Monday, January 10, 2011

Hot off the presses! Jan 11 curr biol

The Jan 11 issue of the curr biol is now up on Pubget (About curr biol): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

  • Climate change talks stumble on
    - curr biol 21(1):R1-R2 (2011)
    Nations are increasingly aware of the threats from rising global temperature and the need for technological innovations to help cope. Nigel Williams reports.
  • Europe fisheries policy protest
    - curr biol 21(1):R3-R4 (2011)
    A new campaign aims to reduce waste from 'bycatch' discards. Nigel Williams reports.
  • Biodiversity boost to African crop
    - curr biol 21(1):R4-R5 (2011)
    A new study shows mixed planting can greatly boost maize yields. Nigel Williams reports.
  • Herbaria source of new plant species
    - curr biol 21(1):R6-R7 (2011)
    Researchers analysing the time lapse between sample collection and species recognition estimate that half the missing plant species have already been collected. Michael Gross reports.
  • Marcus Stensmyr
    - curr biol 21(1):R7-R9 (2011)
  • Vocal mimicry
    - curr biol 21(1):R9-R10 (2011)
  • Cell competition
    - curr biol 21(1):R11-R15 (2011)
    It is self-evident that cell–cell interactions play important roles in multicellular organisms. Genetic mosaics and chimeras, containing cells of distinct genotypes, have long provided an important way to identify and study these interactions. Beginning in the 1970s, genetic mosaic studies in Drosophila began to reveal an unexpected and intriguing phenomenon called 'cell competition', in which otherwise viable cells could be eliminated if their neighbors were different (Figure 1). Cell competition suggests that the properties of individual cells are monitored during development and that variant clones of progenitor cells can be favored or eliminated accordingly. Interest is now building in the mechanisms of cell competition, how it may be adaptive, and whether cell competition is involved in cancer and other diseases. In recent years, progress has been made in understanding the mechanisms of cell competition through several approaches, although much still remains! to be learned.
  • Parental alarm calls warn nestlings about different predatory threats
    - curr biol 21(1):R15-R16 (2011)
    Animal communication signals can contain surprisingly complex information, which plays a vital role in a variety of social interactions. For example, many species of birds and mammals produce vocal alarm signals when encountering a predator [1] and [2], and these calls often serve to communicate the type of predator and/or the degree of danger to members of a social group [3], [4] and [5]. Similarly, signals used in parent–offspring interactions can encode sophisticated information such as the type and immediacy of threat to the offspring [6], [7] and [8]. Here, I show that differential use of parental alarm calls in great tits (Parus major) functions to elicit different predator-avoidance behaviors in altricial nestlings: great tit parents produce acoustically distinctive alarm calls for the two main nest predators, the jungle crow (Corvus macrorhynchos) and the Japanese rat snake (Elaphe climacophora). Nestlings crouched down inside their nest cavity in response to! alarm calls given for a crow, while they fled the cavity in response to alarm calls given for a snake. The two responses help nestlings to selectively evade those predators, because crows snatch nestlings from the nest entrance, whereas snakes invade the nest cavity. While chicks of some species have been shown to recognize and respond appropriately to parental alarm calls [7], [8], [9] and [10], the present findings demonstrate that nest predation by multiple predator species can drive evolution of complex parent–offspring communication in altricial species.
  • Artificial tethering to nuclear pores promotes partitioning of extrachromosomal DNA during yeast asymmetric cell division
    - curr biol 21(1):R17-R18 (2011)
    Asymmetric cell division in unicellular organisms enables sequestration of senescence factors to specific subpopulations. Accumulation of autonomously replicating sequence (ARS) plasmids, which frequently emerge from recombination within the highly repetitive ribosomal DNA locus, is linked to limited replicative life span of Saccharomyces cerevisiae cells [1]. During budding yeast cell division, ARS plasmids are retained in the ageing mother cell, such that only 1 out of 10 plasmids enters the rejuvenated bud [2]. Binding of ARS plasmids to nuclear structures retained in the mother cell was speculated to explain asymmetric plasmid segregation [2]. Association with nuclear pore complexes (NPCs) was proposed to underlie retention of ARS plasmids in the mother cell [3]. However, the role of NPCs in segregation of ARS plasmids is unclear, as NPCs are partitioned between mother and bud nuclei during mitosis [4] and [5]. Here we analyzed how segregation of ARS plasmids is in! fluenced by their interaction with NPCs. We found that artificial tethering to NPCs promotes transport of ARS plasmids into the bud. Moreover, our experiments provide support for the notion that interaction with ARS plasmids does not affect movement of NPCs into the bud. We conclude that binding to NPCs cannot by itself contribute to asymmetric segregation of ARS plasmids.
  • Neuroanatomy: Decoding the Fly Brain
    - curr biol 21(1):R19-R20 (2011)
    Despite their relatively small brains, with only about 100,000 neurons, fruit flies show many complex behaviours. Understanding how these behaviours are generated will require a wiring diagram of the brain, and significant progress is being made towards this goal. One study has labelled 16,000 individual neurons and generated a coarse wiring diagram of the whole fly brain, identifying subnetworks that may carry out local information processing.
  • Chromatin Reprogramming: Gender Equality during Arabidopsis Germline Differentiation
    - curr biol 21(1):R20-R22 (2011)
    Large-scale histone H3 reprogramming during male germline differentiation is conserved between animals and plants. A new report now shows that histone H3 reprogramming also occurs in the female germline of the flowering plant Arabidopsis thaliana.
  • Photoperiodism: Shall EYA Compare Thee to a Summer's Day?
    - curr biol 21(1):R22-R25 (2011)
    Seasonal changes in day length are used by plants and animals to synchronize annual rhythms in reproduction, physiology, and behavior to the environment. Increasing day length during spring causes sudden changes in the mammalian reproductive system once the critical photoperiod is reached. The molecular mechanism behind this switch is now quickly being elucidated.
  • Photoreceptors: Unconventional Ways of Seeing
    - curr biol 21(1):R25-R27 (2011)
    Animals perceive light typically by photoreceptor neurons assembled in eyes, but some also use non-eye photosensory neurons. Multidendritic neurons in the body wall of Drosophila larvae have now been shown to use an unconventional phototransduction mechanism to sense light.
  • Actin Motility: Formin a SCAry Tail
    - curr biol 21(1):R27-R30 (2011)
    A new biochemical analysis has revealed that the Rickettsia bacterial protein Sca2 — recently shown to be essential for virulence and actin-dependent motility — assembles actin filaments using a mechanism that functionally resembles the processive elongation tactics used by formins.
  • Axon Guidance: Push and Pull with Ephrins and GDNF
    - curr biol 21(1):R30-R32 (2011)
    The pathfinding of motor axons is an important model system for understanding binary axon guidance decisions. Recent work has shown that GDNF attracts motor neuron growth cones, and interacts synergistically with ephrinAs on growth cone directionality.
  • Telomeres: A New Means to an End
    - curr biol 21(1):R32-R34 (2011)
    Gene duplication provides an important evolutionary mechanism for functional diversification. A new study in Drosophila indicates that gene duplication has allowed telomere protection to be partitioned between the soma and the specialized chromatin environment of sperm.
  • Developmental Biology: Extending the Limb and Body with Vectors and Scalars
    - curr biol 21(1):R34-R36 (2011)
    Outgrowth of the embryonic limb in vertebrates is driven by a proximodistal gradient of cell movement, with WNT and FGF activities controlling direction and velocity, respectively. A similar gradient, though without a directional bias, drives caudal body axis extension.
  • Growth Control: Myc and Yorkie Get Connected
    - curr biol 21(1):R37-R39 (2011)
    Recent work shows that the transcriptional coactivator Yorkie, which is negatively regulated by the Hippo tumor suppressor pathway, promotes the transcription of the proto-oncogene Myc and requires Myc function to drive growth. In turn, Myc keeps the concentration of Yorkie in check via negative feedback regulation.
  • Mechanism and Significance of cis-Inhibition in Notch Signalling
    - curr biol 21(1):R40-R47 (2011)
    Notch receptors in a given cell are activated by cell surface ligands in neighbouring cells but can also be inhibited by the ligands present within the same cell. This process is known as cis-inhibition of Notch. Additionally, reciprocal cis-inhibition of the ligands by Notch has also been observed, albeit to a limited extent. Here, we review the mechanisms, functional relevance and potential implications of these cis-inhibitory interactions for Notch-mediated fate decisions.
  • Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution
    - curr biol 21(1):1-11 (2011)
    Background Animal behavior is governed by the activity of interconnected brain circuits. Comprehensive brain wiring maps are thus needed in order to formulate hypotheses about information flow and also to guide genetic manipulations aimed at understanding how genes and circuits orchestrate complex behaviors. Results To assemble this map, we deconstructed the adult Drosophila brain into approximately 16,000 single neurons and reconstructed them into a common standardized framework to produce a virtual fly brain. We have constructed a mesoscopic map and found that it consists of 41 local processing units (LPUs), six hubs, and 58 tracts covering the whole Drosophila brain. Despite individual local variation, the architecture of the Drosophila brain shows invariance for both the aggregation of local neurons (LNs) within specific LPUs and for the connectivity of projection neurons (PNs) between the same set of LPUs. An open-access image database, named FlyCircuit, has been constructed for online data archiving, mining, analysis, and three-dimensional visualization of all single neurons, brain-wide LPUs, their wiring diagrams, and neural tracts. Conclusion We found that the Drosophila brain is assembled from families of multiple LPUs and their interconnections. This provides an essential first step in the analysis of information processing within and between neurons in a complete brain.
  • ATP Hydrolysis Is Required for Relocating Cohesin from Sites Occupied by Its Scc2/4 Loading Complex
    - curr biol 21(1):12-24 (2011)
    Background The Cohesin complex that holds sister chromatins together until anaphase is comprised of three core subunits: Smc1 and Smc3, two long-rod-shaped proteins with an ABC-like ATPase head (nucleotide-binding domain [NBD]) and a dimerization domain linked by a 50 nm long intramolecular antiparallel coiled-coil, and Scc1, an α-kleisin subunit interconnecting the NBD domains of Smc1 and Smc3. Cohesin's stable association with chromosomes is thought to involve entrapment of chromatin fibers by its tripartite Smc1-Smc3-Scc1 ring via a poorly understood mechanism dependent on a separate Scc2/4 loading complex. A key issue concerns where entrapment initially takes place: at sites where cohesin is found stably associated or at distinct "loading" sites from which it translocates. Results In this study, we find transition state mutant versions (Smc1E1158Q and SmcE1155Q) defective in disengagement of their nucleotide binding domains (NBDs), unlike functional cohesin, colocalize with Scc2/4 at core centromeres, sites that catalyze wild-type cohesin's recruitment to sequences 20 kb or more away. In addition to Scc2/4, the unstable association of transition state complexes with core centromeres requires Scc1's association with Smc1 and Smc3 NBDs, ATP-driven NBD engagement, cohesin's Scc3 subunit, and its hinge domain. Conclusion We propose that cohesin's association with chromosomes is driven by two key events. NBD engagement driven by ATP binding produces an unstable association with specific loading sites like core centromeres, whereas subsequent ATP hydrolysis triggers DNA entrapment, which permits translocation along chromatin fibers.
  • Nuclear Geometry and Rapid Mitosis Ensure Asymmetric Episome Segregation in Yeast
    - curr biol 21(1):25-33 (2011)
    Background Asymmetric cell division drives the generation of differentiated cells and maintenance of stem cells. In budding yeast, autonomously replicating sequence (ARS) plasmids lacking centromere elements are asymmetrically segregated into the mother cell, where they are thought to contribute to cellular senescence. This phenomenon has been proposed to result from the active retention of plasmids through an interaction with nuclear pores. Results To investigate the mother-daughter segregation bias of plasmids, we used live-cell imaging to follow the behavior of extrachromosomal DNA. We show that both an excised DNA ring and a centromere-deficient ARS plasmid move freely in the nucleoplasm yet show a strong segregation bias for the mother cell. Computational modeling shows that the geometrical shape of the dividing yeast nucleus and length of mitosis severely restrict the passive diffusion of episomes into daughter nuclei. Predictions based on simulated nuclear division were tested with mutants that extend the length of mitosis. Finally, explaining how various anchors can improve mitotic segregation, we show that plasmid partitioning is improved by tethering the plasmid to segregating structures, such as the nuclear envelope and telomeres. Conclusions The morphology and brevity of mitotic division in budding yeast impose physical constraints on the diffusion of material into the daughter, obviating the need for a retention mechanism to generate rejuvenated offspring.
  • The Human Amygdala and the Induction and Experience of Fear
    - curr biol 21(1):34-38 (2011)
    Although clinical observations suggest that humans with amygdala damage have abnormal fear reactions and a reduced experience of fear [[1], [2] and [3]], these impressions have not been systematically investigated. To address this gap, we conducted a new study in a rare human patient, SM, who has focal bilateral amygdala lesions [4]. To provoke fear in SM, we exposed her to live snakes and spiders, took her on a tour of a haunted house, and showed her emotionally evocative films. On no occasion did SM exhibit fear, and she never endorsed feeling more than minimal levels of fear. Likewise, across a large battery of self-report questionnaires, 3 months of real-life experience sampling, and a life history replete with traumatic events, SM repeatedly demonstrated an absence of overt fear manifestations and an overall impoverished experience of fear. Despite her lack of fear, SM is able to exhibit other basic emotions and experience the respective feelings. The findings sup! port the conclusion that the human amygdala plays a pivotal role in triggering a state of fear and that the absence of such a state precludes the experience of fear itself.
  • A Role for Vasa in Regulating Mitotic Chromosome Condensation in Drosophila
    - curr biol 21(1):39-44 (2011)
    Vasa (Vas) is a conserved DEAD-box RNA helicase expressed in germline cells [1] that localizes to a characteristic perinuclear structure called nuage [[2] and [3]]. Previous studies have shown that Vas has diverse functions, with roles in regulating mRNA translation, germline differentiation, pole plasm assembly, and piwi-interacting RNA (piRNA)-mediated transposon silencing [[1], [4], [5], [6], [7], [8], [9] and [10]]. Although vas has also been implicated in the regulation of germline proliferation in Drosophila and mice [[1] and [11]], little is known about whether Vas plays a role during the mitotic cell cycle. Here, we report a translation-independent function of vas in regulating mitotic chromosome condensation in the Drosophila germline. During mitosis, Vas facilitates robust chromosomal localization of the condensin I components Barren (Barr) and CAP-D2. Vas specifically associates with Barr and CAP-D2, but not with CAP-D3 (a condensin II component). The mitoti! c function of Vas is mediated by the formation of perichromosomal Vas bodies during mitosis, which requires the piRNA pathway components aubergine and spindle-E. Our results suggest that Vas functions during mitosis and may link the piRNA pathway to mitotic chromosome condensation in Drosophila.
  • A High Proliferation Rate Is Required for Cell Reprogramming and Maintenance of Human Embryonic Stem Cell Identity
    - curr biol 21(1):45-52 (2011)
    Human embryonic stem (hES) cells show an atypical cell-cycle regulation characterized by a high proliferation rate and a short G1 phase [[1] and [2]]. In fact, a shortened G1 phase might protect ES cells from external signals inducing differentiation, as shown for certain stem cells [3]. It has been suggested that self-renewal and pluripotency are intimately linked to cell-cycle regulation in ES cells [[4], [5] and [6]], although little is known about the overall importance of the cell-cycle machinery in maintaining ES cell identity. An appealing model to address whether the acquisition of stem cell properties is linked to cell-cycle regulation emerged with the ability to generate induced pluripotent stem (iPS) cells by expression of defined transcription factors [[7], [8], [9], [10] and [11]]. Here, we show that the characteristic cell-cycle signature of hES cells is acquired as an early event in cell reprogramming. We demonstrate that induction of cell proliferation ! increases reprogramming efficiency, whereas cell-cycle arrest inhibits successful reprogramming. Furthermore, we show that cell-cycle arrest is sufficient to drive hES cells toward irreversible differentiation. Our results establish a link that intertwines the mechanisms of cell-cycle control with the mechanisms underlying the acquisition and maintenance of ES cell identity.
  • Influence of Combinatorial Histone Modifications on Antibody and Effector Protein Recognition
    - curr biol 21(1):53-58 (2011)
    Increasing evidence suggests that histone posttranslational modifications (PTMs) function in a combinatorial fashion to regulate the diverse activities associated with chromatin. Yet how these patterns of histone PTMs influence the adapter proteins known to bind them is poorly understood. In addition, how histone-specific antibodies are influenced by these same patterns of PTMs is largely unknown. Here we examine the binding properties of histone-specific antibodies and histone-interacting proteins using peptide arrays containing a library of combinatorially modified histone peptides. We find that modification-specific antibodies are more promiscuous in their PTM recognition than expected and are highly influenced by neighboring PTMs. Furthermore, we find that the binding of histone-interaction domains from BPTF, CHD1, and RAG2 to H3 lysine 4 trimethylation is also influenced by combinatorial PTMs. These results provide further support for the histone code hypothesis a! nd raise specific concerns with the quality of the currently available modification-specific histone antibodies.
  • THRUMIN1 Is a Light-Regulated Actin-Bundling Protein Involved in Chloroplast Motility
    - curr biol 21(1):59-64 (2011)
    Chloroplast movement in response to changing light conditions optimizes photosynthetic light absorption [1]. This repositioning is stimulated by blue light perceived via the phototropin photoreceptors [[2], [3] and [4]] and is transduced to the actin cytoskeleton [5]. Some actin-based motility systems use filament reorganizations rather than myosin-based translocations [6]. Recent research favors the hypothesis that chloroplast movement is driven by actin reorganization at the plasma membrane [[7] and [8]], but no proteins affecting chloroplast movements have been shown to associate with both the plasma membrane and actin filaments in vivo. Here we identified THRUMIN1 as a critical link between phototropin photoreceptor activity at the plasma membrane and actin-dependent chloroplast movements. THRUMIN1 bundles filamentous actin in vitro, and it localizes to the plasma membrane and displays light- and phototropin-dependent localization to microfilaments in vivo. These r! esults suggest that phototropin-induced actin bundling via THRUMIN1 is important for chloroplast movement. A mammalian homolog of THRUMIN1, GRXCR1, has been implicated in auditory responses and hair cell stereocilla development as a regulator of actin architecture [[9] and [10]]. Studies of THRUMIN1 will help elucidate the function of this family of eukaryotic proteins.
  • Nanog Overcomes Reprogramming Barriers and Induces Pluripotency in Minimal Conditions
    - curr biol 21(1):65-71 (2011)
    Induced pluripotency requires the expression of defined factors and culture conditions that support the self-renewal of embryonic stem (ES) cells [1]. Small molecule inhibition of MAP kinase (MEK) and glycogen synthase kinase 3 (GSK3) with LIF (2i/LIF) provides an optimal culture environment for mouse ES cells [2] and promotes transition to naive pluripotency in partially reprogrammed (pre-iPS) cells [3]. Here we show that 2i/LIF treatment in clonal lines of pre-iPS cells results in the activation of endogenous Nanog and rapid downregulation of retroviral Oct4 expression. Nanog enables somatic cell reprogramming in serum-free medium supplemented with LIF, a culture condition which does not support induced pluripotency or the self-renewal of ES cells, and is sufficient to reprogram epiblast-derived stem cells to naive pluripotency in serum-free medium alone. Nanog also enhances reprogramming in cooperation with kinase inhibition or 5-aza-cytidine, a small molecule inhib! itor of DNA methylation. These results highlight the capacity of Nanog to overcome multiple barriers to reprogramming and reveal a synergy between Nanog and chemical inhibitors that promote reprogramming. We conclude that Nanog induces pluripotency in minimal conditions. This provides a strategy for imposing naive pluripotency in mammalian cells independently of species-specific culture requirements.
  • Environmental Uncertainty and the Global Biogeography of Cooperative Breeding in Birds
    - curr biol 21(1):72-78 (2011)
    Understanding why organisms as different as amoebas, ants, and birds cooperate remains an important question in evolutionary biology. Although ecology can influence cooperation and conflict within animal societies and has been implicated in species differences in sociality [1], the environmental predictors of sociality across broad geographic and taxonomic scales remain poorly understood [2]. In particular, the importance of temporal variation in selection pressure has been underestimated in most evolutionary studies [[3] and [4]]. Environmental uncertainty resulting from climatic variation is likely to be an important driver of temporal variation in selection pressure and therefore is expected to impact the evolution of behavioral, morphological, and physiological traits, including cooperation [5]. Using a data set of over 95% of the world's birds, we examine the global geography and environmental, biotic, and historical biogeographic predictors of avian social behavi! or. We find dramatic spatial variation in social behavior for which environmental and biotic factors—namely, among-year environmental variability in precipitation—are important predictors. Although the clear global biogeographic structure in avian social behavior carries a strong signal of evolutionary history, environmental uncertainty plays an additional key role in explaining the incidence and distribution of avian cooperative breeding behavior.
  • Zebrafish Neural Tube Morphogenesis Requires Scribble-Dependent Oriented Cell Divisions
    - curr biol 21(1):79-86 (2011)
    How control of subcellular events in single cells determines morphogenesis on the scale of the tissue is largely unresolved. The stereotyped cross-midline mitoses of progenitors in the zebrafish neural keel [[1], [2], [3] and [4]] provide a unique experimental paradigm for defining the role and control of single-cell orientation for tissue-level morphogenesis in vivo. We show here that the coordinated orientation of individual progenitor cell division in the neural keel is the cellular determinant required for morphogenesis into a neural tube epithelium with a single straight lumen. We find that Scribble is required for oriented cell division and that its function in this process is independent of canonical apicobasal and planar polarity pathways. We identify a role for Scribble in controlling clustering of α-catenin foci in dividing progenitors. Loss of either Scrib or N-cadherin results in abnormally oriented mitoses, reduced cross-midline cell divisions, and simila! r neural tube defects. We propose that Scribble-dependent nascent cell-cell adhesion clusters between neuroepithelial progenitors contribute to define orientation of their cell division. Finally, our data demonstrate that while oriented mitoses of individual cells determine neural tube architecture, the tissue can in turn feed back on its constituent cells to define their polarization and cell division orientation to ensure robust tissue morphogenesis.
  • AP-1 Controls the Trafficking of Notch and Sanpodo toward E-Cadherin Junctions in Sensory Organ Precursors
    - curr biol 21(1):87-95 (2011)
    In Drosophila melanogaster, external sensory organs develop from a single sensory organ precursor (SOP). The SOP divides asymmetrically to generate daughter cells, whose fates are governed by differential Notch activation. Here we show that the clathrin adaptor AP-1 complex, localized at the trans Golgi network and in recycling endosomes, acts as a negative regulator of Notch signaling. Inactivation of AP-1 causes ligand-dependent activation of Notch, leading to a fate transformation within sensory organs. Loss of AP-1 affects neither cell polarity nor the unequal segregation of the cell fate determinants Numb and Neuralized. Instead, it causes apical accumulation of the Notch activator Sanpodo and stabilization of both Sanpodo and Notch at the interface between SOP daughter cells, where DE-cadherin is localized. Endocytosis-recycling assays reveal that AP-1 acts in recycling endosomes to prevent internalized Spdo from recycling toward adherens junctions. Because AP-1 ! does not prevent endocytosis and recycling of the Notch ligand Delta, our data indicate that the DE-cadherin junctional domain may act as a launching pad through which endocytosed Notch ligand is trafficked for signaling.
  • Apoptosis: Opening PANdora's BoX
    - curr biol 21(1):96 (2011)

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