December 2018

Research articles

1. 1. Cell Biology

   The ULK1-FBXW5-SEC23B nexus controls autophagy

   Yeon-Tae Jeong, Daniele Simoneschi ... Michele Pagano

   The control of SEC23B degradation by SCF^FBXW5 and ULK1 regulates the autophagy.
2. 1. Neuroscience

   Spinal Shox2 interneuron interconnectivity related to function and development

   Ngoc T Ha, Kimberly J Dougherty

   Spinal Shox2 interneurons are strongly interconnected by gap junctional coupling in a function-specific manner, which provides a mechanism for synchronization of rhythm-generating neurons and may contribute to locomotor rhythmicity.
3. 1. Neuroscience

   Pre-saccadic remapping relies on dynamics of spatial attention

   Martin Szinte, Donatas Jonikaitis ... Heiner Deubel

   To see the world stable across saccades, the brain compensates retinal shifts induced by the movements, pre-saccadic maps of sensitivity reveal that this process takes time and follows attentional dynamics.
4. 1. Cell Biology
   2. Neuroscience

   Cumulative mitochondrial activity correlates with ototoxin susceptibility in zebrafish mechanosensory hair cells

   Sarah B Pickett, Eric D Thomas ... David W Raible

   The history of mitochondrial activity predicts whether zebrafish mechanosensory hair cells live or die after toxic drug exposure.
5. 1. Evolutionary Biology
   2. Microbiology and Infectious Disease

   Symbiont location, host fitness, and possible coadaptation in a symbiosis between social amoebae and bacteria

   Longfei Shu, Debra A Brock ... Susanne DiSalvo

   Morphological and fitness defects imposed on amoebae hosts by Burkholderia symbionts demonstrates symbiont species-specific effects and provides evidence of host adaptation to naturally acquired symbionts.
6. 1. Immunology and Inflammation
   2. Microbiology and Infectious Disease

   Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination

   Joseph J Campo, Timothy Q Le ... Nicholas J Croucher

   Panproteome array analysis of antibody responses to a pneumococcal whole cell vaccine reveals consistent induction of immune responses to multiple surface proteins, despite individuals' unique pre-existing antibody profiles.
7. 1. Developmental Biology

   The flow responsive transcription factor Klf2 is required for myocardial wall integrity by modulating Fgf signaling

   Seyed Javad Rasouli, Mohamed El-Brolosy ... Didier Y Stainier

   Endocardial Klf2 regulates cardiomyocyte adhesion and myocardial wall integrity by modulating FGF signaling in zebrafish.
8. 1. Computational and Systems Biology
   2. Genetics and Genomics

   Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

   Florian Heigwer, Christian Scheeder ... Michael Boutros

   Genetic interaction analysis by combinatorial genetic perturbation and high-throughput imaging maps time- and context-dependent crosstalk between signaling pathways.
9. 1. Neuroscience

   Two central pattern generators from the crab, Cancer borealis, respond robustly and differentially to extreme extracellular pH

   Jessica A Haley, David Hampton, Eve Marder

   The rhythms generated by the stomatogastric and cardiac ganglia of the Jonah crab are surprisingly robust but differentially sensitive to acute changes in extracellular pH from pH 5.5 to 10.4.
10. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Cisplatin-induced DNA double-strand breaks promote meiotic chromosome synapsis in PRDM9-controlled mouse hybrid sterility

    Liu Wang, Barbora Valiskova, Jiri Forejt

    The exogenous DNA DSBs improve meiotic chromosome pairing in mouse inter-subspecific hybrids, thus providing an evidence for a DSB-dependent mechanism of the PRDM9-controlled synapsis failure and infertility.
11. 1. Medicine

    Myocardial NADPH oxidase-4 regulates the physiological response to acute exercise

    Matthew Hancock, Anne D Hafstad ... Min Zhang

    Cardiomyocyte Nox4 is a crucial physiological mediator of Nrf2 activation during acute exercise, triggering an adaptive response that preserves redox balance, mitochondrial and cardiac function to support normal physical exercise.
12. 1. Microbiology and Infectious Disease

    Transcriptomic analysis reveals reduced transcriptional activity in the malaria parasite Plasmodium cynomolgi during progression into dormancy

    Nicole L Bertschi, Annemarie Voorberg-van der Wel ... Guglielmo Roma

    Transcriptome profiling of malaria liver-stage parasites provides unprecedented knowledge on genes and pathways expressed in truly dormant hypnozoites and indicates that dormancy is associated with a switch in energy metabolism.
13. 1. Chromosomes and Gene Expression
    2. Developmental Biology

    Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

    Mustafa Mir, Michael R Stadler ... Michael B Eisen

    The probability of transcription factors binding to their target sites is choreographed through the formation of dynamic multi-protein hubs that transiently interact with actively transcribing genes.
14. 1. Developmental Biology

    Spatial patterning of liver progenitor cell differentiation mediated by cellular contractility and Notch signaling

    Kerim B Kaylan, Ian C Berg ... Gregory H Underhill

    Mechanical stress plays a cooperative role with Notch in biliary differentiation of liver progenitors, supporting a model of liver development in which biomechanical cues are key inducers of cell fate.
15. 1. Neuroscience

    Thalamic reticular control of local sleep in mouse sensory cortex

    Laura MJ Fernandez, Gil Vantomme ... Anita Lüthi

    Local cortical sleep features arise subcortically due to heterogeneous burst discharge in neurons of a sleep rhythm pacemaker previously thought to act uniformly.
16. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Mechanisms of opening and closing of the bacterial replicative helicase

    Jillian Chase, Andrew Catalano ... David Jeruzalmi

    Analysis of the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex provides insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
17. 1. Microbiology and Infectious Disease

    Quorum sensing controls Vibrio cholerae multicellular aggregate formation

    Matthew Jemielita, Ned S Wingreen, Bonnie L Bassler

    A quorum-sensing-controlled program of multicellularity, aggregation, is identified in Vibrio cholerae, which may be important for transitions between the marine niche and the human host.
18. 1. Cell Biology

    The unfolded protein response and endoplasmic reticulum protein targeting machineries converge on the stress sensor IRE1

    Diego Acosta-Alvear, G Elif Karagöz ... Peter Walter

    The coordination of protein targeting to the endoplasmic reticulum and the unfolded protein response through the stress sensor IRE1 ensures quality control of the secreted and transmembrane proteomes.
19. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans

    Gregory M Davis, Shikui Tu ... Peter R Boag

    The RNA-binding protein NHL-2 is required for small-RNA mediated transgenerational epigenetic gene regulation.
20. 1. Neuroscience

    NMDA spikes mediate amplification of inputs in the rat piriform cortex

    Amit Kumar, Oded Schiff ... Jackie Schiller

    Dendrites of pyramidal neurons in piriform cortex can initiate NMDA spikes, which may serve to amplify odor responses, and provide combination selectivity underlying 'discontinuous' odor receptive fields in these neurons.
21. 1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    A herpesvirus encoded Qa-1 mimic inhibits natural killer cell cytotoxicity through CD94/NKG2A receptor engagement

    Xiaoli Wang, Sytse J Piersma ... Daved H Fremont

    Rodent herpesvirus Peru overcomes NK ‘missing-self’ killing using a non-classical MHC-I like protein resistant todownregulation by its own ubiquitin ligase that potently sabotages antigen presentation to T-cells.
22. 1. Neuroscience

    Temporally specific engagement of distinct neuronal circuits regulating olfactory habituation in Drosophila

    Ourania Semelidou, Summer F Acevedo, Efthimios MC Skoulakis

    Habituation to brief olfactory stimulation is biphasic and mediated by distinct neuronal circuits where an initial latency phase is rapidly followed by stimulus devaluation signifying behavioral habituation in Drosophila.
23. 1. Neuroscience

    Developmental 'awakening' of primary motor cortex to the sensory consequences of movement

    James C Dooley, Mark S Blumberg

    Early in development, before neurons in primary motor cortex are involved in motor control, they undergo a rapid transition in how they process sensory information following sleep and wake movements.
24. 1. Neuroscience

    Specific lexico-semantic predictions are associated with unique spatial and temporal patterns of neural activity

    Lin Wang, Gina Kuperberg, Ole Jensen

    The prediction of specific words is associated with distinct spatial and temporal patterns of neural activity within the left inferior and medial temporal regions before the predicted word is presented.
25. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Cooperative cobinding of synthetic and natural ligands to the nuclear receptor PPARγ

    Jinsai Shang, Richard Brust ... Douglas J Kojetin

    Synthetic PPARγ ligands push and cobind with natural endogenous ligands, instead of compete and displace, which synergistically affects the structure and function of PPARγ.
26. 1. Genetics and Genomics

    Genome-wide quantification of the effects of DNA methylation on human gene regulation

    Amanda J Lea, Christopher M Vockley ... Jenny Tung

    mSTARR-seq identifies regions of the genome where DNA methylation causally impacts gene expression, providing a map of which epigenetic marks may influence trait variation.
27. 1. Neuroscience

    'Artiphysiology' reveals V4-like shape tuning in a deep network trained for image classification

    Dean A Pospisil, Anitha Pasupathy, Wyeth Bair

    Single units in a deep convolutional neural network trained for image classification develop shape selectivity that is similar to that found in the primate visual cortex.
28. 1. Physics of Living Systems

    Measuring cis-regulatory energetics in living cells using allelic manifolds

    Talitha L Forcier, Andalus Ayaz ... Justin B Kinney

    A novel strategy is presented for quantitatively measuring protein-DNA and protein-protein interactions that regulate transcription in living cells.
29. 1. Computational and Systems Biology
    2. Developmental Biology

    A re-inducible gap gene cascade patterns the anterior–posterior axis of insects in a threshold-free fashion

    Alena Boos, Jutta Distler ... Ezzat El-Sherif

    The body axis of insects is divided into different fates using a self-regulatory and threshold-free mechanism.
30. 1. Neuroscience

    Evoked transients of pH-sensitive fluorescent false neurotransmitter reveal dopamine hot spots in the globus pallidus

    Jozsef Meszaros, Timothy Cheung ... David Sulzer

    Dopamine release within the mouse external globus pallidus, an area of very sparse innervation, is observed and described for the first time through a new technique: flashing false fluorescent neurotransmitters.
31. 1. Physics of Living Systems

    Downsizing the molecular spring of the giant protein titin reveals that skeletal muscle titin determines passive stiffness and drives longitudinal hypertrophy

    Ambjorn Brynnel, Yaeren Hernandez ... Henk L Granzier

    Genetically altering the size of the molecular spring element in the giant protein titin established that titin determines the stiffness of skeletal muscle and the number of sarcomeres in series.
32. 1. Developmental Biology
    2. Neuroscience

    Conserved and divergent development of brainstem vestibular and auditory nuclei

    Marcela Lipovsek, Richard JT Wingate

    The development of brainstem auditory nuclei echoes the divergent evolutionary history of amniote auditory systems.
33. 1. Neuroscience

    NKB signaling in the posterodorsal medial amygdala stimulates gonadotropin release in a kisspeptin-independent manner in female mice

    Chrysanthi Fergani, Silvia Leon ... Victor M Navarro

    Kiss1 neurons and NKB-responsive neurons of the medial amygdala stimulate LH release in females through different (previously unknown) pathways which, in the case of NKB-responsive neurons, are kisspeptin-independent but estradiol-dependent.
34. 1. Neuroscience

    Neuronal variability and tuning are balanced to optimize naturalistic self-motion coding in primate vestibular pathways

    Diana E Mitchell, Annie Kwan ... Kathleen E Cullen

    A match between neuronal variability and tuning enables optimized coding of natural self-motion in early vestibular pathways.
35. 1. Neuroscience

    Large and fast human pyramidal neurons associate with intelligence

    Natalia A Goriounova, Djai B Heyer ... Huibert D Mansvelder

    Neurons from individuals with higher IQ scores have larger dendrites, are able to maintain faster action potentials, and thus process information more efficiently.
36. 1. Evolutionary Biology
    2. Plant Biology

    An unexpected noncarpellate epigynous flower from the Jurassic of China

    Qiang Fu, Jose Bienvenido Diez ... Xin Wang

    Flowers did bloom in the Early Jurassic.
37. 1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Heterogeneous absorption of antimicrobial peptide LL37 in Escherichia coli cells enhances population survivability

    Mehdi Snoussi, John Paul Talledo ... Sattar Taheri-Araghi

    A rapid absorption and retention of antimicrobial peptides by dead Escherichia coli cells can increase the survivability of the cell population in a "cooperative" fashion.
38. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogen Acinetobacter baumannii

    Lucile Moynié, Ilaria Serra ... James H Naismith

    The pathogen Acinetobacter baumannii recognises preacinetobactin not acinetobactin, yet appears likely to translocate both compounds through a mixed complex.
39. 1. Evolutionary Biology

    Multifactorial processes underlie parallel opsin loss in neotropical bats

    Alexa Sadier, Kalina TJ Davies ... Karen E Sears

    Parallel losses of short-wave light sensitivity in diverse bats occurred through independent changes at multiple steps in the conversion of genotype into functional phenotype, including pre-, during, and post-transcription.
40. 1. Neuroscience

    Potentiation of cerebellar Purkinje cells facilitates whisker reflex adaptation through increased simple spike activity

    Vincenzo Romano, Licia De Propris ... Chris I De Zeeuw

    Physiological and behavioral analyses show that expression of cerebellar whisker learning can be mediated by increased simple spike activity, depending on LTP induction at parallel fiber to Purkinje cell synapses.
41. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The distribution of antibiotic use and its association with antibiotic resistance

    Scott W Olesen, Michael L Barnett ... Yonatan H Grad

    Population-level antibiotic resistance correlates with the breadth of antibiotic use, that is, the proportion of people taking an antibiotic, better than with intensity of use the amount of use among users.
42. 1. Neuroscience

    A causal role for right temporo-parietal junction in signaling moral conflict

    Ignacio Obeso, Marius Moisa ... Jean-Claude Dreher

    Disrupting the right temporo-parietal junction did not change the general motivation to give or adapt behavior to social reputation cues, but specifically reduced the impact of moral-material conflict.
43. 1. Stem Cells and Regenerative Medicine

    Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging

    Petter Säwen, Mohamed Eldeeb ... David Bryder

    Using a lineage tracing model, it is demonstrated that adult murine hematopoiesis is contingent on the continuous output from HSCs, with quantitative contributions that are dependent on lineage-type and age.
44. 1. Neuroscience

    Aquaporin-4-dependent glymphatic solute transport in the rodent brain

    Humberto Mestre, Lauren M Hablitz ... Maiken Nedergaard

    An international collaboration between five independent research groups replicates findings confirming the importance of aquaporin-4 in glymphatic solute transport using five different mouse knockout lines.
45. 1. Physics of Living Systems

    Spatial control of neuronal metabolism through glucose-mediated mitochondrial transport regulation

    Anamika Agrawal, Gulcin Pekkurnaz, Elena F Koslover

    A quantitative analysis of glucose-dependent transport regulation indicates that mitochondrial accumulation in regions of high nutrient availability can enhance metabolism in neuronal axons under physiologically relevant conditions.
46. 1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Reciprocal regulation among TRPV1 channels and phosphoinositide 3-kinase in response to nerve growth factor

    Anastasiia Stratiievska, Sara Nelson ... Sharona E Gordon

    A dual-color TIRFM study reveals a new form of inflammatory regulation, in which a lipid kinase and ion channel reciprocally regulate each other to amplify the response to painful stimuli.
47. 1. Neuroscience

    Perineuronal nets control visual input via thalamic recruitment of cortical PV interneurons

    Giulia Faini, Andrea Aguirre ... Alberto Bacci

    Accumulation of perineuronal nets around parvalbumin (PV)-positive inhibitory interneurons closes visual cortical plasticity by selectively down-regulating thalamic synapses onto PV cells in a sensory-dependent manner.
48. 1. Evolutionary Biology

    Privatisation rescues function following loss of cooperation

    Sandra Breum Andersen, Melanie Ghoul ... Ashleigh S Griffin

    A population of pathogenic bacteria is found to respond to the loss of cooperation by privatising an essential function.
49. 1. Cell Biology

    A liquid-like organelle at the root of motile ciliopathy

    Ryan L Huizar, Chanjae Lee ... John B Wallingford

    DynAPs reveal that biological phase separation provides the organizing principle for the complex process of dynein motor assembly in cells with motile cilia.
50. 1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    The role of scaffold reshaping and disassembly in dynamin driven membrane fission

    Martina Pannuzzo, Zachary A McDargh, Markus Deserno

    Computational modeling of a dynamin-constricted membrane neck can rank proposed shape changes of the helical scaffold in terms of their fission aptitude and elucidate the associated pathways.
51. 1. Computational and Systems Biology
    2. Epidemiology and Global Health

    Inference and control of the nosocomial transmission of methicillin-resistant Staphylococcus aureus

    Sen Pei, Flaviano Morone ... Jeffrey L Shaman

    The asymptomatic colonization and importation of methicillin-resistant Staphylococcus aureus (MRSA) in hospital settings can be inferred from observed cases using combined model-inference methods and used to inform improved interventions.
52. 1. Stem Cells and Regenerative Medicine

    Yap1 safeguards mouse embryonic stem cells from excessive apoptosis during differentiation

    Lucy LeBlanc, Bum-Kyu Lee ... Jonghwan Kim

    During ES cell differentiation, Yap1 directly regulates apoptosis-related genes like Bcl-2 and Mcl-1 to attenuate apoptosis and promote cell survival to allow for successful cell fate changes.
53. 1. Neuroscience

    Odor-evoked category reactivation in human ventromedial prefrontal cortex during sleep promotes memory consolidation

    Laura K Shanahan, Eva Gjorgieva ... Jay A Gottfried

    Odor cues in sleep evoke content-specific signatures of neural reactivation in visual and prefrontal brain areas that predict subsequent memory performance in the wake state.
54. 1. Microbiology and Infectious Disease

    Shed EBA-175 mediates red blood cell clustering that enhances malaria parasite growth and enables immune evasion

    May M Paing, Nichole D Salinas ... Niraj H Tolia

    Plasmodium falciparum invasion protein EBA-175, once shed from the parasite surface post invasion, facilitates RBC clustering and enhances parasite growth while simultaneously enabling parasite immune evasion of host neutralizing antibodies.
55. 1. Cell Biology

    Genome-wide interrogation of extracellular vesicle biology using barcoded miRNAs

    Albert Lu, Paulina Wawro ... Suzanne R Pfeffer

    A screen using artificially barcoded, exosomal microRNAs, paired with CRISPR guide RNAs, helped identify new players in multivesicular endosome exocytosis and a role for Wnt signaling.
56. 1. Neuroscience

    G_i/o protein-coupled receptors in dopamine neurons inhibit the sodium leak channel NALCN

    Fabian Philippart, Zayd M Khaliq

    The sodium leak NALCN channel functions as a core effector of GABA-B and D2 receptors that is used along with GIRK channels to regulate action potential firing in dopamine neurons.
57. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Pervasive transcription fine-tunes replication origin activity

    Tito Candelli, Julien Gros, Domenico Libri

    The pervasive transcription environment alters the efficiency of firing of replication origins, which are 'protected' by roadblock termination due to origin recognition complex (ORC) and pre-RC complexes.
58. 1. Evolutionary Biology
    2. Genetics and Genomics

    Predicted glycosyltransferases promote development and prevent spurious cell clumping in the choanoflagellate S. rosetta

    Laura A Wetzel, Tera C Levin ... Nicole King

    A genetic screen reveals that two predicted glycosyltransferases promote rosette development and prevent cell clumping in one of the closest living relatives of animals, the choanoflagellate S. rosetta.
59. 1. Cell Biology

    BUB-1 promotes amphitelic chromosome biorientation via multiple activities at the kinetochore

    Frances Edwards, Gilliane Maton ... Julien Dumont

    During chromosome segregation, BUB-1 performs multiple roles.
60. 1. Neuroscience

    Prediction error and repetition suppression have distinct effects on neural representations of visual information

    Matthew F Tang, Cooper A Smout ... Jason B Mattingley

    Multivariate analyses of human electrophysiological recordings revealed that the brain represents unexpected visual stimuli with greater fidelity than expected stimuli which arose independently of simple habituation arising from repetition.
61. 1. Developmental Biology
    2. Neuroscience

    Tuning of delta-protocadherin adhesion through combinatorial diversity

    Adam J Bisogni, Shila Ghazanfar ... David M Lin

    Combinatorial expression patterns of δ-Pcdhs are defined within single neurons, and in vitro assays are employed to establish guiding principles used by this gene family to mediate cell adhesion.
62. 1. Neuroscience

    Offline replay supports planning in human reinforcement learning

    Ida Momennejad, A Ross Otto ... Kenneth A Norman

    fMRI evidence for off-task replay predicts subsequent replanning behavior in humans, suggesting that learning from simulated experience during replay helps update past policies in reinforcement learning.
63. 1. Biochemistry and Chemical Biology
    2. Genetics and Genomics

    Genetic analysis reveals functions of atypical polyubiquitin chains

    Fernando Meza Gutierrez, Deniz Simsek ... David P Toczyski

    A comprehensive genetic interaction screen uncovered biological roles of K11 linkages in amino acid homeostasis and cell cycle regulation in yeast.
64. 1. Neuroscience

    Neural circuitry of a polycystin-mediated hydrodynamic startle response for predator avoidance

    Luis A Bezares-Calderón, Jürgen Berger ... Gáspár Jékely

    The Platynereis startle circuit links polycystin-dependent hydrodynamic sensors to muscle and ciliary effector cells.
65. 1. Cell Biology

    The sterol-responsive RNF145 E3 ubiquitin ligase mediates the degradation of HMG-CoA reductase together with gp78 and Hrd1

    Sam A Menzies, Norbert Volkmar ... Paul J Lehner

    CRISPR/Cas9 genome-wide screens using sterol-sensitive endogenous HMG-CoA reductase (HMGCR) reporter identify the sterol-responsive RNF145 and gp78 as independently responsible for sterol-accelerated degradation of HMGCR, the rate-limiting enzyme of cholesterol biosynthesis.
66. 1. Evolutionary Biology
    2. Genetics and Genomics

    Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

    Colin D Meiklejohn, Emily L Landeen ... Daven C Presgraves

    Selfish genetic elements may either promote or prevent the evolution of reproductive barriers, depending on the extent of gene flow between species.
67. 1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Structured illumination microscopy combined with machine learning enables the high throughput analysis and classification of virus structure

    Romain F Laine, Gemma Goodfellow ... Clemens F Kaminski

    Machine learning in conjunction with super-resolution imaging allows for the first time to quantitatively analyse large and heterogenous virus samples structure at a high throughput and specificity.
68. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus

    Michael Habig, Gert HJ Kema, Eva Holtgrewe Stukenbrock

    Female-inherited supernumerary chromosomes that lack a male-inherited homolog are transmitted to all meiotic products instead of the expected half, which indicates an additional amplification of unpaired chromosomes during meiosis.
69. 1. Cancer Biology

    miR-34a is a microRNA safeguard for Citrobacter-induced inflammatory colon oncogenesis

    Lihua Wang, Ergang Wang ... Xiling Shen

    miR-34a prevents inflammation-induced colonic regeneration from oncogenesis by simultaneously targeting processes in both immune and epithelial cells, including T helper 17 cell differentiation, recruitment, and IL-17 induced epithelial proliferation.
70. 1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Structural organization of a major neuronal G protein regulator, the RGS7-Gβ5-R7BP complex

    Dipak N Patil, Erumbi S Rangarajan ... Kirill A Martemyanov

    Atomic details on structural organization and conformational dynamics of the key regulator of neuronal signaling shed light on its allosteric regulation and role in regulating cellular pathways.
71. 1. Cell Biology

    Muscle-specific stress fibers give rise to sarcomeres in cardiomyocytes

    Aidan M Fenix, Abigail C Neininger ... Dylan T Burnette

    Sarcomeres in heart muscle cells come from stress fiber-like structures that are mechanistically distinct from stress fibers in non-muscle cells.
72. 1. Neuroscience

    Reactive oxygen species regulate activity-dependent neuronal plasticity in Drosophila

    Matthew CW Oswald, Paul S Brooks ... Matthias Landgraf

    Reactive oxygen species, previously considered damaging agents linked to pathology, are required for normal neuronal plasticity, including adjustment of synaptic terminal size, maintenance of synaptic physiology and adaptive behavioural responses.
73. 1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Munc18-1 catalyzes neuronal SNARE assembly by templating SNARE association

    Junyi Jiao, Mengze He ... Yongli Zhang

    Sec1/Munc18-family proteins chaperone SNARE assembly via a common templating mechanism.
74. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Role of the pre-initiation complex in Mediator recruitment and dynamics

    Elisabeth R Knoll, Z Iris Zhu ... Randall H Morse

    Genome-wide recruitment of Mediator and Pol II is reduced in yeast lacking the Med2-Med3-Med15 tail module triad, and Mediator association with gene promoters depends on Pol II, Taf1, and TBP.
75. 1. Developmental Biology

    HIPPO signaling resolves embryonic cell fate conflicts during establishment of pluripotency in vivo

    Tristan Frum, Tayler M Murphy, Amy Ralston

    HIPPO signaling antagonizes the apical domain of polarized cells, driving cell internalization, regulated gene expression, and cell fate change during formation of pluripotent stem cell progenitors in the mouse embryo.
76. 1. Cancer Biology

    Replication Study: Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET

    Jeewon Kim, Amirali Afshari ... Reproducibility Project: Cancer Biology

    Editors' Summary: This Replication Study has reproduced some parts of the original paper but other parts could not be interpreted.
77. 1. Biochemistry and Chemical Biology
    2. Neuroscience

    Tau monomer encodes strains

    Apurwa M Sharma, Talitha L Thomas ... Marc I Diamond

    Tau monomer from aggregate-containing cell models and tauopathy brains adopts discrete structures that act as templates, dictating the conformation of distinct strains that result from its seeding activity.
78. 1. Neuroscience

    Convergence of monosynaptic and polysynaptic sensory paths onto common motor outputs in a Drosophila feeding connectome

    Anton Miroschnikow, Philipp Schlegel ... Michael J Pankratz

    A parallel neuronal network architecture ensures control of basic feeding reflex circuits via integration of crossmodal sensory information to filter multiple biological events and enhance meaningful behavioral choice.
79. 1. Cancer Biology

    Systematic identification of mutations and copy number alterations associated with cancer patient prognosis

    Joan C Smith, Jason M Sheltzer

    Gene copy number provides more prognostic information than gene mutation status in cancer.
80. 1. Evolutionary Biology

    Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism

    Daria N Shalaeva, Dmitry A Cherepanov ... Armen Y Mulkidjanian

    In potassium-dependent NTPases, insertion of the activating potassium ion into the active site leads to rotation of the gamma-phosphate yielding a near-eclipsed, catalytically productive conformation of the triphosphate chain.
81. 1. Structural Biology and Molecular Biophysics

    Voltage-dependent dynamics of the BK channel cytosolic gating ring are coupled to the membrane-embedded voltage sensor

    Pablo Miranda, Miguel Holmgren, Teresa Giraldez

    Allosteric modulation of BK channels, vital for the physiology of nerve, muscle and endocrine cells, is determined by direct coupling between gating ring RCK1 domains and the voltage sensor function.
82. 1. Biochemistry and Chemical Biology

    SETD3 protein is the actin-specific histidine N-methyltransferase

    Sebastian Kwiatkowski, Agnieszka K Seliga ... Jakub Drozak

    Histone-lysine N-methyltransferase SETD3 (NP_115609.2) was identified as the actin-specific histidine N-methyltransferase, an enzyme catalyzing the extremely well-conserved methylation of H73 in β-actin.
83. 1. Structural Biology and Molecular Biophysics

    Molecular basis of signaling specificity between GIRK channels and GPCRs

    Kouki K Touhara, Roderick MacKinnon

    A single kinetic step in the G protein activation cycle determines whether a G protein-coupled receptor activates G protein-gated K⁺ channels or not.
84. 1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Highly efficient 5' capping of mitochondrial RNA with NAD⁺ and NADH by yeast and human mitochondrial RNA polymerase

    Jeremy G Bird, Urmimala Basu ... Bryce E Nickels

    Eukaryotic mitochondrial RNA polymerases cap RNA with NAD with much higher efficiencies than nuclear RNA polymerase II; as a consequence, mitochondrial RNAs have remarkably high levels of NAD capping.
85. 1. Computational and Systems Biology
    2. Developmental Biology

    A repressor-decay timer for robust temporal patterning in embryonic Drosophila neuroblast lineages

    Inna Averbukh, Sen-Lin Lai ... Naama Barkai

    The demand for robust performance distinguishes the mechanism which progresses the biological timer acting within neural progenitors to determine neuronal fates in the Drosophila embryo.
86. 1. Structural Biology and Molecular Biophysics

    An unexpected INAD PDZ tandem-mediated plcβ binding in Drosophila photo receptors

    Fei Ye, Yuxin Huang ... Mingjie Zhang

    Biochemical and structural studies uncover an unexpected mode of interaction, with unprecedented high affinity, between INAD scaffold and NORPA that is critical for Drosophila compound eye photo-transduction.
87. 1. Neuroscience

    The roles of vision and antennal mechanoreception in hawkmoth flight control

    Ajinkya Dahake, Anna L Stöckl ... Almut Kelber

    Mechanosensors in the antennae of hawkmoths provide rapid sensory feedback for the control of fast flight manoeuvres, which acts in parallel to visual information.
88. 1. Neuroscience

    A prediction model of working memory across health and psychiatric disease using whole-brain functional connectivity

    Masahiro Yamashita, Yujiro Yoshihara ... Hiroshi Imamizu

    Human neuroimaging and machine learning reveals a generalizable relationship between brain connectivity and working memory ability across healthy populations and distinct psychiatric diagnoses.
89. 1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    DNA sequence encodes the position of DNA supercoils

    Sung Hyun Kim, Mahipal Ganji ... Cees Dekker

    Single-molecule experiments reveal that plectonemic supercoils occupy specific positions on DNA and a physical model relates this to the intrinsic curvature, providing an insight into how supercoiling organizes the genome.
90. 1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Sae2/CtIP prevents R-loop accumulation in eukaryotic cells

    Nodar Makharashvili, Sucheta Arora ... Tanya T Paull

    The CtIP DNA repair enzyme is required for the removal of transcription-associated lesions in eukaryotic cells.
91. 1. Immunology and Inflammation

    A novel pathway of LPS uptake through syndecan-1 leading to pyroptotic cell death

    Shigetoshi Yokoyama, Yan Cai ... Shioko Kimura

    A novel pathway was discovered for cellular uptake of LPS through secretory protein secretoglobin3A2 and a receptor syndecan-1, causing activation of non-canonical inflammasome pathway leading to pyroptosis of cancer cells.
92. 1. Neuroscience

    Spatial sampling in human visual cortex is modulated by both spatial and feature-based attention

    Daniel Marten van Es, Jan Theeuwes, Tomas Knapen

    The sampling of visual space is not only warped by attention towards locations but also depends on attended features.
93. 1. Microbiology and Infectious Disease

    A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV

    Molly OhAinle, Louisa Helms ... Michael Emerman

    Host restriction factors that block cross-species transmission also play a role in limiting the replication of highly-adapted HIV-1 in IFN-stimulated cells.
94. 1. Developmental Biology

    Control of neural crest multipotency by Wnt signaling and the Lin28/let-7 axis

    Debadrita Bhattacharya, Megan Rothstein ... Marcos Simoes-Costa

    The developmental potential of neural crest stem cells is regulated by a post-transcriptional mechanism that operates in a position-dependent manner.
95. 1. Developmental Biology

    Screening for insulin-independent pathways that modulate glucose homeostasis identifies androgen receptor antagonists

    Sri Teja Mullapudi, Christian SM Helker ... Didier YR Stainier

    Zebrafish insulin mutants serve as an innovative platform to identify novel mechanisms regulating glucose homeostasis.
96. 1. Neuroscience

    Promoting subjective preferences in simple economic choices during nap

    Sizhi Ai, Yunlu Yin ... Jie Shi

    Neurocognitive processing during sleep selectively biases subjective preferences in simple economic choices when the sleeper is stimulated by covert, reward-associated cues.
97. 1. Cell Biology

    The transcription factors TFE3 and TFEB amplify p53 dependent transcriptional programs in response to DNA damage

    Owen A Brady, Eutteum Jeong ... Rosa Puertollano

    Disruption of TFEB and TFE3 results in diminished p53 signaling capacity and altered cell cycle regulation under genotoxic stress conditions.
98. 1. Neuroscience

    Bayesian analysis of retinotopic maps

    Noah C Benson, Jonathan Winawer

    A novel Bayesian method of modeling retinotopic maps is more accurate than traditional voxel-wise methods and can be used to automatically derive high-quality maps.
99. 1. Evolutionary Biology
    2. Genetics and Genomics

    Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function

    J Grey Monroe, Tyler Powell ... John K McKay

    Gene knockouts provide valuable genetic fuel for climate adaptation in nature.
100. 1. Stem Cells and Regenerative Medicine

     Stem cells repurpose proliferation to contain a breach in their niche barrier

     Kenneth Lay, Shaopeng Yuan ... Elaine Fuchs

     Adult stem cells sense nearby tissue damage and recruit immune cells to help them direct efforts towards containing a breach in the epithelial barrier.
101. 1. Chromosomes and Gene Expression

     General decapping activators target different subsets of inefficiently translated mRNAs

     Feng He, Alper Celik ... Allan Jacobson

     Dhh1, Pat1, and Lsm1 target subsets of cellular mRNAs for decapping via interactions of these regulatory proteins with the C-terminal domain of Dcp2, the catalytic component of the decapping enzyme.
102. 1. Microbiology and Infectious Disease
     2. Physics of Living Systems

     Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria

     Joshua S MacCready, Pusparanee Hakim ... Daniel C Ducat

     Carboxysomes, the carbon-fixation machinery of cyanobacteria, are equidistantly-positioned by dynamic gradients of the protein McdA on the nucleoid that emerge through interaction with a previously unidentified carboxysome factor, McdB.
103. 1. Biochemistry and Chemical Biology

     A secretory pathway kinase regulates sarcoplasmic reticulum Ca²⁺ homeostasis and protects against heart failure

     Adam J Pollak, Canzhao Liu ... Jack E Dixon

     Protein phosphorylation within the lumen of the secretory pathway regulates cardiac function.
104. 1. Structural Biology and Molecular Biophysics

     DNA translocation mechanism of an XPD family helicase

     Kaiying Cheng, Dale B Wigley

     Structures of binary and ternary complexes of DinG reveal translocation mechanism of XPD family helicases.
105. 1. Neuroscience
     2. Structural Biology and Molecular Biophysics

     Auxiliary subunits keep AMPA receptors compact during activation and desensitization

     Jelena Baranovic, Andrew JR Plested

     The auxiliary protein Stargazin limits the conformational dynamics of AMPA-type glutamate receptors in cell membranes, as revealed by 'molecular rulers' deployed on the seconds to milliseconds timescale.
106. 1. Evolutionary Biology
     2. Genetics and Genomics

     Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi

     Eric CH Chen, Stephanie Mathieu ... Nicolas Corradi

     Arbuscular mycorrhizal fungi generate nuclear diversity in the dikaryotic life-stage stage via inter-nucleus recombination.
107. 1. Cell Biology

     Glucose intake hampers PKA-regulated HSP90 chaperone activity

     Yu-Chen Chen, Pei-Heng Jiang ... Shu-Chun Teng

     Food overconsumption impairs cellular protein folding through a novel aging-related signaling pathway.
108. 1. Genetics and Genomics

     Spliceosome factors target timeless (tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila

     Iryna Shakhmantsir, Soumyashant Nayak ... Amita Sehgal

     Alternative splicing provides a mechanism to maintain oscillations of the circadian clock.
109. 1. Developmental Biology

     Wnt11 directs nephron progenitor polarity and motile behavior ultimately determining nephron endowment

     Lori L O'Brien et al.

     Wnt11 maintains nephron progenitor niche integrity during kidney development through its modulation of cellular dynamics.
110. 1. Neuroscience

     Corollary discharge in precerebellar nuclei of sleeping infant rats

     Didhiti Mukherjee, Greta Sokoloff, Mark S Blumberg

     Infant rats distinguish between self- and other-generated movements, and they do so primarily when moving during active sleep.
111. 1. Neuroscience
     2. Physics of Living Systems

     Arterial smooth muscle cell PKD2 (TRPP1) channels regulate systemic blood pressure

     Simon Bulley, Carlos Fernández-Peña ... Jonathan H Jaggar

     Arterial myocyte PKD2 channels are activated by vasoconstrictor stimuli, which increases blood pressure, are upregulated during hypertension and cell-specific knockout in vivo reduces both physiological blood pressure and hypertension.
112. 1. Cell Biology

     Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2

     Mario Ruiz, Rakesh Bodhicharla ... Marc Pilon

     Inhibition of C. elegans FLD-1 or Human TLCD1/2 prevents saturated fat lipotoxicity by allowing increased levels of membrane phospholipids that contain fluidizing long-chain polyunsaturated fatty acids.
113. 1. Cell Biology

     Endothelial-specific FoxO1 depletion prevents obesity-related disorders by increasing vascular metabolism and growth

     Martina Rudnicki, Ghoncheh Abdifarkosh ... Tara L Haas

     Stimulation of endothelial glucose metabolism and vascular growth by genetic depletion of endothelial Foxo1 improves the whole-body response to a high-fat diet, by preserving adipose tissue functions and glucose homeostasis.
114. 1. Chromosomes and Gene Expression
     2. Microbiology and Infectious Disease

     Fragile X mental retardation protein is a Zika virus restriction factor that is antagonized by subgenomic flaviviral RNA

     Ruben Soto-Acosta, Xuping Xie ... Shelton Bradrick

     The Zika virus subgenomic flaviviral RNA binds to and inhibits the fragile X mental retardation protein, a novel Zika virus restriction factor.
115. 1. Cell Biology
     2. Chromosomes and Gene Expression

     Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease

     Ilaria Pettinati, Pawel Grzechnik ... Christopher J Schofield

     MBLAC1 is an endoribonuclease specific for replication dependent histone pre-mRNA processing during S-phase and may represent a new type of cancer target.
116. 1. Neuroscience

     Attention periodically samples competing stimuli during binocular rivalry

     Matthew J Davidson, David Alais ... Naotsugu Tsuchiya

     A combined behavioural and electroencephalographic approach investigating the covert allocation of attention shows evidence for distributed periodic sampling away from a conscious visual image.
117. 1. Neuroscience

     Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1

     Terri M Driessen, Paul J Lee, Janghoo Lim

     Unbiased transcriptomics reveals novel insights into the mechanisms that may contribute to regional neurodegeneration in SCA1, and other SCAs in general.
118. 1. Cancer Biology
     2. Cell Biology

     Global transcriptional analysis identifies a novel role for SOX4 in tumor-induced angiogenesis

     Stephin J Vervoort, Olivier G de Jong ... Paul J Coffer

     Global transcriptome analysis reveals that the transcription factor SOX4 can promote breast tumor development via tumor angiogenesis by promoting paracrine signalling through endothelin-1.