April 2014

Research articles

    1. Biochemistry
    2. Biophysics and Structural Biology

    Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation

    Marta Carroni et al
    Overcoming image-processing problems in the analysis of the ClpB chaperone provides a new structural model and regulatory mechanism, based on clear density for the coiled-coil domain and supported by various biochemical data.
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    1. Neuroscience

    Monosynaptic premotor circuit tracing reveals neural substrates for oro-motor coordination

    Edward Stanek IV et al
    Retrograde tracing of the neural circuits that control movement of the jaw and tongue reveals how shared premotor neurons help to ensure coordinated muscle activity.
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    1. Biochemistry
    2. Cell Biology

    Cell-cycle dependent phosphorylation of yeast pericentrin regulates γ-TuSC-mediated microtubule nucleation

    Tien-chen Lin et al
    Phosphorylation of Spc110 N-terminal domain encompassing conserved motifs and its interaction with conserved GCP3 N-terminal domain regulate the oligomerization of gamma-tubulin small complexes (γ-TuSCs).
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    1. Genes and Chromosomes

    MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability

    Young Eun Choi et al
    MicroRNAs tightly control the cellular level of homologous recombination (HR) factors in the G1 phase, and failure of this control system results in an ectopic increase in HR proteins in G1 cells leading to impaired DNA repair.
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    1. Biochemistry
    2. Microbiology and Infectious Disease

    Transcription inhibition by the depsipeptide antibiotic salinamide A

    David Degen et al
    Salinamide A exerts antibacterial activity by binding to the bridge-helix cap of bacterial RNA polymerase and allosterically inhibiting nucleotide addition
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    1. Biochemistry

    Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation

    Andrei S Avanesov et al
    Aging is a process characterized by gradual metabolome remodeling, deceleration of the remodeling in late life and under conditions that extend lifespan, and a mortality-associated pattern of cumulative damage.
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    1. Genes and Chromosomes

    Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

    Daan Noordermeer et al
    Hox genes are activated sequentially and, at the same time, undergo a transition from an inactive to an active chromatin compartment, most likely to prevent posterior genes being activated too early.
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    1. Cell Biology
    2. Ecology

    Systems analysis of the CO2 concentrating mechanism in cyanobacteria

    Niall M Mangan, Michael P Brenner
    Systems level modeling of cyanobacterial mechanism for concentrating carbon dioxide shows optimal organization and enzymatic activity for enhanced carbon fixation.
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    1. Biophysics and Structural Biology
    2. Cell Biology

    Symmetry breaking in reconstituted actin cortices

    Enas Abu Shah, Kinneret Keren
    A reconstituted system has been developed that self-organizes into dynamic actin cortices capable of spontaneous polarization, similar to the initial cortical polarization observed in cells during embryogenesis and development.
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    1. Biochemistry
    2. Genomics and Evolutionary Biology

    Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

    Iris Jonkers et al
    The elongation rate of RNA Polymerase II varies greatly between and along genes, as this enzyme accelerates from stable pausing to rapid elongation within genes, and is influenced by CG-content, exons and chromatin.
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    1. Plant Biology

    Combining growth-promoting genes leads to positive epistasis in Arabidopsis thaliana

    Hannes Vanhaeren et al
    Pairwise combinations of growth-promoting genes regulating distinct cellular mechanisms lead to synergistic effects on leaf growth, and hence greatly increased leaf size.
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    1. Genes and Chromosomes

    p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes

    Michal Krawczyk, Beverly M Emerson
    A long non-coding RNA removes the transcriptional repressor p50 to regulate recruitment of co-activator p300 and RNA Polymerase II complexes to activate the COX-2 gene in human mammary epithelial cells and macrophages.
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    1. Biophysics and Structural Biology

    Periodic DNA patrolling underlies diverse functions of Pif1 on R-loops and G-rich DNA

    Ruobo Zhou et al
    Analyzing single molecules reveals that Pif1 family helicases periodically patrol DNA, which may explain this enzyme's ability to suppress genome instability at G-quadruplex motifs and transcriptional RNA-DNA hybrids (R-loops).
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    1. Biochemistry
    2. Genes and Chromosomes

    Repair of naturally occurring mismatches can induce mutations in flanking DNA

    Jia Chen et al
    The repair of spontaneous DNA damage can introduce mutators that lead to further genetic changes, which could underlie evolutionary change, disease and aging.
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    1. Biophysics and Structural Biology
    2. Microbiology and Infectious Disease

    Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1

    Xiaofei Jia et al
    HIV-1 viral protein u (Vpu) can stimulate novel versions of canonical interactions with the clathrin adaptor AP1 to counteract the host antiviral protein BST2.
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    1. Biophysics and Structural Biology
    2. Genes and Chromosomes

    Resveratrol modulates the inflammatory response via an estrogen receptor-signal integration network

    Jerome C Nwachukwu et al
    Anti-inflammatory effects of resveratrol are mediated by the estrogen receptor to coordinate a complex array of transcriptional coregulators, suggesting that estrogenic effects must be considered in the complex polypharmacology of resveratrol.
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    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    Genetic interactions affecting human gene expression identified by variance association mapping

    Andrew Anand Brown et al
    Multiple replicated examples of epistasis affecting gene expression in humans are identified, some explaining a substantial proportion of the variation in expression.
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    1. Plant Biology

    Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases

    Yinwei Cheng et al
    Brassinosteroids signal through a pathway involving GSK3-like kinases and the WER-GL3/EGL3-TTG1 transcription factor complex to determine the fate of cells in the root epidermis.
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    1. Biochemistry
    2. Cell Biology

    Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation

    Ivana Petrovska et al
    A starvation-induced drop in cytosolic pH promotes assembly of budding yeast glutamine synthetase into enzymatically inactive filaments that function as enzyme storage depots.
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    A micro-epidemiological analysis of febrile malaria in Coastal Kenya showing hotspots within hotspots

    Philip Bejon et al
    Malaria 'hotspots' can be identified that range in size from a few homesteads to a village, and it will be necessary to eliminate hotspots at varying scales as we progress towards eliminating malaria.
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    1. Cell Biology

    The GTPase IFT27 is involved in both anterograde and retrograde intraflagellar transport

    Diego Huet et al
    A small GTPase within the flagellum can participate in the control of transport from the base to the tip of the flagellum, and back again.
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    1. Biophysics and Structural Biology
    2. Genes and Chromosomes

    AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter

    Ursula Schulze-Gahmen et al
    AFF4 increases the combined selectivity of HIV Tat and TAR for super elongation complexes 330-fold over P-TEFb alone.
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    1. Developmental Biology and Stem Cells

    Precardiac deletion of Numb and Numblike reveals renewal of cardiac progenitors

    Lincoln T Shenje et al
    Cardiac progenitors remain undifferentiated and expansive in the second pharyngeal arch that serves as a microenvironment, and Numb and Numblike are required for their renewal.
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    1. Neuroscience

    Midbrain dopamine neurons sustain inhibitory transmission using plasma membrane uptake of GABA, not synthesis

    Nicolas X Tritsch et al
    The molecular mechanisms by which midbrain dopamine neurons acquire the inhibitory neurotransmitter GABA for synaptic release are revealed.
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    1. Genomics and Evolutionary Biology
    2. Human Biology and Medicine

    APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition

    Sandra R Richardson et al
    Combining in vitro and in vivo assays demonstrates that the cytidine deaminase APOBEC3A can inhibit LINE-1 retrotransposition by deaminating transiently exposed single-strand DNA that arises during the process of LINE-1 integration.
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    1. Biochemistry

    DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase

    Aysen L Erdem et al
    DNA synthesis by DNA polymerase V is regulated by an intrinsic DNA-dependent ATPase activity which has not been observed for any other polymerase.
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    1. Genomics and Evolutionary Biology

    A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning

    Nicky Wybouw et al
    The enzyme that allows some mites and insects to detoxify the hydrogen cyanide produced by plants has been identified.
    Research Article
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    1. Genes and Chromosomes

    Targeted genome editing by lentiviral protein transduction of zinc-finger and TAL-effector nucleases

    Yujia Cai et al
    Lentiviral protein transduction offers a new approach for administration of custom-designed nucleases, leading to high-efficacy targeted gene editing and reduced off-target activity after virus-directed delivery of programmable nuclease proteins.
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    1. Neuroscience

    RGS7/Gβ5/R7BP complex regulates synaptic plasticity and memory by modulating hippocampal GABABR-GIRK signaling

    Olga Ostrovskaya et al
    A critical regulator of inhibitory neurotransmitter signaling in the hippocampus has been identified in experiments on mice and been shown to play essential role in synaptic plasticity and memory.
    Research Article
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    1. Neuroscience

    SIR-2.1 integrates metabolic homeostasis with the reproductive neuromuscular excitability in early aging male Caenorhabditis elegans

    Xiaoyan Guo, L René García
    A protein called SIR-2.1 helps to protect worms from the effects of aging by regulating metabolic processes that would otherwise generate damaging reactive oxygen species.
    Research Article
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    1. Neuroscience

    Gating of neural error signals during motor learning

    Rhea R Kimpo et al
    Electrode recordings and optogenetics reveal that the cerebellum can modulate its response to error signals from the brainstem during motor learning.
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    1. Biochemistry
    2. Microbiology and Infectious Disease

    GE23077 binds to the RNA polymerase ‘i’ and ‘i+1’ sites and prevents the binding of initiating nucleotides

    Yu Zhang et al
    The cyclic-peptide antibiotic GE23077 inhibits bacterial RNA polymerase through a novel target that exhibits low susceptibility to target-based resistance and that enables synthesis of bipartite inhibitors that are exceptionally potent and refractory to target-based resistance.
    Research Article
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    1. Developmental Biology and Stem Cells

    Transgressions of compartment boundaries and cell reprogramming during regeneration in Drosophila

    Salvador C Herrera, Ginés Morata
    The reconstruction of damaged structures during regeneration requires cell reprogramming mediated by the up regulation of the JNK pathway and the transient debilitation of the epigenetic control mechanism.
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    1. Developmental Biology and Stem Cells
    2. Genes and Chromosomes

    Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development

    Leonardo Gastón Guilgur et al
    The need for efficient pre-RNA splicing during early embryonic development of Drosophila indicates that the constraints imposed by the cell cycle are a force capable of driving changes in Eukaryotic gene architecture.
    Research Article
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    1. Neuroscience

    Regulation of branching dynamics by axon-intrinsic asymmetries in Tyrosine Kinase Receptor signaling

    Marlen Zschätzsch et al
    Asymmetric localization of the receptor EGFR within branches of axons is required to establish the precise wiring of neuronal networks within the Drosophila brain.
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    1. Cell Biology
    2. Plant Biology

    Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells

    Arun Sampathkumar et al
    In the Arabidopsis epidermis, the internal mechanical stress of a cell competes with the external stress to control microtubule behavior, providing a framework to understand the mechanical feedbacks that underlie plant morphogenesis.
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    1. Biophysics and Structural Biology
    2. Cell Biology

    The influence of dynein processivity control, MAPs, and microtubule ends on directional movement of a localising mRNA

    Harish Chandra Soundararajan, Simon L Bullock
    In vitro reconstitution of mRNA motility reveals the basis of directionally biased motion by groups of motors, their response to potential obstacles, and the consequences of reaching microtubule ends.
    Research Article
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    1. Cell Biology
    2. Plant Biology

    Abscisic acid dynamics in roots detected with genetically encoded FRET sensors

    Alexander M Jones et al
    Fluorescent sensors for the hormone abscisic acid have been developed using a high-throughput platform, and used to monitor hormone dynamics in plant roots and leaves.
    Research Article
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    1. Cell Biology

    Nuclear receptor LRH-1/NR5A2 is required and targetable for liver endoplasmic reticulum stress resolution

    Jennifer L Mamrosh et al
    LRH-1/NR5A2 responds to ER stress by inducing a novel pathway that is required for stress resolution in mice and can be targeted by LRH-1 agonists.
    Research Article
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    1. Developmental Biology and Stem Cells

    Selective amputation of the pharynx identifies a FoxA-dependent regeneration program in planaria

    Carolyn E Adler et al
    A chemical method has been developed for studying single organ regeneration and fate specification of stem cells in an adult organism.
    Research Article
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    1. Genes and Chromosomes

    The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1

    Peter J Skene et al
    The ATP-dependent chromatin remodeler Chd1 controls nucleosome turnover to allow RNA Polymerase to transcribe in vivo.
    Research Article
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    1. Cell Biology
    2. Plant Biology

    FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis

    Rainer Waadt et al
    Fluorescent sensors can track the movement and distribution of the plant hormone abscisic acid in roots and leaves in Arabidopsis.
    Research Article
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    1. Genes and Chromosomes

    The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

    Steven Henikoff et al
    A stable tetrameric nucleosome occupies the central segment of each ∼120-bp budding yeast centromere in two rotational phases of both reflectional orientations in vivo.
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    1. Biophysics and Structural Biology
    2. Immunology

    T cells translate individual, quantal activation into collective, analog cytokine responses via time-integrated feedbacks

    Karen E Tkach et al
    Experiment-driven quantitative model of IL-2 secretion demonstrates how T cells integrate their digital antigen responses into an analog-scaled output.
    Research Article
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    1. Neuroscience

    A frontal cortex event-related potential driven by the basal forebrain

    David P Nguyen, Shih-Chieh Lin
    Contrary to the common belief that cognitive event-related potentials are generated by local activity within the cerebral cortex, it is shown that some of these potentials are modulated by subcortical inputs.
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    1. Cell Biology
    2. Plant Biology

    Delivery of endocytosed proteins to the cell–division plane requires change of pathway from recycling to secretion

    Sandra Richter et al
    The same membrane trafficking cargo can change pathways mediated by different members of ARF-GEF family of vesicle formation regulators.
    Research Article
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    1. Genes and Chromosomes
    2. Genomics and Evolutionary Biology

    Holocentromeres are dispersed point centromeres localized at transcription factor hotspots

    Florian A Steiner, Steven Henikoff
    Worm holocentromeres show a polycentric distribution, with each site containing a single centromeric nucleosome and also being targeted by multiple transcription factors.
    Research Article
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    1. Biochemistry
    2. Cell Biology

    Aim24 and MICOS modulate respiratory function, tafazzin-related cardiolipin modification and mitochondrial architecture

    Max Emanuel Harner et al
    Interactions between Aim24 and the mitochondrial outer and inner membrane contact site complex (MICOS) are essential for mitochondrial ultrastructure, lipid composition and oxidative phosphorylation.
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    1. Biophysics and Structural Biology
    2. Cell Biology

    Structural basis for the assembly of the mitotic motor Kinesin-5 into bipolar tetramers

    Jessica E Scholey et al
    The Bipolar Assembly domain of kinesin-5 comprises an anti-parallel four-helix bundle, which explains how kinesin-5 subunits assemble into bipolar tetramers with two motile ends that transmit forces while crosslinking and sliding adjacent microtubules during mitosis.
    Research Article
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    1. Developmental Biology and Stem Cells

    In vivo reprogramming of pancreatic acinar cells to three islet endocrine subtypes

    Weida Li et al
    Combinations of transcription factors can convert pancreatic acinar cells into endocrine α-, β- and δ-cells in vivo.
    Research Article
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    1. Immunology

    Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells

    Dorothy K Sojka et al
    Natural killer cells that were commonly thought to circulate around the body can actually reside in distinct tissues, such as in the liver, skin or uterus, and do not re-circulate.
    Research Article
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    1. Biophysics and Structural Biology

    Encounter complexes and dimensionality reduction in protein–protein association

    Dima Kozakov et al
    Analysis of protein–protein encounter complexes shows that proteins associate along preferred pathways, similar to the sliding of a protein along DNA.
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