cell line

   Yize Li, Shuvojit Banerjee ... Susan R Weiss

   Endogenous double-stranded RNA is generated in human cells and leads to RNase L activation and consequent cell death unless neutralized by adenosine deaminase acting on RNA1 (ADAR1).
8. 1. Cancer Biology
   2. Cell Biology

   Inhibitor of ppGalNAc-T3-mediated O-glycosylation blocks cancer cell invasiveness and lowers FGF23 levels

   Lina Song, Adam D Linstedt

   The first inhibitor identified against an iso-enzyme that initiates O-glycosylation in the Golgi complex promises new therapeutic approaches for cancer and chronic kidney disease.
9. 1. Cancer Biology
   2. Cell Biology

   Ambra1 spatially regulates Src activity and Src/FAK-mediated cancer cell invasion via trafficking networks

   Christina Schoenherr, Adam Byron ... Margaret C Frame

   Ambra1 is a Src "spatial rheostat".
10. 1. Plant Biology

    Regulation of plant immune receptor accumulation through translational repression by a glycine-tyrosine-phenylalanine (GYF) domain protein

    Zhongshou Wu, Shuai Huang ... Xin Li

    A GYF protein regulates plant immune receptor homeostasis through translational repression, a previously unknown mechanism.
11. 1. Structural Biology and Molecular Biophysics

    An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump

    Zhao Wang, Guizhen Fan ... Dijun Du

    The tripartite drug efflux pump AcrA-AcrB-TolC, representative of a wide group of pumps from Gram-negative bacteria, enters a transport-competent state through long-distance conformational changes that switch the channel from a closed to an open state.
12. 1. Developmental Biology

    Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells

    Daniela Roellig, Johanna Tan-Cabugao ... Marianne E Bronner

    The vertebrate neural plate border is comprised of precursors that coexpress multiple lineage markers and small changes in their levels can bias border cell fate.
13. 1. Cell Biology

    Angiopoietin-2 in white adipose tissue improves metabolic homeostasis through enhanced angiogenesis

    Yu A An, Kai Sun ... Philipp E Scherer

    Gain- and loss-of-function studies highlight the important role for angiopoietin-2 to maintain adipose tissue health during metabolic challenges.
14. 1. Cell Biology
    2. Neuroscience

    The interactome of the copper transporter ATP7A belongs to a network of neurodevelopmental and neurodegeneration factors

    Heather S Comstra, Jacob McArthy ... Victor Faundez

    The ATP7A interactome is the first comprehensive view of putative Menkes disease neurodegeneration mechanisms.
15. 1. Computational and Systems Biology
    2. Ecology

    Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

    Babak Momeni, Li Xie, Wenying Shou

    With mathematical modeling being an important source of insight for microbial communities, we may need to move beyond commonly-used pairwise models that do not capture microbial interactions.
16. 1. Ecology
    2. Epidemiology and Global Health

    Tracking zoonotic pathogens using blood-sucking flies as 'flying syringes'

    Paul-Yannick Bitome-Essono, Benjamin Ollomo ... Christophe Paupy

    A field study coupled with a molecular analysis demonstrates that using hematophagous flies as 'flying syringes' could be used to investigate blood-borne pathogen diversity in wild vertebrates and act as an early detection tool of zoonotic pathogens.
17. 1. Cell Biology
    2. Neuroscience

    Mechanotransduction current is essential for stability of the transducing stereocilia in mammalian auditory hair cells

    A Catalina Vélez-Ortega, Mary J Freeman ... Gregory I Frolenkov

    The remarkable lifelong stability of mechanotransducing stereocilia of the inner ear hair cells depends on the activity of the transduction ion channels located at the tips of these mechanosensory projections.
18. 1. Neuroscience

    Dopamine signaling tunes spatial pattern selectivity in C. elegans

    Bicheng Han, Yongming Dong ... Jihong Bai

    Natural variations in touch-dependent dopamine signaling tune the perception of spatial patterns in C. elegans.
19. 1. Neuroscience

    Lack of IL-1R8 in neurons causes hyperactivation of IL-1 receptor pathway and induces MECP2-dependent synaptic defects

    Romana Tomasoni, Raffaella Morini ... Michela Matteoli

    Excessive inflammation of the brain in early life predisposes individuals to neurodevelopmental disorders by preventing synapses from developing correctly.
20. 1. Cell Biology
    2. Microbiology and Infectious Disease

    Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense

    Annette Fischer, Kelly S Harrison ... Thomas Rudel

    Obligate intracellular Chlamydia secrete a deubiquitinating enzyme (Cdu1) into the membrane of the Chlamydia-containing vacuole to deubiquitinate selected host proteins and support the survival of the bacteria during genital infection.
21. 1. Developmental Biology
    2. Neuroscience

    A mutant with bilateral whisker to barrel inputs unveils somatosensory mapping rules in the cerebral cortex

    Nicolas Renier, Chloé Dominici ... Alain Chédotal

    The somatosensory cortex doesn't integrate mixed bilateral inputs, as partially uncrossing projections from the whiskers duplicates their representation by segregating lateralized inputs from each side of the head.
22. 1. Cell Biology
    2. Developmental Biology

    Dual role for Jumu in the control of hematopoietic progenitors in the Drosophila lymph gland

    Yangguang Hao, Li Hua Jin

    Jumu is required for the proper differentiation of prohemocytes and the proliferation and location of PSC cells.
23. 1. Cancer Biology

    Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression

    Viviana Anelli, Jacques A Villefranc ... Yariv Houvras

    Transformation mediated by oncogenic BRAF requires transcriptional activation of TWIST at the earliest stage of neoplastic transformation.
24. 1. Cell Biology
    2. Chromosomes and Gene Expression

    Polo-like kinase-dependent phosphorylation of the synaptonemal complex protein SYP-4 regulates double-strand break formation through a negative feedback loop.

    Saravanapriah Nadarajan, Talley J Lambert ... Monica P Colaiácovo

    PLK-1/2-mediated SYP-4 phosphorylation is dependent on crossover precursor formation, triggering a switch in the dynamic state of the synaptonemal complex that reduces the formation of further double-strand breaks at late meiotic prophase.
25. 1. Biochemistry and Chemical Biology

    Action of CMG with strand-specific DNA blocks supports an internal unwinding mode for the eukaryotic replicative helicase

    Lance Langston, Mike O’Donnell

    The CMG complex, the replicative helicase in eukaryotes, uses a different mechanism from bacterial and viral helicases by engaging both strands of parental DNA with substantial force and unwinding the duplex within the central channel of CMG.
26. 1. Neuroscience

    EM connectomics reveals axonal target variation in a sequence-generating network

    Jörgen Kornfeld, Sam E Benezra ... Michael A Long

    Combining light microscopy and electron microscopy uncovered patterns of neural connectivity in a zebra finch forebrain region capable of generating song-related sequential activity, contributing to our understanding of the neural circuitry that underlies skilled motor performance.
27. 1. Chromosomes and Gene Expression

    Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases

    Ryan Janke, Anthony T Iavarone, Jasper Rine

    Mutations in budding yeast modeled after cancer-associated isocitrate dehydrogenase mutations lead to stabilization of heterochromatin and enhanced gene silencing through inhibition of specific histone demethylases by the oncometabolite D-2-hydroxyglutarate.
28. 1. Developmental Biology
    2. Neuroscience

    Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome

    Melinda S Modrell, Mike Lyne ... Clare VH Baker

    An unbiased transcriptomic approach reveals that developing paddlefish electrosensory organs express genes essential for mechanosensory hair cell development and synaptic transmission, and identifies candidates for mediating electroreceptor development and function.
29. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity

    Michael P Meers, Telmo Henriques ... A Gregory Matera

    Post-translational modification of histone H3K36 is not required to suppress cryptic transcription initiation or to include alternative exons in Drosophila; instead it promotes expression of active genes by stimulating polyadenylation.
30. 1. Structural Biology and Molecular Biophysics
    2. Cell Biology

    Dilation of fusion pores by crowding of SNARE proteins

    Zhenyong Wu, Oscar D Bello ... Erdem Karatekin

    A few SNARE complexes suffice to fuse membranes, but many more are needed to dilate the nascent fusion pore by molecular crowding for efficient neurotransmitter or hormone release during exocytosis.
31. 1. Computational and Systems Biology
    2. Evolutionary Biology

    Environment determines evolutionary trajectory in a constrained phenotypic space

    David T Fraebel, Harry Mickalide ... Seppe Kuehn

    Experimental evolution shows that when selection acts on two traits constrained by a trade-off, the direction of phenotypic evolution depends on the environment.
32. 1. Biochemistry and Chemical Biology
    2. Neuroscience

    The neuropeptide F/nitric oxide pathway is essential for shaping locomotor plasticity underlying locust phase transition

    Li Hou, Pengcheng Yang ... Le Kang

    Two neuropeptides, NPF1a and NPF2, act via the nitric oxide signaling pathway in the locust brain to regulate the trait transition between solitary and swarming behavior.
33. 1. Cancer Biology

    CRISPR/Cas9 mutagenesis invalidates a putative cancer dependency targeted in on-going clinical trials

    Ann Lin, Christopher J Giuliano ... Jason M Sheltzer

    A putative therapeutic target undergoing clinical trials in breast cancer is non-essential and the drug used in those trials blocks cell division through an off-target effect.
34. 1. Stem Cells and Regenerative Medicine
    2. Chromosomes and Gene Expression

    Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

    Paula Freire-Pritchett, Stefan Schoenfelder ... Mikhail Spivakov

    Promoter interactome maps in human embryonic stem cells (ESCs) and ESC-derived early neuroectodermal progenitors link distal enhancers to putative target genes, reveal lineage-specific cis-regulatory architecture and shed light on the logic of gene regulation by multiple enhancers.
35. 1. Chromosomes and Gene Expression
    2. Neuroscience

    A receptor and neuron that activate a circuit limiting sucrose consumption

    Ryan M Joseph, Jennifer S Sun ... John R Carlson

    Although sugar-sensing taste neurons typically promote feeding, a taste neuron in the Drosophila pharynx limits feeding via the IR60b receptor; thus, revealing a new element in the circuit logic of feeding control.
36. 1. Neuroscience

    NPTX2 and cognitive dysfunction in Alzheimer’s Disease

    Mei-Fang Xiao, Desheng Xu ... Paul F Worley

    Dysfunction of pyramidal neuron-PV interneuron circuits contributes to cognitive failure in Alzheimer's disease.
37. 1. Structural Biology and Molecular Biophysics
    2. Chromosomes and Gene Expression

    Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

    Ramasubramanian Sundaramoorthy, Amanda L Hughes ... Tom Owen-Hughes

    Structural models of the chromatin remodeling enzyme Chd1 in solution and when bound to chromatin indicate that conformational changes to both the enzyme and the nucleosome occur upon nucleotide dependent engagement.
38. 1. Cell Biology
    2. Stem Cells and Regenerative Medicine

    The PERK arm of the unfolded protein response regulates satellite cell-mediated skeletal muscle regeneration

    Guangyan Xiong, Sajedah M Hindi ... Ashok Kumar

    Genetic and biochemical analyses reveal that PERK is important for the survival of activated satellite stem cells during regeneration of injured skeletal muscle.
39. 1. Developmental Biology
    2. Chromosomes and Gene Expression

    Atrophin controls developmental signaling pathways via interactions with Trithorax-like

    Kelvin Yeung, Ann Boija ... Helen McNeill

    ChIP-seq and phenotypic analyses reveal Atrophin from Drosophila directly regulates Notch and Dpp signaling components, and engrailed gene expression, via interactions with GAGA Factor.
40. 1. Cell Biology

    Age-dependent diastolic heart failure in an in vivo Drosophila model

    Matthew P Klassen, Christian J Peters ... Yuh Nung Jan

    As in humans, Drosophila hearts are able to maintain contractile performance during healthy aging, but this maintenance is associated with an increased susceptibility to progressive dysrhythmias that can lead to fibrillatory arrest.
41. 1. Genetics and Genomics

    Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator

    Isabel Nocedal, Eugenio Mancera, Alexander D Johnson

    Rapid evolutionary rewiring of the meiosis transcription network facilitated a switch in the function of a master regulator from regulating meiosis to regulating biofilm formation.
42. 1. Microbiology and Infectious Disease

    Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins

    Leonor García-Bayona, Monica S Guo, Michael T Laub

    Genetic, biochemical, and cell biological approaches reveal a new form of contact-dependent inhibition in bacteria involving bacteriocin-like proteins that aggregate on the surface of cells.
43. 1. Developmental Biology

    Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

    Yun Huang, Jong Kyoung Kim ... M Azim Surani

    Soon after fertilisation, a critical portion of the embryonic genome is switched on through the actions of maternally inherited Stella, in part through controlling the activation of transposable elements.
44. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Nucleosomes influence multiple steps during replication initiation

    Ishara F Azmi, Shinya Watanabe ... Stephen P Bell

    Nucleosomal DNAs assembled or modified by different chromatin remodeling enzymes differentially impact the origin licensing and helicase activation steps of replication initiation.
45. 1. Neuroscience

    Fast-spiking GABA circuit dynamics in the auditory cortex predict recovery of sensory processing following peripheral nerve damage

    Jennifer Resnik, Daniel B Polley

    Dynamic regulation of feedforward inhibition from parvalbumin-expressing inhibitory neurons is linked to the gradual restoration of cortical sensory processing following auditory nerve damage.
46. 1. Cell Biology
    2. Developmental Biology

    Discovery of novel determinants of endothelial lineage using chimeric heterokaryons

    Wing Tak Wong, Gianfranco Matrone ... John P Cooke

    Bioinformatic analysis of gene expression in chimeric heterokaryons can identify novel regulators of cell lineage.
47. 1. Developmental Biology

    SMOC can act as both an antagonist and an expander of BMP signaling

    J Terrig Thomas, D Eric Dollins ... Malcolm Moos

    SMOC inhibits BMP signaling locally, but also expands the range of BMP signaling by competing for heparan sulfate binding sites.
48. 1. Cell Biology
    2. Microbiology and Infectious Disease

    Toxoplasma gondii F-actin forms an extensive filamentous network required for material exchange and parasite maturation

    Javier Periz, Jamie Whitelaw ... Markus Meissner

    In contrast to current knowledge that predicts that apicomplexan actin is unconventional, use of Chromobodies demonstrate that Toxoplasma F-actin forms a long, stable, highly dynamic tubular network that is required for material transfer and parasite maturation.
49. 1. Developmental Biology

    YAP is essential for mechanical force production and epithelial cell proliferation during lung branching morphogenesis

    Chuwen Lin, Erica Yao ... Pao-Tien Chuang

    The control of local cell properties such as epithelial cell number and mechanical force production by Hippo signaling is a major determinant of lung branching.
50. 1. Structural Biology and Molecular Biophysics
    2. Microbiology and Infectious Disease

    CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin

    Katharina van Pee, Alexander Neuhaus ... Özkan Yildiz

    The near-atomic cryoEM pore complex structure of pneumolysin, the main virulence factor of Streptococcus pneumoniae, shows how the individual domains rearrange during the pore formation.
51. 1. Neuroscience

    Valosin-containing protein (VCP/p97) inhibitors relieve Mitofusin-dependent mitochondrial defects due to VCP disease mutants

    Ting Zhang, Prashant Mishra ... Ming Guo

    A potential medication has been found for the brain and muscle degenerative diseases caused by mutant forms of Valosin-Containing Protein.
52. 1. Plant Biology

    A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

    Wannarat Pornsiriwong, Gonzalo M Estavillo ... Barry J Pogson

    Molecular signals from chloroplasts can synergistically interact with the plant hormone, abscisic acid (ABA), to regulate non-canonical signaling pathways mediating fundamental cellular processes including stomatal closure, seed dormancy and germination.
53. 1. Neuroscience

    Activity patterns of serotonin neurons underlying cognitive flexibility

    Sara Matias, Eran Lottem ... Zachary F Mainen

    Recordings from serotonin-producing neurons in the brain reveal that these neurons are highly activated by sudden changes in previously familiar environments, potentially explaining why serotonin is important for learning to adapt to such changes.
54. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex

    Jin Young Kang, Paul Dominic B Olinares ... Seth A Darst

    Cryo-electron microscopy structures show how coliphage HK022 Nun blocks Escherichia coli RNA polymerase translocation by mediating multiple interactions between the RNA polymerase and nucleic acids.
55. 1. Cancer Biology
    2. Chromosomes and Gene Expression

    Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma

    Floris Foijer, Lee A Albacker ... Peter K Sorger

    Chromosomal instability through spindle assembly checkpoint alleviation facilitates malignant transformation of hepatocytes and T-cells in vivo, resulting in cancers with recurrent karyotypes.
56. 1. Chromosomes and Gene Expression

    A high-resolution map of transcriptional repression

    Ziwei Liang, Karen E Brown ... Matthias Merkenschlager

    High resolution mapping of transcriptional repression reveals complex and interdependent mechanisms that underpin rapid transitions between transcriptional states.
57. 1. Neuroscience

    Computational models of O-LM cells are recruited by low or high theta frequency inputs depending on h-channel distributions

    Vladislav Sekulić, Frances K Skinner

    The contribution of biophysical ion channels to neuron function can be predicted by taking advantage of an ongoing dialogue between model and experiment.
58. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    DNA-mediated association of two histone-bound complexes of yeast Chromatin Assembly Factor-1 (CAF-1) drives tetrasome assembly in the wake of DNA replication

    Francesca Mattiroli, Yajie Gu ... Karolin Luger

    After DNA replication, nucleosomes are assembled by two histone chaperone complexes each bound to an H3-H4 histone dimer, suggesting the feasibility for a semi-conservative mode of epigenome inheritance.
59. 1. Neuroscience

    A cellular mechanism for inverse effectiveness in multisensory integration

    Torrey LS Truszkowski, Oscar A Carrillo ... Carlos D Aizenman

    Building on previous work (Felch et al., 2016), it is shown that inverse effectiveness, a central property of multisensory integration, in the optic tectum is mediated by the activation of NMDA-type glutamate receptors, resulting in a response greater than the sum of responses to each individual sensory modality.
60. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1

    Paul Victor Sauer, Jennifer Timm ... Daniel Panne

    The CAF1 complex binds single histone H3-H4 dimers, and two such complexes associate with extended DNA elements to ensure the deposition of H3-H4 tetramers, the first step in the assembly of nucleosomes.
61. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Fail-safe control of translation initiation by dissociation of eIF2α phosphorylated ternary complexes

    Martin D Jennings, Christopher J Kershaw ... Graham D Pavitt

    Phosphorylated translation initiation factor eIF2, a potent inhibitor of protein synthesis in eukaryotic cells, is also inhibitory to protein synthesis when bound to GTP and initiator tRNA broadening the reach and immediacy of eIF2-mediated control.
62. 1. Computational and Systems Biology

    Systematic morphological profiling of human gene and allele function via Cell Painting

    Mohammad Hossein Rohban, Shantanu Singh ... Anne E Carpenter

    Gene function can be revealed based on characteristic phenotypes using a Cell Painting microscopy assay.
63. 1. Medicine

    Human cardiac fibroblasts adaptive responses to controlled combined mechanical strain and oxygen changes in vitro

    Giovanni Stefano Ugolini, Andrea Pavesi ... Monica Soncini

    Human cardiac fibroblasts regulate their cellular responses according to the combination of multiple environmental stimuli namely oxygen changes and mechanical signals.
64. 1. Neuroscience

    Stimulus background influences phase invariant coding by correlated neural activity

    Michael G Metzen, Maurice J Chacron

    Building on previous work (Metzen et al., 2016), a combination of neurophysiological and behavioral approaches reveals that changes in the background strongly impacts invariant coding and perception of behaviourally relevant signals.
65. 1. Cell Biology
    2. Stem Cells and Regenerative Medicine

    PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes

    Mitsuhiro Endoh, Takaho A Endo ... Haruhiko Koseki

    PCGF6 links sequence specific target recognition by the MAX/MGA transcription factor complex to PRC1 (polycomb repressive complex 1) -dependent transcriptional silencing of germ cell-specific genes in mouse pluripotent stem cells.
66. 1. Cell Biology

    Scaffold-mediated gating of Cdc42 signalling flux

    Péter Rapali, Romain Mitteau ... Derek McCusker

    The scaffold Bem1 increases the rate of GEF-mediated Cdc42 activation, while also increasing the rate and extent of GEF phosphorylation by PAK, which attenuates further scaffold stimulation.
67. 1. Evolutionary Biology

    Membranes, energetics, and evolution across the prokaryote-eukaryote divide

    Michael Lynch, Georgi K Marinov

    The common view that the mitochondrion endowed eukaryotes with a boost in bioenergetic capacity above that in prokaryotes is inconsistent with a diversity of cellular features.
68. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Mechanism of ribosome rescue by ArfA and RF2

    Gabriel Demo, Egor Svidritskiy ... Andrei A Korostelev

    Cryo-EM structures reveal the structural dynamics of ArfA*RF2-mediated rescue of stalled ribosomes.
69. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation

    Anzhalika Sidarovich, Cindy L Will ... Reinhard Lührmann

    Stalling spliceosome assembly at a novel step before Bact complex formation reveals new insights into the extensive RNP rearrangements and compositional changes that accompany the intricate process of spliceosome activation.
70. 1. Biochemistry and Chemical Biology
    2. Genetics and Genomics

    Genome mining unearths a hybrid nonribosomal peptide synthetase-like-pteridine synthase biosynthetic gene cluster

    Hyun Bong Park, Corey E Perez ... Jason M Crawford

    A new type of hybrid nonribosomal peptide synthetase (NRPS)-like-pteridine synthase biosynthetic pathway has been illuminated via genome mining.
71. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress

    Alicia N McMurchy, Przemyslaw Stempor ... Julie Ahringer

    Genome-wide profiling and functional analyses reveal a network of heterochromatin and small RNA factors that silences repetitive elements and prevents genotoxic stress to ensure fertility.
72. 1. Neuroscience

    The computational nature of memory modification

    Samuel J Gershman, Marie-H Monfils ... Yael Niv

    A computational model explains how the brain chooses between creating a new memory versus updating an old one when faced with an event that defies expectations.
73. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels

    Anna L Miles, Stephen P Burr ... James A Nathan

    An unbiased genome-wide human forward genetic screen identifies the vacuolar ATPase complex and assembly factors as regulators of HIF stability through their actions on intracellular iron metabolism.
74. 1. Plant Biology

    Natural haplotypes of FLM non-coding sequences fine-tune flowering time in ambient spring temperatures in Arabidopsis

    Ulrich Lutz, Thomas Nussbaumer ... Claus Schwechheimer

    Gene expression changes associated with polymorphisms in non-coding sequences of the flowering time regulator FLM directly influence flowering time in ambient temperature in Arabidopsis over an extended vegetative period.
75. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Constitutive scaffolding of multiple Wnt enhanceosome components by Legless/BCL9

    Laurens M van Tienen, Juliusz Mieszczanek ... Mariann Bienz

    BCL9/Legless is an integral component of the Wnt enhanceosome, harboring binding sites in its conserved C-terminus for multiple core components of this complex including ChiLS and Groucho/TLE.
76. 1. Computational and Systems Biology
    2. Developmental Biology

    Discovering sparse transcription factor codes for cell states and state transitions during development

    Leon A Furchtgott, Samuel Melton ... Sharad Ramanathan

    Sparse patterns in gene expression allow simultaneous discovery of cell states, lineage relationships and key genes controlling developmental decisions.
77. 1. Computational and Systems Biology
    2. Stem Cells and Regenerative Medicine

    Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states

    Sumin Jang, Sandeep Choubey ... Sharad Ramanathan

    Mammalian germ layer differentiation is characterized by transitions through discrete cell states, which are transcriptionally as well as functionally distinct.
78. 1. Structural Biology and Molecular Biophysics
    2. Neuroscience

    Identification of a pre-active conformation of a pentameric channel receptor

    Anaïs Menny, Solène N Lefebvre ... Pierre-Jean Corringer

    Allosteric reorganizations of a bacterial channel receptor are mapped along the protein structure, using the site-directed bimane quenching fluorescence technique, through parallel real-time conformational and electrophysiological recordings.
79. 1. Neuroscience

    Synaptic transmission and plasticity require AMPA receptor anchoring via its N-terminal domain

    Jake F Watson, Hinze Ho, Ingo H Greger

    The positioning of AMPA-type glutamate receptors at synapses – a requirement for effective neurotransmission and synaptic plasticity – is orchestrated by their extracellular, N-terminal domain.
80. 1. Biochemistry and Chemical Biology

    Total biosynthesis of the cyclic AMP booster forskolin from Coleus forskohlii

    Irini Pateraki, Johan Andersen-Ranberg ... Björn Hamberger

    The entire biosynthetic pathway for the diterpenoid forskolin in Coleus forskohlii has been reconstituted in yeast.
81. 1. Developmental Biology
    2. Evolutionary Biology

    Mating and male pheromone kill Caenorhabditis males through distinct mechanisms

    Cheng Shi, Alexi M Runnels, Coleen T Murphy

    Male C. elegans die through two distinct mechanisms – mating-induced germline activation, and potent male pheromone toxicity – but the latter is unique to males of androdioecious species (made up of hermaphrodites and males).
82. 1. Structural Biology and Molecular Biophysics
    2. Cell Biology

    Kinesin-4 KIF21B is a potent microtubule pausing factor

    Wilhelmina E van Riel, Ankit Rai ... Anna Akhmanova

    Kinesin-4 KIF21B combines a processive motor activity with two non-motor microtubule-binding domains and an autoregulatory region to induce pausing of microtubule plus ends.
83. 1. Neuroscience

    Externally induced frontoparietal synchronization modulates network dynamics and enhances working memory performance

    Ines R Violante, Lucia M Li ... David J Sharp

    Externally induced synchronous/desynchronous oscillations during working memory performance reveal distinct patterns of brain activity and connectivity across large-scale networks recruited by the task.
84. 1. Computational and Systems Biology
    2. Neuroscience

    A molecular mechanism for the topographic alignment of convergent neural maps

    Elise Savier, Stephen J Eglen ... Michael Reber

    Retinal ephrin-As gradients provide positional information, through retino-collicular map in the superior colliculus, for topographic alignment of cortico-collicular projections.
85. 1. Stem Cells and Regenerative Medicine
    2. Chromosomes and Gene Expression

    The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

    Hamish W King, Robert J Klose

    The chromatin remodeller BRG1 is recruited to pluripotency-associated gene regulatory elements by the pioneer transcription factor OCT4 to support further transcription factor binding and gene regulation.
86. 1. Cancer Biology
    2. Cell Biology

    p27^Kip1 promotes invadopodia turnover and invasion through the regulation of the PAK1/Cortactin pathway

    Pauline Jeannot, Ada Nowosad ... Arnaud Besson

    p27Kip1 directly controls invadopodia turnover by promoting the interaction of PAK1 with Cortactin, which induces Cortactin phosphorylation, invadopodia disassembly and facilitates invasion through extracellular matrix.
87. 1. Cell Biology
    2. Computational and Systems Biology

    Decoupling global biases and local interactions between cell biological variables

    Assaf Zaritsky, Uri Obolski ... Gaudenz Danuser

    DeBias is a generic method to decompose and quantify the confounding, global factors and direct interactions of pairwise interacting variables.
88. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Quantitative proteomics reveal proteins enriched in tubular endoplasmic reticulum of Saccharomyces cerevisiae

    Xinbo Wang, Shanshan Li ... Junjie Hu

    Immunoisolation combined with quantitative proteomics identifies 79 proteins enriched in the tubular endoplasmic reticulum and provides useful tool for analyzing this organelle's functions.
89. 1. Structural Biology and Molecular Biophysics
    2. Chromosomes and Gene Expression

    Single-molecule observation of DNA compaction by meiotic protein SYCP3

    Johanna L Syrjänen, Iddo Heller ... Luca Pellegrini

    Building on previous work (Syrjänen, Pellegrini, & Davies, 2014), it is shown that SYCP3 contributes to the architecture of meiotic chromosomes through local bridging interactions that result in large-scale compaction of the chromosome axis.
90. 1. Computational and Systems Biology
    2. Immunology and Inflammation

    Memory CD4 T cell subsets are kinetically heterogeneous and replenished from naive T cells at high levels

    Graeme Gossel, Thea Hogan ... Andrew J Yates

    The maintenance of memory CD4 T cells in mice relies on a continual and strikingly high level of replenishment from naive precursors, and older memory T cells may resist the influx of newer ones.
91. 1. Structural Biology and Molecular Biophysics

    Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals

    Ho Yee Joyce Fung, Szu-Chin Fu, Yuh Min Chook

    Building on previous work (Fung et al., 2015), the structures of eight new nuclear export signal (NES) peptides bound to Exportin CRM1 are reported, revealing striking diversity in NES structures, a small conserved secondary structural element, and a CRM1 residue that functions as a selectivity filter.
92. 1. Structural Biology and Molecular Biophysics
    2. Cell Biology

    Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks

    Jenna R Christensen, Glen M Hocky ... David R Kovar

    Both cooperative and competitive associations of actin binding proteins with actin filaments help drive the self-organization of functionally diverse F-actin networks in fission yeast.
93. 1. Developmental Biology

    Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta

    Lyad Zamir, Reena Singh ... Eldad Tzahor

    Live imaging coupled with cell lineage tracing in chick and mouse embryos reveal that the cardiac regulatory gene Nkx2.5 is also transiently expressed in early extra-cardiac hemogenic angioblasts that migrate to the heart, yolk sac and dorsal aorta.
94. 1. Developmental Biology
    2. Neuroscience

    Transcription factor Emx2 controls stereociliary bundle orientation of sensory hair cells

    Tao Jiang, Katie Kindt, Doris K Wu

    Emx2 reverses hair bundle orientation in sensory hair cells.
95. 1. Immunology and Inflammation
    2. Neuroscience

    Peptidoglycan sensing by octopaminergic neurons modulates Drosophila oviposition

    C Leopold Kurz, Bernard Charroux ... Julien Royet

    Female fruit flies sense bacteria-derived peptidoglycan via the octopaminergic neurons to adapt their egg laying behavior to their infection status.
96. 1. Plant Biology
    2. Developmental Biology

    Autocrine regulation of stomatal differentiation potential by EPF1 and ERECTA-LIKE1 ligand-receptor signaling

    Xingyun Qi, Soon-Ki Han ... Keiko U Torii

    The stomatal precursor cell uses autocrine peptide-receptor kinase signaling to self-inhibit its differentiation potential in order to ensure proper stomatal development on the plant epidermis.
97. 1. Biochemistry and Chemical Biology
    2. Cell Biology

    Substrate specificity of TOR complex 2 is determined by a ubiquitin-fold domain of the Sin1 subunit

    Hisashi Tatebe, Shinichi Murayama ... Kazuhiro Shiozaki

    Sin1, a regulatory subunit of TOR protein kinase, has an evolutionarily conserved domain that specifically binds and recruits substrate for phosphorylation, and may represent a potential target for anti-cancer drugs.
98. 1. Structural Biology and Molecular Biophysics

    Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel

    Sandip Basak, Nicolaus Schmandt ... Sudha Chakrapani

    Polyunsaturated fatty acids enhance desensitization in pentameric ligand-gated ion channels.
99. 1. Neuroscience

    Detecting changes in dynamic and complex acoustic environments

    Yves Boubenec, Jennifer Lawlor ... Bernhard Englitz

    Psychophysics experiments and EEG recordings reveal that people's performance in detecting unexpected changes in complex auditory scenes can be modeled as a process of sensory evidence accumulation.
100. 1. Developmental Biology
     2. Neuroscience

     Supporting cells remove and replace sensory receptor hair cells in a balance organ of adult mice

     Stephanie A Bucks, Brandon C Cox ... Jennifer S Stone

     Cell fate-mapping with genetically-modified mouse models and cellular markers demonstrates that sensory hair cells in the vestibular portion of the inner ear are a dynamic population in adult mice that undergo cell death and replacement under normal conditions.
101. 1. Cell Biology
     2. Developmental Biology

     Uncoupling apical constriction from tissue invagination

     SeYeon Chung, Sangjoon Kim, Deborah J Andrew

     Spatially coordinated apical constriction occurs during Drosophila salivary gland invagination, but the salivary gland can form fully internalized and elongated tubes even when this process is completely blocked.
102. 1. Cell Biology

     KChIP2 is a core transcriptional regulator of cardiac excitability

     Drew M Nassal, Xiaoping Wan ... Isabelle Deschênes

     The ion channel accessory subunit KChIP2 has a transcriptional role that provides regulation over miRNA targets, driving the adverse remodeling of key ion channels during cardiac stress and leading to the development of arrhythmia.
103. 1. Biochemistry and Chemical Biology
     2. Microbiology and Infectious Disease

     Novel mechanism of metabolic co-regulation coordinates the biosynthesis of secondary metabolites in Pseudomonas protegens

     Qing Yan, Benjamin Philmus ... Joyce E Loper

     The production of two secondary metabolites is co-regulated in a bacterium via an intermediate in one pathway that is converted into signals to activate the second pathway.
104. 1. Structural Biology and Molecular Biophysics
     2. Microbiology and Infectious Disease

     Bacterial flagella grow through an injection-diffusion mechanism

     Thibaud T Renault, Anthony O Abraham ... Marc Erhardt

     Single cell, fluorescent microscopy and mathematical modeling reveal how bacterial flagella dynamically assemble outside the cell.
105. 1. Chromosomes and Gene Expression

     The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription

     Eva Torreira, Jaime Alegrio Louro ... Carlos Fernández-Tornero

     Live-cell imaging, genetic analysis and electron cryomicroscopy identify structural motifs involved in the differential assembly of Pol I-Rrn3 complexes and Pol I homodimers in response to nutrient availability.
106. 1. Computational and Systems Biology
     2. Neuroscience

     Mapping the function of neuronal ion channels in model and experiment

     William F Podlaski, Alexander Seeholzer ... Tim P Vogels

     The ion channel genealogy resource is a comprehensive and intuitive comparison tool for ion channel models and experimental data, helping to visualize their similarity and function to facilitate better experimentally-constrained modeling.
107. 1. Cell Biology
     2. Plant Biology

     Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains

     Christoph A Bücherl, Iris K Jarsch ... Cyril Zipfel

     Although genetically and biochemically linked, the plant immune and growth receptors FLS2 and BRI1 form dispersed receptor clusters within the plasma membrane that are spatiotemporally separated.
108. 1. Cell Biology
     2. Neuroscience

     Olfactory receptor accessory proteins play crucial roles in receptor function and gene choice

     Ruchira Sharma, Yoshiro Ishimaru ... Hiroaki Matsunami

     G protein-coupled odorant receptors regulate their own gene transcription based on their cell surface trafficking, which is facilitated by receptor transporting protein (RTP) family members.
109. 1. Biochemistry and Chemical Biology
     2. Plant Biology

     Origin and evolution of transporter substrate specificity within the NPF family

     Morten Egevang Jørgensen, Deyang Xu ... Barbara Ann Halkier

     Phylogenetic and biochemical analyses reveals a shared evolutionary path between biosynthesis and transport of defense metabolites in plants.
110. 1. Biochemistry and Chemical Biology
     2. Cell Biology

     An unexpected role for the yeast nucleotide exchange factor Sil1 as a reductant acting on the molecular chaperone BiP

     Kevin D Siegenthaler, Kristeen A Pareja ... Carolyn S Sevier

     Building on previous work (Wang et al., 2014), it is shown that the nucleotide exchange factor of the chaperone BiP (Sil1) unexpectedly facilitates the reduction of oxidized BiP.
111. 1. Cell Biology
     2. Microbiology and Infectious Disease

     Plasmodium falciparum parasites deploy RhopH2 into the host erythrocyte to obtain nutrients, grow and replicate

     Natalie A Counihan, Scott A Chisholm ... Tania F de Koning-Ward

     Plasmodium parasites secrete RhopH2 from the rhoptry organelle into their host red blood cell to facilitate the uptake of essential nutrients required for parasite replication and survival.
112. 1. Microbiology and Infectious Disease
     2. Cell Biology

     The Plasmodium falciparum rhoptry protein RhopH3 plays essential roles in host cell invasion and nutrient uptake

     Emma S Sherling, Ellen Knuepfer ... Christiaan van Ooij

     The rhoptry protein RhopH3 is crucial for the invasion and growth of the malaria parasite and disruption of it provides insight into the binding of the parasite to the host red blood cell and into the formation of new import pathways.
113. 1. Structural Biology and Molecular Biophysics
     2. Microbiology and Infectious Disease

     Chlamydia interfere with an interaction between the mannose-6-phosphate receptor and sorting nexins to counteract host restriction

     Cherilyn A Elwell, Nadine Czudnochowski ... Oren S Rosenberg

     Structure of a pathogen effector complexed to Sorting Nexin 5 reveals an evolutionarily conserved interface that is required for retromer-dependent host restriction.