October 2015

Research articles

    1. Biochemistry
    2. Genomics and Evolutionary Biology

    Non-classical amine recognition evolved in a large clade of olfactory receptors

    Qian Li et al.
    Fish trace amine-associated receptors evolved a novel structural motif that enables the detection of chemically diverse amine odors in a non-canonical 'inverted' orientation.
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Resolving dual binding conformations of cellulosome cohesin-dockerin complexes using single-molecule force spectroscopy

    Markus A Jobst et al.
    A single-molecule approach is able to discriminate the redundant binding conformations of cellulosomal dockerin based on differences in their mechanical properties.
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    1. Epidemiology and Global Health

    Childhood injury after a parental cancer diagnosis

    Ruoqing Chen et al.
    Children with a parent of cancer have a higher rate of hospital contact for injury, especially immediately after the cancer diagnosis.
    Research Article
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    1. Neuroscience

    Retroactive modulation of spike timing-dependent plasticity by dopamine

    Zuzanna Brzosko et al.
    Dopamine, a reward signal in the brain, can retroactively convert hippocampal synaptic depression into potentiation, suggesting an elegant biological solution to the distal reward problem.
    Short Report
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    1. Computational and Systems Biology
    2. Neuroscience

    Mapping nonlinear receptive field structure in primate retina at single cone resolution

    Jeremy Freeman et al.
    Multi-electrode recordings and modeling are combined to reveal the transformations of signals from cones to bipolar cells and then to ganglion cells within the primate retina.
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    1. Biochemistry
    2. Immunology

    LynA regulates an inflammation-sensitive signaling checkpoint in macrophages

    Tanya S Freedman et al.
    Degradation of kinase LynA protects macrophages from activation unless cells sense a receptor-binding pathogen or inflammation
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    1. Microbiology and Infectious Disease

    pp32 and APRIL are host cell-derived regulators of influenza virus RNA synthesis from cRNA

    Kenji Sugiyama et al.
    The host-derived factors, pp32 and APRIL, interact with influenza viral RNA polymerase to support viral genomic RNA synthesis from complementary RNA.
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    1. Biochemistry
    2. Microbiology and Infectious Disease

    Fucosylation and protein glycosylation create functional receptors for cholera toxin

    Amberlyn M Wands et al.
    Cholera intoxication of human colonic epithelial cells is dependent on recognition of protein glycosylation and fucosylation, not exclusively on ganglioside recognition as proposed previously.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    The Rho-guanine nucleotide exchange factor PDZ-RhoGEF governs susceptibility to diet-induced obesity and type 2 diabetes

    Ying-Ju Chang et al.
    PDZ-RhoGEF controls adipose tissue abundance and whole body metabolism.
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    1. Neuroscience

    Filopodial dynamics and growth cone stabilization in Drosophila visual circuit development

    Mehmet Neset Özel et al.
    Long-term live imaging in intact developing Drosophila brains reveals a role for N-Cadherin-mediated fast filopodial dynamics and growth cone stabilization during neural circuit assembly.
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    1. Genomics and Evolutionary Biology
    2. Immunology

    Genetic and epigenetic variation in the lineage specification of regulatory T cells

    Aaron Arvey et al.
    There is limited epigenetic conservation of lineage-specific DNA elements in Treg cells, and genetic variation in Treg cell specific enhancers is associated with autoimmune disease.
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    1. Genes and Chromosomes
    2. Human Biology and Medicine

    A deleterious gene-by-environment interaction imposed by calcium channel blockers in Marfan syndrome

    Jefferson J Doyle et al.
    Calcium channel blockers accelerate aortic aneurysm and cause premature aortic rupture in a mouse model of Marfan syndrome through protein kinase C-mediated activation of extracellular signal-regulated kinase.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Coordination of planar cell polarity pathways through Spiny-legs

    Abhijit A Ambegaonkar, Kenneth D Irvine
    A direct connection between distinct planar cell polarity systems orients cells, answering long-standing questions regarding the relationship between systems and the orientation of cell polarity.
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    1. Cell Biology
    2. Computational and Systems Biology

    Self-establishing communities enable cooperative metabolite exchange in a eukaryote

    Kate Campbell et al.
    A eukaryotic cell model overcomes metabolic deficiencies within a complex, self-establishing community that enables the growth-relevant exchange of metabolic intermediates.
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    1. Biochemistry
    2. Genomics and Evolutionary Biology

    Circularization restores signal recognition particle RNA functionality in Thermoproteus

    André Plagens et al.
    Archaea can contain permuted versions of the universal signal recognition particle RNA, which require a moonlighting activity of the tRNA splicing machinery to generate functional circular RNAs.
    Short Report
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    1. Biophysics and Structural Biology

    cryo-EM structures of the E. coli replicative DNA polymerase reveal its dynamic interactions with the DNA sliding clamp, exonuclease and τ

    Rafael Fernandez-Leiro et al.
    Structures of the replicative DNA polymerase Pol IIIα, the DNA sliding clamp, the proofreading exonuclease, and the processivity switch Tau (τ) suggest a mechanism for quick release during lagging strand synthesis.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Functional genomic screening reveals asparagine dependence as a metabolic vulnerability in sarcoma

    Simone Hettmer et al.
    The availability of asparagine is important for cell growth and nascent peptide synthesis in certain sarcoma cells, and could be targeted therapeutically to inhibit tumor growth.
    Research Article
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    1. Neuroscience

    Nonlinear circuits for naturalistic visual motion estimation

    James E Fitzgerald, Damon A Clark
    New computational models provide insights into how the insect brain estimates the speed and direction of movement.
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    1. Cell Biology
    2. Immunology

    Attenuation of AMPK signaling by ROQUIN promotes T follicular helper cell formation

    Roybel R Ramiscal et al.
    The ubiquitin ligase ROQUIN cross-talks with cellular metabolic signals to generate protective T cell-dependent antibody responses.
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    1. Biophysics and Structural Biology
    2. Genes and Chromosomes

    Dna2 nuclease-helicase structure, mechanism and regulation by Rpa

    Chun Zhou et al.
    X-ray crystallography reveals that the Dna2 nuclease-helicase contains a long tunnel through which single-stranded DNA threads, and an allosteric mechanism for displacing the DNA-binding protein Rpa that restricts cleavage to the proper polarity.
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    1. Computational and Systems Biology
    2. Human Biology and Medicine

    Expression signature based on TP53 target genes doesn't predict response to TP53-MDM2 inhibitor in wild type TP53 tumors

    Dmitriy Sonkin
    A previously suggested expression signature based on thirteen TP53 transcriptional target genes does not predict the response of wild type TP53 tumors to TP53-MDM2 inhibitors.
    Short Report
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    1. Developmental Biology and Stem Cells

    Developmental compartments in the larval trachea of Drosophila

    Prashanth R Rao et al.
    Cells in the tracheal systems of fruit fly larvae are organised into compartments with precisely located boundaries, which pattern the formation of branched tubular networks.
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    1. Genes and Chromosomes

    HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells

    Jonathan E Reeder et al.
    Tat uses unexpected regulatory mechanisms to reprogram target immune cells to promote viral replication and rewire pathways beneficial for HIV.
    Research Article
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    1. Computational and Systems Biology
    2. Immunology

    Digital signaling decouples activation probability and population heterogeneity

    Ryan A Kellogg et al.
    Digital NF-κB signaling achieves orthogonal control over the probability of activation (percentage of activated cells) and dynamic response heterogeneity in the population via the area and shape of the input profile.
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    1. Biophysics and Structural Biology
    2. Cell Biology

    Assembly and positioning of actomyosin rings by contractility and planar cell polarity

    Ivonne M Sehring et al.
    Contractility wins over the polarity pathway in a tug-of-war to position a cytokinesis-like actomyosin ring at the equator of notochord cells.
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    1. Neuroscience

    Human blindsight is mediated by an intact geniculo-extrastriate pathway

    Sara Ajina et al.
    White matter microstructure in hemianopia patients indicates that blindsight requires an intact connection between the lateral geniculate nucleus and extrastriate cortex.
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    1. Ecology
    2. Genomics and Evolutionary Biology

    The evolution of non-reproductive workers in insect colonies with haplodiploid genetics

    Jason W Olejarz et al.
    A mathematical model predicts the precise conditions for natural selection to favor the evolution of non-reproductive workers in insect colonies with haplodiploid genetics.
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Environmental changes in oxygen tension reveal ROS-dependent neurogenesis and regeneration in the adult newt brain

    L Shahul Hameed et al.
    Control of neural stem cells by reactive oxygen species (ROS) provides a link between systemic shifts in oxygen tension and neuronal regeneration, and suggests an evolutionary driving force for the inherent ability of newts to regenerate their brain cells.
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    1. Neuroscience

    Episodic-like memory trace in awake replay of hippocampal place cell activity sequences

    Susumu Takahashi
    What will happen where and when could be predicted by the sequential reactivation of place cells that occurs while an animal pauses, suggesting that the replay is linked to mental time travel.
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    1. Developmental Biology and Stem Cells

    Pericytes are progenitors for coronary artery smooth muscle

    Katharina S Volz et al.
    Progenitor cells for the muscle layer around the coronary arteries have been identified revealing a key step in how the embryo forms these important blood vessels.
    Research Article
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    1. Human Biology and Medicine

    ANGPTL4 mediates shuttling of lipid fuel to brown adipose tissue during sustained cold exposure

    Wieneke Dijk et al.
    During sustained cold exposure, lipid fuel is specifically directed towards brown adipose tissue, but not white adipose tissue, via cold-induced regulation of Angiopoietin-like 4 (ANGPTL4).
    Research Article
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    1. Neuroscience

    Localized hypoxia within the subgranular zone determines the early survival of newborn hippocampal granule cells

    Christina Chatzi et al.
    Neural progenitors reside in relative low oxygen in the subgranular zone (SGZ), and the higher tissue oxygen levels that these cells must face as they migrate away from the hypoxic areas and differentiate appear to cause oxidative damage and an early phase of cell death.
    Research Article
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    1. Neuroscience

    Distinct roles of NMDA receptors at different stages of granule cell development in the adult brain

    Yangling Mu et al.
    NMDARs promote spine formation to control survival of adult-born granule cells, but gauge spine enlargement and recruitment of AMPARs in both developing and mature neurons.
    Research Article
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    1. Neuroscience

    A nap to recap or how reward regulates hippocampal-prefrontal memory networks during daytime sleep in humans

    Kinga Igloi et al.
    Sleep plays a critical role in the selectivity of memory by promoting the retention of important memories at the expense of less relevant ones.
    Short Report
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    1. Computational and Systems Biology

    Calibration and analysis of genome-based models for microbial ecology

    Stilianos Louca, Michael Doebeli
    A novel computation tool for microbial community modeling predicts the evolution and diversification of E. coli in laboratory evolution experiments and gives insight into the underlying metabolic processes.
    Tools and Resources
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    1. Human Biology and Medicine

    An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish

    Jun Zou et al.
    The newly discovered Titin internal promoter may explain why the severity of dilated cardiomyopathy in patients with truncating mutations in Titin varies dramatically depending on position of the mutation.
    Research Article
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    1. Biochemistry
    2. Cell Biology

    Physiological modulation of BiP activity by trans-protomer engagement of the interdomain linker

    Steffen Preissler et al.
    Interdomain linker-mediated oligomerization of the endoplasmic reticulum chaperone protein BiP responds to the unfolded protein burden
    Research Article
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    1. Biochemistry
    2. Genomics and Evolutionary Biology

    Protein kinase C coordinates histone H3 phosphorylation and acetylation

    Zoulfia Darieva et al.
    Chromatin structure is altered following DNA replication stress through the activity of protein kinase C signalling which leads to functionally coupled histone H3 phosphorylation and acetylation events.
    Research Article
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    1. Computational and Systems Biology
    2. Developmental Biology and Stem Cells

    Reconstructing the in vivo dynamics of hematopoietic stem cells from telomere length distributions

    Benjamin Werner et al.
    Telomere length distributions can be used to infer important properties of stem cell proliferation.
    Research Article
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    1. Developmental Biology and Stem Cells
    2. Genomics and Evolutionary Biology

    Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals

    Alex de Mendoza et al.
    Functional genomics reveal complex genome regulation during the coenocytic development of the ichthyosporean Creolimax fragrantissima, a protist closely related to animals.
    Research Article
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    1. Microbiology and infectious disease

    Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase

    Niels Bradshaw, Richard Losick
    Asymmetric cell division is linked to cell-specific transcription by handoff of a key developmental regulator from the cytokinetic machinery to the adjacent cell pole where it oligomerizes to become stabilized and activated.
    Research Article
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    1. Neuroscience

    A genetically defined asymmetry underlies the inhibitory control of flexor–extensor locomotor movements

    Olivier Britz et al.
    Two classes of premotor inhibitory neurons have specific roles in controlling flexor-extensor behaviors in mice, which is the underlying neural mechanism for limb driven movements in terrestrial vertebrates.
    Research Article
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    1. Genomics and Evolutionary Biology

    Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

    Erik M Quandt et al.
    A long-term evolution experiment with Escherichia coli shows that the appearance and optimization of a new trait can require both co-opting existing cellular pathways for new roles and reversing a history of previous adaptation.
    Research Article
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    1. Neuroscience

    VTA neurons coordinate with the hippocampal reactivation of spatial experience

    Stephen N Gomperts et al.
    During quiet wakefulness but not slow wave sleep, reward modulated VTA neurons coordinate selectively with hippocampal replay sequences and are biased in their timing towards the reactivated representation of reward locations.
    Research Article
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    In vivo dynamics of skeletal muscle Dystrophin in zebrafish embryos revealed by improved FRAP analysis

    Fernanda Bajanca et al.
    A multidisciplinary approach was used to translate the mathematical analysis of Dystrophin movements inside muscle cells into the biology of how Dystrophin interacts with the cell membrane.
    Research Article
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    1. Neuroscience

    Thalamic reticular nucleus induces fast and local modulation of arousal state

    Laura D Lewis et al.
    A neural circuit that can selectively induce sleep-like patterns in small regions of the brain demonstrates how sleep and arousal states may be controlled in local brain regions.
    Research Article
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    1. Neuroscience

    Complementary control of sensory adaptation by two types of cortical interneurons

    Ryan G Natan et al.
    Two distinct types of inhibitory neurons increase the brain's sensitivity to unexpected acoustic signals by amplifying selective suppression of cortical responses to frequent, but not rare sounds.
    Research Article
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Loss of neurofibromin Ras-GAP activity enhances the formation of cardiac blood islands in murine embryos

    Amanda D Yzaguirre et al.
    Ras-GAP activity suppresses the hemogenic potential of the embryonic heart.
    Research Article
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    1. Plant Biology

    Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate

    Miin-Feng Wu et al.
    SWI/SNF chromatin remodeling complexes act as ‘gatekeepers’ for auxin responses and directly interact with the auxin response factor MONOPTEROS.
    Research Article
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    1. Epidemiology and Global Health
    2. Human Biology and Medicine

    A meta-analysis of threats to valid clinical inference in preclinical research of sunitinib

    Valerie C Henderson et al.
    Preclinical efficacy experiments testing sunitinib in animal cancer models display a lack of methodological rigour, with trim-and-fill analysis suggesting prominent publication bias that leads to an overestimation of treatment effect.
    Research Article
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    1. Cell Biology

    Super-resolution kinetochore tracking reveals the mechanisms of human sister kinetochore directional switching

    Nigel J Burroughs et al.
    Directional switching of sister chromatids during mitosis is regulated by a mechanical clock that is sensitive to the stretch of centromeric chromatin between the chromatids.
    Research Article
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    1. Biophysics and Structural Biology
    2. Genes and Chromosomes

    Single-molecule imaging of telomerase reverse transcriptase in human telomerase holoenzyme and minimal RNP complexes

    Robert Alexander Wu et al.
    New labeling approaches for single-molecule fluorescence microscopy detect the monomeric catalytic subunit of human telomerase within cellular holoenzyme and minimal active recombinant enzyme.
    Research Article
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Egr-5 is a post-mitotic regulator of planarian epidermal differentiation

    Kimberly C Tu et al.
    The dynamic homeostasis of the planarian epidermis serves as an experimental paradigm to study stem cell dynamics and post-mitotic specification of diverse functional cell fates.
    Research Article
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    1. Developmental Biology and Stem Cells
    2. Neuroscience

    Epithelial cells supply Sonic Hedgehog to the perinatal dentate gyrus via transport by platelets

    Youngshik Choe et al.
    During development the Sonic Hedgehog protein is produced by epithelial structures and acts at a distance in the brain and perhaps in other organs.
    Research Article
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    1. Developmental Biology and Stem Cells

    Wnt signaling-mediated redox regulation maintains the germ line stem cell differentiation niche

    Su Wang et al.
    Wnt signaling regulates cellular redox in the germline stem cell differentiation niche via a novel regulatory mechanism, thereby controlling germ line stem cell progeny differentiation.
    Research Article
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    1. Cell Biology
    2. Genes and Chromosomes

    Vilya, a component of the recombination nodule, is required for meiotic double-strand break formation in Drosophila

    Cathleen M Lake et al.
    The Zip3-like protein Vilya links the initiation of meiotic recombination with crossover formation.
    Research Article
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    1. Neuroscience

    A molecular mechanism underlying gustatory memory trace for an association in the insular cortex

    Chinnakkaruppan Adaikkan, Kobi Rosenblum
    The role of CaMKII-GluA1 in the cortex in maintaining a given taste memory trace for an aversive association has been elucidated.
    Short Report
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    1. Biophysics and Structural Biology

    Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

    Ninning Liu et al.
    The subunits of the SpoIIIE motor contact the 5'→3' strand of DNA in sequence to rapidly translocate the DNA across a membrane.
    Research Article
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    1. Computational and Systems Biology

    Paracrine communication maximizes cellular response fidelity in wound signaling

    L Naomi Handly et al.
    There are inherent tradeoffs in the control of cellular response variability by paracrine communication during the establishment of initial wound response signaling gradients.
    Research Article
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    1. Biochemistry
    2. Cell Biology

    Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage

    Koichiro Akiyama et al.
    Mutational analysis and biochemical experiments suggest that the conserved β-hairpin-like membrane-reentrant loop of RseP - an S2P family intramembrane cleaving protease - helps to discriminate substrates by directly interacting with their transmembrane segments.
    Research Article
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    1. Cell Biology
    2. Developmental Biology and Stem Cells

    Precise let-7 expression levels balance organ regeneration against tumor suppression

    Linwei Wu et al.
    Mouse genetic studies reveal that let-7 performs potent tumor suppressive roles, but at the expense of regeneration and tissue homeostasis in the liver, findings with unanticipated therapeutic implications.
    Research Article
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    1. Biochemistry
    2. Computational and Systems Biology

    Snf1/AMPK promotes the formation of Kog1/Raptor-bodies to increase the activation threshold of TORC1 in budding yeast

    James E Hughes Hallett et al.
    The key Target of Rapamycin Complex (TORC1) component Kog1 moves into bodies during glucose starvation to limit reactivation of the complex.
    Research Article
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    1. Microbiology and Infectious Disease

    Impact of a decade of successful antiretroviral therapy initiated at HIV-1 seroconversion on blood and rectal reservoirs

    Eva Malatinkova et al.
    An early start to long-term antiretroviral therapy limits the size of the HIV-1 reservoir more effectively than treatment that starts later.
    Research Article
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    1. Neuroscience

    Odor-identity dependent motor programs underlie behavioral responses to odors

    Seung-Hye Jung et al.
    Flies respond to odors by modulating multiple independently modulated motor programs.
    Research Article
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    1. Biophysics and Structural Biology
    2. Cell Biology

    A mutation uncouples the tubulin conformational and GTPase cycles, revealing allosteric control of microtubule dynamics

    Elisabeth A Geyer et al.
    A buried mutation in αβ-tubulin reveals an allosteric response to GDP in the lattice that dictates microtubule catastrophe and shrinking.
    Research Article
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    1. Cell Biology
    2. Immunology

    TAPBPR alters MHC class I peptide presentation by functioning as a peptide exchange catalyst

    Clemens Hermann et al.
    We reveal TAPBPR is a peptide exchange catalyst which restricts the peptide repertoire presented by MHC I on cells, a finding which has important implications for all aspects of immune recognition.
    Research Article
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    1. Computational and Systems Biology
    2. Microbiology and Infectious Disease

    Cell-to-cell infection by HIV contributes over half of virus infection

    Shingo Iwami et al.
    The human immunodeficiency virus HIV-1 primarily spreads between cells using a method called cell-to-cell infection, suggesting that this process may be a target for anti-viral drugs.
    Research Article
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    1. Biochemistry
    2. Biophysics and Structural Biology

    Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM

    Anna Zhou et al.
    Structural analysis of the ATP synthase – in combination with evolutionary covariance analysis – reveals the fold of the a subunit and shows that the enzyme can adopt several different conformations, which support the Brownian ratchet model for generating rotation.
    Research Article
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    1. Ecology
    2. Neuroscience

    Patterns of call communication between group-housed zebra finches change during the breeding cycle

    Lisa F Gill et al.
    Call-based vocal communication of individually recorded zebra finches changes in social groups across reproductive stages and is related with successful egg laying.
    Research Article
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    1. Human Biology and Medicine
    2. Immunology

    Nanoparticulate carbon black in cigarette smoke induces DNA cleavage and Th17-mediated emphysema

    Ran You et al.
    The accumulation of carbon black nanoparticles in smokers' lungs causes sterile inflammation, double-strand DNA breaks and emphysema.
    Research Article
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    1. Cell Biology

    Ferritinophagy via NCOA4 is required for erythropoiesis and is regulated by iron dependent HERC2-mediated proteolysis

    Joseph D Mancias et al.
    NCOA4, the ferritin autophagy receptor, is regulated by HERC2 in an iron-dependent manner and is critical for red blood cell development.
    Research Article
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    1. Neuroscience

    Human observers have optimal introspective access to perceptual processes even for visually masked stimuli

    Megan A K Peters, Hakwan Lau
    Despite the widely held belief among researchers in consciousness that healthy observers can show unconscious perception, a study using a novel method to control for response biases finds no evidence for this phenomenon.
    Research Article
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    1. Neuroscience

    A quantitative framework for whole-body coordination reveals specific deficits in freely walking ataxic mice

    Ana S Machado et al.
    Analysis of 3D paw kinematics and whole-body coordination in freely walking mice isolates specific features of gait ataxia and supports the hypothesis that the cerebellum provides an internal forward model for motor control.
    Research Article
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    1. Genes and Chromosomes

    Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

    Todd Blevins et al.
    The 24-nucleotide long siRNAs that guide cytosine methylation in Arabidopsis are made by dicing short double-stranded RNAs that are only around 30 nucleotides long.
    Research Article
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    1. Biochemistry
    2. Computational and Systems Biology

    Rapid cell-free forward engineering of novel genetic ring oscillators

    Henrike Niederholtmeyer et al.
    Rapid forward engineering can be accomplished using cell-free systems, as demonstrated by the implementation and characterization of novel genetic oscillators in a cell-free system and their consequent transfer to cells.
    Research Article
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