Thursday, April 30, 2009

Hot off the presses! May 02 Lancet

The May 02 issue of the Lancet is now up on Pubget (About Lancet): 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:

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Hot off the presses! May 01 Cell

The May 01 issue of the Cell is now up on Pubget (About Cell): 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:

  • In This Issue
    - Cell 137(3):383, 385 (2009)
  • Neurobiology Select
    - Cell 137(3):387, 389 (2009)
    Sleep is one of the most fundamental, yet least understood, facets of animal physiology—its universality reflected in the saying, "life is one long process of getting tired." This issue's Neurobiology Select describes the latest progress toward understanding sleep, including its role in maintaining synaptic homeostasis, its role in long-term memory formation, and the causes and consequences of sleep disruption.
  • Commonality but Diversity in Cancer Gene Fusions
    - Cell 137(3):391-395 (2009)
    Recent findings of gene fusions in carcinomas recapitulate the discovery of chromosomal abnormalities in leukemias and sarcomas decades ago. A recurring feature of carcinoma gene fusions, in contrast to those in hematopoietic and mesenchymal malignancies, is that they result in aberrant cell signaling. This may reflect differences in the differentiation programs of these tissues.
  • Rfu1: Stimulus for the Ubiquitin Economy
    - Cell 137(3):397-398 (2009)
    During cellular stress, monoubiquitin is in demand due to the accumulation of misfolded proteins that require proteasomal degradation. Kimura et al. (2009) now show in yeast that monoubiquitin levels are bolstered during stress conditions by downregulation of the protein Rfu1, an inhibitor of the deubiquitinating enzyme Doa4.
  • Specifying Mouse Embryonic Germ Cells
    - Cell 137(3):398-400 (2009)
    Male germ cells are induced to form from the epiblast of the mouse embryo by a combination of WNT and bone morphogenetic protein signals. Ohinata et al. (2009) now clarify the steps of mouse germ cell formation and use this genetic insight to direct the specification and differentiation of germline progenitor cells in vitro.
  • Opening Windows to the Genome
    - Cell 137(3):400-402 (2009)
    Recent mapping of nucleosome positioning has added a new dimension to the study of transcriptional regulation. Hartley and Madhani (2009) now demonstrate the power of this approach and show that a chromatin regulator alters nucleosome positioning in the promoters of a large number of genes in the budding yeast Saccharomyces cerevisiae.
  • HIV Entry Revisited
    - Cell 137(3):402-404 (2009)
    HIV has long served as a model for viruses that enter cells by direct fusion at the plasma membrane. Miyauchi et al. (2009) now provide compelling evidence that HIV enters cells primarily by endocytosis.
  • Ure(k)a! Sirtuins Regulate Mitochondria
    - Cell 137(3):404-406 (2009)
    Increasing evidence suggests that multiple metabolic pathways are regulated by sirtuin-dependent protein deacetylation in the mitochondria. In this issue, Nakagawa et al. (2009) show that the sirtuin SIRT5 deacetylates and activates a mitochondrial enzyme, carbamoyl phosphate synthetase 1, which mediates the first step in the urea cycle.
  • Frodos Found: Behold the CENP-A "Ring" Bearers
    - Cell 137(3):409-412 (2009)
    CENP-A is a histone H3-like protein specific to centromeres that is essential for kinetochore formation and accurate chromosome segregation in eukaryotes. Recent studies ([Dunleavy et al., 2009], [Foltz et al., 2009], [Perpelescu et al., 2009], [Pidoux et al., 2009] and [Williams et al., 2009]) analyze CENP-A binding proteins required for the recruitment of CENP-A to centromeres in humans and in fission yeast, bringing us closer to understanding how centromere identity is faithfully propagated.
  • Blinded by the Light: The Growing Complexity of p53
    - Cell 137(3):413-431 (2009)
    While the tumor suppressor functions of p53 have long been recognized, the contribution of p53 to numerous other aspects of disease and normal life is only now being appreciated. This burgeoning range of responses to p53 is reflected by an increasing variety of mechanisms through which p53 can function, although the ability to activate transcription remains key to p53's modus operandi. Control of p53's transcriptional activity is crucial for determining which p53 response is activated, a decision we must understand if we are to exploit efficiently the next generation of drugs that selectively activate or inhibit p53.
  • HIV Enters Cells via Endocytosis and Dynamin-Dependent Fusion with Endosomes
    - Cell 137(3):433-444 (2009)
    Enveloped viruses that rely on a low pH-dependent step for entry initiate infection by fusing with acidic endosomes, whereas the entry sites for pH-independent viruses, such as HIV-1, have not been defined. These viruses have long been assumed to fuse directly with the plasma membrane. Here we used population-based measurements of the viral content delivery into the cytosol and time-resolved imaging of single viruses to demonstrate that complete HIV-1 fusion occurred in endosomes. In contrast, viral fusion with the plasma membrane did not progress beyond the lipid mixing step. HIV-1 underwent receptor-mediated internalization long before endosomal fusion, thus minimizing the surface exposure of conserved viral epitopes during fusion and reducing the efficacy of inhibitors targeting these epitopes. We also show that, strikingly, endosomal fusion is sensitive to a dynamin inhibitor, dynasore. These findings imply that HIV-1 infects cells via endocytosis and envelope glyc! oprotein- and dynamin-dependent fusion with intracellular compartments.
  • Mechanisms that Specify Promoter Nucleosome Location and Identity
    - Cell 137(3):445-458 (2009)
    The chromatin architecture of eukaryotic gene promoters is generally characterized by a nucleosome-free region (NFR) flanked by at least one H2A.Z variant nucleosome. Computational predictions of nucleosome positions based on thermodynamic properties of DNA-histone interactions have met with limited success. Here we show that the action of the essential RSC remodeling complex in S. cerevisiae helps explain the discrepancy between theory and experiment. In RSC-depleted cells, NFRs shrink such that the average positions of flanking nucleosomes move toward predicted sites. Nucleosome positioning at distinct subsets of promoters additionally requires the essential Myb family proteins Abf1 and Reb1, whose binding sites are enriched in NFRs. In contrast, H2A.Z deposition is dispensable for nucleosome positioning. By regulating H2A.Z deposition using a steroid-inducible protein splicing strategy, we show that NFR establishment is necessary for H2A.Z deposition. These studies ! suggest an ordered pathway for the assembly of promoter chromatin architecture.
  • RAD6-Mediated Transcription-Coupled H2B Ubiquitylation Directly Stimulates H3K4 Methylation in Human Cells
    - Cell 137(3):459-471 (2009)
    H2B ubiquitylation has been implicated in active transcription but is not well understood in mammalian cells. Beyond earlier identification of hBRE1 as the E3 ligase for H2B ubiquitylation in human cells, we now show (1) that hRAD6 serves as the cognate E2-conjugating enzyme; (2) that hRAD6, through direct interaction with hPAF-bound hBRE1, is recruited to transcribed genes and ubiquitylates chromatinized H2B at lysine 120; (3) that hPAF-mediated transcription is required for efficient H2B ubiquitylation as a result of hPAF-dependent recruitment of hBRE1-hRAD6 to the Pol II transcription machinery; (4) that H2B ubiquitylation per se does not affect the level of hPAF-, SII-, and p300-dependent transcription and likely functions downstream; and (5) that H2B ubiquitylation directly stimulates hSET1-dependent H3K4 di- and trimethylation. These studies establish the natural H2B ubiquitylation factors in human cells and also detail the mechanistic basis for H2B ubiquitylatio! n and function during transcription.
  • Centromere-Specific Assembly of CENP-A Nucleosomes Is Mediated by HJURP
    - Cell 137(3):472-484 (2009)
    The centromere is responsible for accurate chromosome segregation. Mammalian centromeres are specified epigenetically, with all active centromeres containing centromere-specific chromatin in which CENP-A replaces histone H3 within the nucleosome. The proteins responsible for assembly of human CENP-A into centromeric nucleosomes during the G1 phase of the cell cycle are shown here to be distinct from the chromatin assembly factors previously shown to load other histone H3 variants. Here we demonstrate that prenucleosomal CENP-A is complexed with histone H4, nucleophosmin 1, and HJURP. Recruitment of new CENP-A into nucleosomes at replicated centromeres is dependent on HJURP. Recognition by HJURP is mediated through the centromere targeting domain (CATD) of CENP-A, a region that we demonstrated previously to induce a unique conformational rigidity to both the subnucleosomal CENP-A heterotetramer and the corresponding assembled nucleosome. We propose HJURP to be a cell-cy! cle-regulated CENP-A-specific histone chaperone required for centromeric chromatin assembly.
  • HJURP Is a Cell-Cycle-Dependent Maintenance and Deposition Factor of CENP-A at Centromeres
    - Cell 137(3):485-497 (2009)
    The histone H3 variant CenH3, called CENP-A in humans, is central in centromeric chromatin to ensure proper chromosome segregation. In the absence of an underlying DNA sequence, it is still unclear how CENP-A deposition at centromeres is determined. Here, we purified non-nucleosomal CENP-A complexes to identify direct CENP-A partners involved in such a mechanism and identified HJURP. HJURP was not detected in H3.1- or H3.3-containing complexes, indicating its specificity for CENP-A. HJURP centromeric localization is cell cycle regulated, and its transient appearance at the centromere coincides precisely with the proposed time window for new CENP-A deposition. Furthermore, HJURP downregulation leads to a major reduction in CENP-A at centromeres and impairs deposition of newly synthesized CENP-A, causing mitotic defects. We conclude that HJURP is a key factor for CENP-A deposition and maintenance at centromeres.
  • An Effector of RNA-Directed DNA Methylation in Arabidopsis Is an ARGONAUTE 4- and RNA-Binding Protein
    - Cell 137(3):498-508 (2009)
    DNA methylation is a conserved epigenetic mark in plants and mammals. In Arabidopsis, DNA methylation can be triggered by small interfering RNAs (siRNAs) through an RNA-directed DNA methylation (RdDM) pathway. Here, we report the identification of an RdDM effector, KTF1. Loss-of-function mutations in KTF1 reduce DNA methylation and release the silencing of RdDM target loci without abolishing the siRNA triggers. KTF1 has similarity to the transcription elongation factor SPT5 and contains a C-terminal extension rich in GW/WG repeats. KTF1 colocalizes with ARGONAUTE 4 (AGO4) in punctate nuclear foci and binds AGO4 and RNA transcripts. Our results suggest KTF1 as an adaptor protein that binds scaffold transcripts generated by Pol V and recruits AGO4 and AGO4-bound siRNAs to form an RdDM effector complex. The dual interaction of an effector protein with AGO and small RNA target transcripts may be a general feature of RNA-silencing effector complexes.
  • Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies
    - Cell 137(3):509-521 (2009)
    Piwi-interacting RNAs (piRNAs) silence transposons in animal germ cells. piRNAs are thought to derive from long transcripts spanning transposon-rich genomic loci and to direct an autoamplification loop in which an antisense piRNA, bound to Aubergine or Piwi protein, triggers production of a sense piRNA bound to the PIWI protein Argonaute3 (Ago3). In turn, the new piRNA is envisioned to produce a second antisense piRNA. Here, we describe strong loss-of-function mutations in ago3, allowing a direct genetic test of this model. We find that Ago3 acts to amplify piRNA pools and to enforce on them an antisense bias, increasing the number of piRNAs that can act to silence transposons. We also detect a second, Ago3-independent piRNA pathway centered on Piwi. Transposons targeted by this second pathway often reside in the flamenco locus, which is expressed in somatic ovarian follicle cells, suggesting a role for piRNAs beyond the germline.
  • Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary
    - Cell 137(3):522-535 (2009)
    In Drosophila gonads, Piwi proteins and associated piRNAs collaborate with additional factors to form a small RNA-based immune system that silences mobile elements. Here, we analyzed nine Drosophila piRNA pathway mutants for their impacts on both small RNA populations and the subcellular localization patterns of Piwi proteins. We find that distinct piRNA pathways with differing components function in ovarian germ and somatic cells. In the soma, Piwi acts singularly with the conserved flamenco piRNA cluster to enforce silencing of retroviral elements that may propagate by infecting neighboring germ cells. In the germline, silencing programs encoded within piRNA clusters are optimized via a slicer-dependent amplification loop to suppress a broad spectrum of elements. The classes of transposons targeted by germline and somatic piRNA clusters, though not the precise elements, are conserved among Drosophilids, demonstrating that the architecture of piRNA clusters has coevol! ved with the transposons that they are tasked to control.
  • Disassembly of Exon Junction Complexes by PYM
    - Cell 137(3):536-548 (2009)
    Exon junction complexes (EJCs) are deposited onto mRNAs during splicing, serve as positional landmarks for the intron exon structure of genes, and direct posttranscriptional processes in the cytoplasm. EJC removal and recycling by translation are ill understood and have been attributed to ribosomal passage. This work identifies the ribosome-associated protein PYM as an EJC disassembly factor and defines its mechanism of function. Whereas EJC assembly intermediates are resistant to PYM, fully assembled EJCs are dissociated from spliced mRNAs by PYM. This disassembly involves PYM binding to the EJC proteins MAGOH-Y14. PYM overexpression in cells disrupts EJC association with spliced mRNA and inhibits nonsense-mediated mRNA decay. In cells depleted of PYM, EJCs accumulate on spliced mRNAs and EJC protein recycling is impaired. Hence, PYM is an EJC disassembly factor that acts both in vitro and in living cells, and that antagonizes important EJC functions.
  • An Inhibitor of a Deubiquitinating Enzyme Regulates Ubiquitin Homeostasis
    - Cell 137(3):549-559 (2009)
    The dynamic and reversible process of ubiquitin modification controls various cellular activities. Ubiquitin exists as monomers, unanchored chains, or protein-conjugated forms, but the regulation of these interconversions remains largely unknown. Here, we identified a protein designated Rfu1 (regulator of free ubiquitin chains 1), which regulates intracellular concentrations of monomeric ubiquitins and free ubiquitin chains in Saccharomyces cerevisiae. Rfu1 functions as an inhibitor of Doa4, a deubiquitinating enzyme. Rapid loss of free ubiquitin chains upon heat shock, a condition in which more proteins require ubiquitin conjugation, was mediated in part by Doa4 and Rfu1. Thus, regulation of ubiquitin homeostasis is controlled by a balance between a deubiquitinating enzyme and its inhibitor. We propose that free ubiquitin chains function as a ubiquitin reservoir that allows maintenance of monomeric ubiquitins at adequate levels under normal conditions and rapid supply! for substrate conjugation under stress conditions.
  • SIRT5 Deacetylates Carbamoyl Phosphate Synthetase 1 and Regulates the Urea Cycle
    - Cell 137(3):560-570 (2009)
    Sirtuins are NAD-dependent protein deacetylases that connect metabolism and aging. In mammals, there are seven sirtuins (SIRT1-7), three of which are associated with mitochondria. Here, we show that SIRT5 localizes in the mitochondrial matrix and interacts with carbamoyl phosphate synthetase 1 (CPS1), an enzyme, catalyzing the initial step of the urea cycle for ammonia detoxification and disposal. SIRT5 deacetylates CPS1 and upregulates its activity. During fasting, NAD in liver mitochondria increases, thereby triggering SIRT5 deacetylation of CPS1 and adaptation to the increase in amino acid catabolism. Indeed, SIRT5 KO mice fail to upregulate CPS1 activity and show elevated blood ammonia during fasting. Similar effects occur during long-term calorie restriction or a high protein diet. These findings demonstrate SIRT5 plays a pivotal role in ammonia detoxification and disposal by activating CPS1.
  • A Signaling Principle for the Specification of the Germ Cell Lineage in Mice
    - Cell 137(3):571-584 (2009)
    Specification of the germ cell lineage is vital to development and heredity. In mice, the germ cell fate is induced in pluripotent epiblast cells by signaling molecules, yet the underlying mechanism remains unknown. Here we demonstrate that germ cell fate in the epiblast is a direct consequence of Bmp4 signaling from the extraembryonic ectoderm (ExE), which is antagonized by the anterior visceral endoderm (AVE). Strikingly, Bmp8b from the ExE restricts AVE development, thereby contributing to Bmp4 signaling. Furthermore, Wnt3 in the epiblast ensures its responsiveness to Bmp4. Serum-free, defined cultures revealed that, in response to Bmp4, competent epiblast cells uniformly expressed key transcriptional regulators Blimp1 and Prdm14 and acquired germ-cell properties, including genome-wide epigenetic reprogramming, in an orderly fashion. Notably, the induced cells contributed to both spermatogenesis and fertility of offspring. By identifying a signaling principle in ger! m cell specification, our study establishes a robust strategy for reconstituting the mammalian germ cell lineage in vitro.
  • SnapShot: MicroRNAs in Cancer
    - Cell 137(3):586-586.e1 (2009)
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Hot off the presses! May 01 Nat Cell Biol

The May 01 issue of the Nat Cell Biol is now up on Pubget (About Nat Cell 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:

  • Genetic privacy and piracy
    - Nat Cell Biol 11(5):509 (2009)
  • Focus on host subversion
    - Nat Cell Biol 11(5):509 (2009)
  • Virus entry by macropinocytosis
    - Nat Cell Biol 11(5):510-520 (2009)
    As obligatory intracellular parasites, viruses rely on host-cell functions for most aspects of their replication cycle. This is born out during entry, when most viruses that infect vertebrate and insect cells exploit the endocytic activities of the host cell to move into the cytoplasm. Viruses belonging to vaccinia, adeno, picorna and other virus families have been reported to take advantage of macropinocytosis, an endocytic mechanism normally involved in fluid uptake. The virus particles first activate signalling pathways that trigger actin-mediated membrane ruffling and blebbing. Usually, this is followed by the formation of large vacuoles (macropinosomes) at the plasma membrane, internalization of virus particles and penetration by the viruses or their capsids into the cytosol through the limiting membrane of the macropinosomes. We review the molecular machinery involved in macropinocytosis and describe what is known about its role in virus entry.
  • Targeting of immune signalling networks by bacterial pathogens
    - Nat Cell Biol 11(5):521-526 (2009)
    Host defence against microbial pathogens requires appropriate coordination of multiple signalling pathways. These pathways are triggered by innate immune recognition of conserved microbial molecules, and initiate an inflammatory cascade that involves recruitment of leukocytes to the site of infection, activation of antimicrobial effector mechanisms and induction of an adaptive immune response that promotes clearance of infection and long-term immune memory. Microbial pathogens possess specialized proteins termed virulence factors, which interfere with host defence at several levels. Many virulence factors from diverse pathogens have been identified in recent years and their functions linked to disruption of essential processes of immune defence, from signalling to phagocytosis. Although the diversity of pathogens and virulence factors is immense, common themes have emerged with regard to how microbial pathogens interfere with immune responses. Here we discuss recent ad! vances in our understanding of how virulence factors target innate and adaptive immune responses, focusing on bacterial pathogens. We also propose that pathogens responsible for causing acute infection tend to target central components (hubs) of cellular signalling pathways, causing global disruption of the host response. By contrast, pathogens that cause chronic or persistent infections tend to target more peripheral signalling network components (nodes) to promote pathogen persistence.
  • Viral avoidance and exploitation of the ubiquitin system
    - Nat Cell Biol 11(5):527-534 (2009)
    The versatility of ubiquitin in regulating protein function and cell behaviour through post-translational protein modification makes it a particularly attractive target for viruses. Here we review how viruses manipulate the ubiquitin system to favour their propagation by redirecting cellular ubiquitin enzymes or encoding their own ubiquitin components to enable replication, egress and immune evasion. These studies not only reveal the many cellular processes requiring ubiquitin but also illustrate how viruses usurp their host cells.
  • From cell differentiation to the cell cycle: how failing in biochemistry led to success in morphology
    - Nat Cell Biol 11(5):535 (2009)
  • Breaking a temporal barrier: signalling crosstalk regulates the initiation of border cell migration
    - Nat Cell Biol 11(5):536-538 (2009)
  • Smurf1 zaps the talin head
    - Nat Cell Biol 11(5):538-540 (2009)
  • SCAI blocks MAL-evolent effects on cancer cell invasion
    - Nat Cell Biol 11(5):540-542 (2009)
  • Research highlights
    - Nat Cell Biol 11(5):543 (2009)
  • Protein kinase D1 regulates cofilin-mediated F-actin reorganization and cell motility through slingshot
    - Nat Cell Biol 11(5):545-556 (2009)
    Dynamic actin remodelling processes at the leading edge of migrating tumour cells are concerted events controlled by a fine-tuned temporal and spatial interplay of kinases and phosphatases. Actin severing is regulated by actin depolymerizing factor (ADF)/cofilin, which regulates stimulus-induced lamellipodia protrusion and directed cell motility. Cofilin is activated by dephosphorylation through phosphatases of the slingshot (SSH) family. SSH activity is strongly increased by its binding to filamentous actin (F-actin); however, other upstream regulators remain unknown. Here we show that in response to RhoA activation, protein kinase D1 (PKD1) phosphorylates the SSH enzyme SSH1L at a serine residue located in its actin-binding motif. This generates a 14-3-3-binding motif and blocks the localization of SSH1L to F-actin-rich structures in the lamellipodium by sequestering it in the cytoplasm. Consequently, expression of constitutively active PKD1 in invasive tumour cells ! enhanced the phosphorylation of cofilin and effectively blocked the formation of free actin-filament barbed ends and directed cell migration.
  • SCAI acts as a suppressor of cancer cell invasion through the transcriptional control of beta1-integrin
    - Nat Cell Biol 11(5):557-568 (2009)
    Gene expression reprogramming governs cellular processes such as proliferation, differentiation and cell migration through the complex and tightly regulated control of transcriptional cofactors that exist in multiprotein complexes. Here we describe SCAI (suppressor of cancer cell invasion), a novel and highly conserved protein that regulates invasive cell migration through three-dimensional matrices. SCAI acts on the RhoA–Dia1 signal transduction pathway and localizes in the nucleus, where it binds and inhibits the myocardin-related transcription factor MAL by forming a ternary complex with serum response factor (SRF). Genome-wide expression analysis surprisingly reveals that one of the strongest upregulated genes after suppression of SCAI is beta1-integrin. Decreased levels of SCAI are tightly correlated with increased invasive cell migration, and SCAI is downregulated in several human tumours. Functional analysis of the beta1-integrin gene strongly argues that SCAI! is a novel transcriptional cofactor that controls gene expression downstream of Dia1 to dictate changes in cell invasive behaviour.
  • Border-cell migration requires integration of spatial and temporal signals by the BTB protein Abrupt
    - Nat Cell Biol 11(5):569-579 (2009)
    During development, elaborate patterns of cell differentiation and movement must occur in the correct locations and at the proper times. Developmental timing has been studied less than spatial pattern formation, and the mechanisms integrating the two are poorly understood. Border-cell migration in the Drosophila ovary occurs specifically at stage 9. Timing of the migration is regulated by the steroid hormone ecdysone, whereas spatial patterning of the migratory population requires localized activity of the JAK–STAT pathway. Ecdysone signalling is patterned spatially as well as temporally, although the mechanisms are not well understood. In stage 9 egg chambers, ecdysone signalling is highest in anterior follicle cells including the border cells. We identify the gene abrupt as a repressor of ecdysone signalling and border-cell migration. Abrupt protein is normally lost from border-cell nuclei during stage 9, in response to JAK–STAT activity. This contributes to the ! spatial pattern of the ecdysone response. Abrupt attenuates ecdysone signalling by means of a direct interaction with the basic helix–loop–helix (bHLH) domain of the P160 ecdysone receptor coactivator Taiman (Tai). Taken together, these findings provide a molecular mechanism by which spatial and temporal cues are integrated.
  • KRAB-type zinc-finger protein Apak specifically regulates p53-dependent apoptosis
    - Nat Cell Biol 11(5):580-591 (2009)
    Only a few p53 regulators have been shown to participate in the selective control of p53-mediated cell cycle arrest or apoptosis. How p53-mediated apoptosis is negatively regulated remains largely unclear. Here we report that Apak (ATM and p53-associated KZNF protein), a Krüppel-associated box (KRAB)-type zinc-finger protein, binds directly to p53 in unstressed cells, specifically downregulates pro-apoptotic genes, and suppresses p53-mediated apoptosis by recruiting KRAB-box-associated protein (KAP)-1 and histone deacetylase 1 (HDAC1) to attenuate the acetylation of p53. Apak inhibits p53 activity by interacting with ATM, a previously identified p53 activator. In response to stress, Apak is phosphorylated by ATM and dissociates from p53, resulting in activation of p53 and induction of apoptosis. These findings revealed Apak to be a negative regulator of p53-mediated apoptosis and showed the dual role of ATM in p53 regulation.
  • RAD18 transmits DNA damage signalling to elicit homologous recombination repair
    - Nat Cell Biol 11(5):592-603 (2009)
    To maintain genome stability, cells respond to DNA damage by activating signalling pathways that govern cell-cycle checkpoints and initiate DNA repair. Cell-cycle checkpoint controls should connect with DNA repair processes, however, exactly how such coordination occurs in vivo is largely unknown. Here we describe a new role for the E3 ligase RAD18 as the integral component in translating the damage response signal to orchestrate homologous recombination repair (HRR). We show that RAD18 promotes homologous recombination in a manner strictly dependent on its ability to be recruited to sites of DNA breaks and that this recruitment relies on a well-defined DNA damage signalling pathway mediated by another E3 ligase, RNF8. We further demonstrate that RAD18 functions as an adaptor to facilitate homologous recombination through direct interaction with the recombinase RAD51C. Together, our data uncovers RAD18 as a key factor that orchestrates HRR through surveillance of the D! NA damage signal.
  • Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity
    - Nat Cell Biol 11(5):604-615 (2009)
    The accumulation of stochastic DNA damage throughout an organism's lifespan is thought to contribute to ageing. Conversely, ageing seems to be phenotypically reproducible and regulated through genetic pathways such as the insulin-like growth factor-1 (IGF-1) and growth hormone (GH) receptors, which are central mediators of the somatic growth axis. Here we report that persistent DNA damage in primary cells from mice elicits changes in global gene expression similar to those occurring in various organs of naturally aged animals. We show that, as in ageing animals, the expression of IGF-1 receptor and GH receptor is attenuated, resulting in cellular resistance to IGF-1. This cell-autonomous attenuation is specifically induced by persistent lesions leading to stalling of RNA polymerase II in proliferating, quiescent and terminally differentiated cells; it is exacerbated and prolonged in cells from progeroid mice and confers resistance to oxidative stress. Our findings sugg! est that the accumulation of DNA damage in transcribed genes in most if not all tissues contributes to the ageing-associated shift from growth to somatic maintenance that triggers stress resistance and is thought to promote longevity.
  • Telomere recombination requires the MUS81 endonuclease
    - Nat Cell Biol 11(5):616-623 (2009)
    Telomerase-negative cancer cells maintain their telomeres through the alternative lengthening of telomeres (ALT) pathway1, 2, 3. Although a growing body of evidence demonstrates that the ALT mechanism is a post-replicative telomere recombination process, molecular details of this pathway are largely unknown. Here we demonstrate that MUS81, a DNA structure specific recombination endonuclease, has a key role in the maintenance of telomeres in human ALT cells. We find that MUS81 specifically localizes to ALT-associated promyelocytic leukaemia (PML) nuclear bodies (APBs) and associates with telomeric DNA in ALT cells, which is enriched during the G2 phase of the cell cycle. Depletion of MUS81 results in the reduction of ALT-specific telomere recombination and leads to proliferation arrest of ALT cells. In addition, the endonuclease activity of MUS81 is required for recombination-based ALT cell survival, and the interaction of MUS81 with the telomeric repeat-binding factor ! TRF2 regulates this enzymatic activity, thereby maintaining telomere recombination. Thus, our results suggest that MUS81 is involved in the maintenance of ALT cell survival at least in part by homologous recombination of telomeres.
  • Talin phosphorylation by Cdk5 regulates Smurf1-mediated talin head ubiquitylation and cell migration
    - Nat Cell Biol 11(5):624-630 (2009)
    Cell migration is a dynamic process that requires temporal and spatial regulation of integrin activation and focal adhesion assembly/disassembly1. Talin, an actin and beta-integrin tail-binding protein, is essential for integrin activation and focal adhesion formation2, 3. Calpain-mediated cleavage of talin has a key role in focal adhesion turnover3; however, the talin head domain, one of the two cleavage products, stimulates integrin activation, localizes to focal adhesions and maintains cell edge protrusions2, 4, 5, suggesting that other steps, downstream of talin proteolysis, are required for focal adhesion disassembly. Here we show that talin head binds Smurf1, an E3 ubiquitin ligase involved in cell polarity and migration6, 7, more tightly than full-length talin does and that this interaction leads to talin head ubiquitylation and degradation. We found that talin head is a substrate for Cdk5, a cyclin-dependent protein kinase that is essential for cell migration, ! synaptic transmission and cancer metastasis8, 9, 10, 11. Cdk5 phosphorylated talin head at Ser 425, inhibiting its binding to Smurf1, thus preventing talin head ubiquitylation and degradation. Expression of the mutant talS425A, which resists Cdk5 phosphorylation thereby increasing its susceptibility to Smurf1-mediated ubiqitylation, resulted in extensive focal adhesion turnover and inhibited cell migration. Thus, talin head produced by calpain-induced cleavage of talin is degraded through Smurf1-mediated ubiquitylation; moreover, phosphorylation by Cdk5 regulates the binding of Smurf1 to talin head, controlling talin head turnover, adhesion stability and ultimately, cell migration.
  • Production of offspring from a germline stem cell line derived from neonatal ovaries
    - Nat Cell Biol 11(5):631-636 (2009)
    The idea that females of most mammalian species have lost the capacity for oocyte production at birth1, 2, 3, 4, 5 has been challenged recently by the finding that juvenile and adult mouse ovaries possess mitotically active germ cells6. However, the existence of female germline stem cells (FGSCs) in postnatal mammalian ovaries still remains a controversial issue among reproductive biologists and stem cell researchers6, 7, 8, 9, 10. We have now established a neonatal mouse FGSC line, with normal karyotype and high telomerase activity, by immunomagnetic isolation and culture for more than 15 months. FGSCs from adult mice were isolated and cultured for more than 6 months. These FGSCs were infected with GFP virus and transplanted into ovaries of infertile mice. Transplanted cells underwent oogenesis and the mice produced offspring that had the GFP transgene. These findings contribute to basic research into oogenesis and stem cell self-renewal and open up new possibilities ! for use of FGSCs in biotechnology and medicine.
  • Bone morphogenetic protein heterodimers assemble heteromeric type I receptor complexes to pattern the dorsoventral axis
    Little SC Mullins MC - Nat Cell Biol 11(5):637-643 (2009)
    Patterning the embryonic dorsoventral axis of both vertebrates and invertebrates requires signalling through bone morphogenetic proteins (BMPs)1. Although a well-studied process, the identity of the physiologically relevant BMP signalling complex in the Drosophila melanogaster embryo is controversial2, 3, is generally inferred from cell culture studies and has not been investigated in vertebrates. Here, we demonstrate that dorsoventral patterning in zebrafish, Danio rerio, requires two classes of non-redundant type I BMP receptors, Alk3/6 and Alk8 (activin-like kinases 3/6 and 8). We show, under physiological conditions in the embryo, that these two type I receptor classes form a complex in a manner that depends on Bmp2 and Bmp7. We found that both Bmp2–7 heterodimers, as well as Bmp2 and Bmp7 homodimers, form in the embryo. However, only recombinant ligand heterodimers can activate BMP signalling in the early embryo, whereas a combination of Bmp2 and Bmp7 homodimers! cannot. We propose that only heterodimers, signalling through two distinct classes of type I receptor, possess sufficient receptor affinity in an environment of extracellular antagonists to elicit the signalling response required for dorsoventral patterning.
  • PP1-mediated dephosphorylation of phosphoproteins at mitotic exit is controlled by inhibitor-1 and PP1 phosphorylation
    - Nat Cell Biol 11(5):644-651 (2009)
    Loss of cell division cycle 2 (Cdc2, also known as Cdk1) activity after cyclin B degradation is necessary, but not sufficient, for mitotic exit. Proteins phosphorylated by Cdc2 and downstream mitotic kinases must be dephosphorylated. We report here that protein phosphatase-1 (PP1) is the main catalyst of mitotic phosphoprotein dephosphorylation. Suppression of PP1 during early mitosis is maintained through dual inhibition by Cdc2 phosphorylation and the binding of inhibitor-1. Protein kinase A (PKA) phosphorylates inhibitor-1, mediating binding to PP1. As Cdc2 levels drop after cyclin B degradation, auto-dephosphorylation of PP1 at its Cdc2 phosphorylation site (Thr 320) allows partial PP1 activation. This promotes PP1-regulated dephosphorylation at the activating site of inhibitor-1 (Thr 35) followed by dissociation of the inhibitor-1–PP1 complex and then full PP1 activation to promote mitotic exit. Thus, Cdc2 both phosphorylates multiple mitotic substrates and inhi! bits their PP1-mediated dephosphorylation.
  • Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability
    - Nat Cell Biol 11(5):652-658 (2009)
    Piwi family proteins are essential for germline development and bind piwi-interacting RNAs (piRNAs)1, 2, 3. The grandchildless gene aub of Drosophila melanogaster encodes the piRNA-binding protein Aubergine (Aub), which is essential for formation of primordial germ cells (PGCs)4. Here we report that Piwi family proteins of mouse, Xenopus laevis and Drosophila contain symmetrical dimethylarginines (sDMAs). We found that Piwi proteins are expressed in Xenopus oocytes and we identified numerous Xenopus piRNAs. We report that the Drosophila homologue of protein methyltransferase 5 (dPRMT5, csul/dart5), which is also the product of a grandchildless gene5, 6, is required for arginine methylation of Drosophila Piwi, Ago3 and Aub proteins in vivo. Loss of dPRMT5 activity led to a reduction in the levels of piRNAs, Ago3 and Aub proteins, and accumulation of retrotransposons in the Drosophila ovary. Our studies explain the relationship between aub and dPRMT5 (csul/dart5) genes b! y demonstrating that dPRMT5 is the enzyme that methylates Aub. Our findings underscore the significance of sDMA modification of Piwi proteins in the germline and suggest an interacting pathway of genes that are required for piRNA function and PGC specification.
  • WIP1 phosphatase is a negative regulator of NF-kappaB signalling
    - Nat Cell Biol 11(5):659-666 (2009)
    Post-translational modifications of NF-kappaB through phosphorylations enhance its transactivation potential. Much is known about the kinases that phosphorylate NF-kappaB, but little is known about the phosphatases that dephosphorylate it. By using a genome-scale siRNA screen, we identified the WIP1 phosphatase as a negative regulator of NF-kappaB signalling. WIP1-mediated regulation of NF-kappaB occurs in both a p38-dependent and independent manner. Overexpression of WIP1 resulted in decreased NF-kappaB activation in a dose-dependent manner, whereas WIP1 knockdown resulted in increased NF-kappaB function. We show that WIP1 is a direct phosphatase of Ser 536 of the p65 subunit of NF-kappaB. Phosphorylation of Ser 536 is known to be essential for the transactivation function of p65, as it is required for recruitment of the transcriptional co-activator p300. WIP1-mediated regulation of p65 regulated binding of NF-kappaB to p300 and hence chromatin remodelling. Consistent! with our results, mice lacking WIP1 showed enhanced inflammation. These results provide the first genetic proof that a phosphatase directly regulates NF-kappaB signalling in vivo.
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Wednesday, April 29, 2009

Hot off the presses! Apr 30 Nature

The Apr 30 issue of the Nature is now up on Pubget (About Nature): 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:

  • Time to act
    - Nature 458(7242):1077-1078 (2009)
    Without a solid commitment from the world's leaders, innovative ways to combat climate change are likely to come to nothing.
  • Authorship policies
    - Nature 458(7242):1078 (2009)
    We are clarifying the duties of lead authors and making author-contribution statements mandatory.
  • Fluid dynamics: Dynamics of a dance
    - Nature 458(7242):1080 (2009)
  • Chemistry: Fuel from thin air
    - Nature 458(7242):1080 (2009)
  • Biochemistry: DNA base maker
    - Nature 458(7242):1080 (2009)
  • Stem-cell biology: New stem-cell formula
    - Nature 458(7242):1080 (2009)
  • Photonics: E-ink goes colour
    - Nature 458(7242):1080 (2009)
  • Chemical biology: Getting the glow
    - Nature 458(7242):1081 (2009)
  • Materials: Improving on nature
    - Nature 458(7242):1081 (2009)
  • Genomics: X-linked mysteries
    - Nature 458(7242):1081 (2009)
  • Climate: Ground truths
    - Nature 458(7242):1081 (2009)
  • Journal club
    - Nature 458(7242):1081 (2009)
  • Swine flu goes global
    - Nature 458(7242):1082-1083 (2009)
  • California in clean-fuel drive
    - Nature 458(7242):1083 (2009)
  • Japan goes for the sun
    - Nature 458(7242):1084-1085 (2009)
  • Basic researchers protest UK budget
    - Nature 458(7242):1084-1085 (2009)
  • Obama says more money
    - Nature 458(7242):1085 (2009)
  • Funding cut for US nuclear waste dump
    - Nature 458(7242):1086-1087 (2009)
  • Brain imaging skewed
    - Nature 458(7242):1087 (2009)
  • Fake Facebook pages spin web of deceit
    - Nature 458(7242):1089 (2009)
  • Close shave for Austrian science budget
    - Nature 458(7242):1090 (2009)
  • Nobel laureate celebrates her centenary
    - Nature 458(7242):1090 (2009)
  • Japan cuts red tape holding up stem-cell work
    - Nature 458(7242):1090 (2009)
  • New UK coal must be partly 'clean'
    - Nature 458(7242):1090 (2009)
  • Texas agencies sue over national disease lab
    - Nature 458(7242):1090 (2009)
  • Researchers rally to support animal studies
    - Nature 458(7242):1090 (2009)
  • Correction
    - Nature 458(7242):1090 (2009)
  • Climate crunch: A burden beyond bearing
    - Nature 458(7242):1091-1094 (2009)
  • Sucking it up
    - Nature 458(7242):1094-1097 (2009)
  • Great white hope
    - Nature 458(7242):1097-1100 (2009)
  • Stem-cell treatments for spinal-cord injury may be worth the risk
    - Nature 458(7242):1101 (2009)
    In his Correspondence 'Caution urged in trial of stem cells to treat spinal-cord injury' (Nature 458, 29; 2009), Yves Barde questions the wisdom of testing oligodendrocyte precursors derived from embryonic stem (ES) cells in patients, despite the promise that such cells hold for repairing these injuries in rodents.
  • A lesson or two from a regional economic argument
    - Nature 458(7242):1101 (2009)
    In his Commentary on how to survive the recession, 'Work for the greater good' (Nature 457, 959–960; 2009), Eric Rauchway discusses the role that science and technology had in improving living conditions in the Tennessee Valley in the 1930s.
  • Romanian funding cuts call for more stringent criteria
    - Nature 458(7242):1101 (2009)
    The Lisbon summit in 2000 persuaded many governments that it was in the interest of Europe's long-term economic growth to restore priorities in science and research expenditure; this would also help found the next generation of researchers, innovators and technicians. But these laudable aims are being undermined by the current economic crisis, which disproportionately affects the Eastern European economies.
  • Overshoot, adapt and recover
    - Nature 458(7242):1102-1103 (2009)
    We will probably overshoot our current climate targets, so policies of adaptation and recovery need much more attention, say Martin Parry, Jason Lowe and Clair Hanson.
  • The worst-case scenario
    - Nature 458(7242):1104-1105 (2009)
    Stephen Schneider explores what a world with 1,000 parts per million of CO2 in its atmosphere might look like.
  • Could climate change capitalism?
    - Nature 458(7242):1107-1108 (2009)
    Economist Nicholas Stern's latest book is a rare and masterly synthesis of climate-change science and economics. His 'global deal' could change capitalism for the better, says Robert Costanza.
  • New in Paperback
    - Nature 458(7242):1107-1116 (2009)
  • Why inequality is fatal
    - Nature 458(7242):1109-1110 (2009)
  • Fiction beyond the grave
    - Nature 458(7242):1110 (2009)
  • Genes, games and the sexes
    - Nature 458(7242):1111-1112 (2009)
  • Managing nature as Earth warms
    - Nature 458(7242):1112-1113 (2009)
  • Tales of top models
    - Nature 458(7242):1113-1114 (2009)
  • A billionaire's vision for India
    - Nature 458(7242):1114-1115 (2009)
  • An eye on the Universe
    - Nature 458(7242):1116 (2009)
  • Climate change: Too much of a bad thing
    - Nature 458(7242):1117-1118 (2009)
    There are various — and confusing — targets to limit global warming due to emissions of greenhouse gases. Estimates based on the total slug of carbon emitted are possibly the most robust, and are worrisome.
  • Cell biology: Another way to get rid of fat
    - Nature 458(7242):1118-1119 (2009)
    When starved, cells resort to breaking down their assets — proteins, lipids and even whole organelles. An investigation of lipid metabolism indicates that one process — autophagy — targets all three cellular components.
  • X-ray astronomy: When appearances are deceptive
    - Nature 458(7242):1119-1121 (2009)
    The sharpest X-ray image ever obtained of a portion of the Milky Way resolves a seemingly diffuse X-ray emission into discrete sources. These sources are likely to be stars of the 'garden variety' in the Sun's vicinity.
  • Miniature devices: Voyage of the microrobots
    - Nature 458(7242):1121-1122 (2009)
    Nanobots — tiny robots that can be injected into the body to perform medical procedures — are the stuff of science fiction. Swimming microrobots propelled by artificial flagella bring that fantasy closer to reality.
  • Ecology: Speciation affects ecosystems
    - Nature 458(7242):1122-1123 (2009)
    Evidence that speciation and adaptive radiation can change the properties of an ecosystem is a reminder of the pressing need to integrate ecosystems science and evolutionary biology.
  • Solid-state physics: Lost magnetic moments
    - Nature 458(7242):1123-1124 (2009)
    A neat study gives clear-cut evidence that when a wire made of a magnetic material such as iron is squashed to the atomic scale, the material's magnetism disappears via an exotic physical process.
  • Neuroscience: A social hub for worms
    - Nature 458(7242):1124-1125 (2009)
    There are more connections in the human brain than there are stars in the Milky Way, so scientists use simple organisms to search for universal neural-circuit motifs. Their latest find is a neuron for social behaviour.
  • Correction
    - Nature 458(7242):1125 (2009)
    filled circle In the News & Views article "Quantum chemistry: The little molecules that could" by Cris H. Greene (Nature 458, 975–976; 2009
  • Cytoplasmic functions of the tumour suppressor p53
    - Nature 458(7242):1127-1130 (2009)
    The principal tumour-suppressor protein, p53, accumulates in cells in response to DNA damage, oncogene activation and other stresses. It acts as a nuclear transcription factor that transactivates genes involved in apoptosis, cell cycle regulation and numerous other processes. An emerging area of research unravels additional activities of p53 in the cytoplasm, where it triggers apoptosis and inhibits autophagy. These previously unknown functions contribute to the mission of p53 as a tumour suppressor.
  • Autophagy regulates lipid metabolism
    - Nature 458(7242):1131-1135 (2009)
    The intracellular storage and utilization of lipids are critical to maintain cellular energy homeostasis. During nutrient deprivation, cellular lipids stored as triglycerides in lipid droplets are hydrolysed into fatty acids for energy. A second cellular response to starvation is the induction of autophagy, which delivers intracellular proteins and organelles sequestered in double-membrane vesicles (autophagosomes) to lysosomes for degradation and use as an energy source. Lipolysis and autophagy share similarities in regulation and function but are not known to be interrelated. Here we show a previously unknown function for autophagy in regulating intracellular lipid stores (macrolipophagy). Lipid droplets and autophagic components associated during nutrient deprivation, and inhibition of autophagy in cultured hepatocytes and mouse liver increased triglyceride storage in lipid droplets. This study identifies a critical function for autophagy in lipid metabolism that co! uld have important implications for human diseases with lipid over-accumulation such as those that comprise the metabolic syndrome.
  • Structural basis for leucine-rich nuclear export signal recognition by CRM1
    - Nature 458(7242):1136-1141 (2009)
    CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 Å structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Si! milar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.
  • Discrete sources as the origin of the Galactic X-ray ridge emission
    - Nature 458(7242):1142-1144 (2009)
    An unresolved X-ray glow (at energies above a few kiloelectronvolts) was discovered about 25 years ago and found to be coincident with the Galactic disk—the Galactic ridge X-ray emission1, 2. This emission3, 4, 5, 6, 7, 8, 9, 10 has a spectrum characteristic of a approx108 K optically thin thermal plasma, with a prominent iron emission line at 6.7 keV. The gravitational well of the Galactic disk, however, is far too shallow to confine such a hot interstellar medium; instead, it would flow away at a velocity of a few thousand kilometres per second, exceeding the speed of sound in the gas. To replenish the energy losses requires a source of 1043 erg s-1, exceeding by orders of magnitude all plausible energy sources in the Milky Way11. An alternative is that the hot plasma is bound to a multitude of faint sources12, which is supported by the recently observed similarities in the X-ray and near-infrared surface brightness distributions13, 14 (the latter traces the Galact! ic stellar distribution). Here we report that at energies of approx6–7 keV, more than 80 per cent of the seemingly diffuse X-ray emission is resolved into discrete sources, probably accreting white dwarfs and coronally active stars.
  • Serial time-encoded amplified imaging for real-time observation of fast dynamic phenomena
    - Nature 458(7242):1145-1149 (2009)
    Ultrafast real-time optical imaging is an indispensable tool for studying dynamical events such as shock waves1, 2, chemical dynamics in living cells3, 4, neural activity5, 6, laser surgery7, 8, 9 and microfluidics10, 11. However, conventional CCDs (charge-coupled devices) and their complementary metal–oxide–semiconductor (CMOS) counterparts are incapable of capturing fast dynamical processes with high sensitivity and resolution. This is due in part to a technological limitation—it takes time to read out the data from sensor arrays. Also, there is the fundamental compromise between sensitivity and frame rate; at high frame rates, fewer photons are collected during each frame—a problem that affects nearly all optical imaging systems. Here we report an imaging method that overcomes these limitations and offers frame rates that are at least 1,000 times faster than those of conventional CCDs. Our technique maps a two-dimensional (2D) image into a serial time-domain! data stream and simultaneously amplifies the image in the optical domain. We capture an entire 2D image using a single-pixel photodetector and achieve a net image amplification of 25 dB (a factor of 316). This overcomes the compromise between sensitivity and frame rate without resorting to cooling and high-intensity illumination. As a proof of concept, we perform continuous real-time imaging at a frame speed of 163 ns (a frame rate of 6.1 MHz) and a shutter speed of 440 ps. We also demonstrate real-time imaging of microfluidic flow and phase-explosion effects that occur during laser ablation.
  • The Kondo effect in ferromagnetic atomic contacts
    - Nature 458(7242):1150-1153 (2009)
    Iron, cobalt and nickel are archetypal ferromagnetic metals. In bulk, electronic conduction in these materials takes place mainly through the s and p electrons, whereas the magnetic moments are mostly in the narrow d-electron bands, where they tend to align. This general picture may change at the nanoscale because electrons at the surfaces of materials experience interactions that differ from those in the bulk. Here we show direct evidence for such changes: electronic transport in atomic-scale contacts of pure ferromagnets (iron, cobalt and nickel), despite their strong bulk ferromagnetism, unexpectedly reveal Kondo physics, that is, the screening of local magnetic moments by the conduction electrons below a characteristic temperature1. The Kondo effect creates a sharp resonance at the Fermi energy, affecting the electrical properties of the system; this appears as a Fano–Kondo resonance2 in the conductance characteristics as observed in other artificial nanostructur! es3, 4, 5, 6, 7, 8, 9, 10, 11. The study of hundreds of contacts shows material-dependent log-normal distributions of the resonance width that arise naturally from Kondo theory12. These resonances broaden and disappear with increasing temperature, also as in standard Kondo systems4, 5, 6, 7. Our observations, supported by calculations, imply that coordination changes can significantly modify magnetism at the nanoscale. Therefore, in addition to standard micromagnetic physics, strong electronic correlations along with atomic-scale geometry need to be considered when investigating the magnetic properties of magnetic nanostructures.
  • The ITQ-37 mesoporous chiral zeolite
    - Nature 458(7242):1154-1157 (2009)
    The synthesis of crystalline molecular sieves with pore dimensions that fill the gap between microporous and mesoporous materials is a matter of fundamental and industrial interest1, 2, 3. The preparation of zeolitic materials with extralarge pores and chiral frameworks would permit many new applications. Two important steps in this direction include the synthesis4 of ITQ-33, a stable zeolite with 18 times 10 times 10 ring windows, and the synthesis5 of SU-32, which has an intrinsically chiral zeolite structure and where each crystal exhibits only one handedness. Here we present a germanosilicate zeolite (ITQ-37) with extralarge 30-ring windows. Its structure was determined by combining selected area electron diffraction (SAED) and powder X-ray diffraction (PXRD) in a charge-flipping algorithm6. The framework follows the SrSi2 (srs) minimal net7 and forms two unique cavities, each of which is connected to three other cavities to form a gyroidal channel system. These ca! vities comprise the enantiomorphous srs net of the framework. ITQ-37 is the first chiral zeolite with one single gyroidal channel. It has the lowest framework density (10.3 T atoms per 1,000 Å3) of all existing 4-coordinated crystalline oxide frameworks, and the pore volume of the corresponding silica polymorph would be 0.38 cm3 g-1.
  • Greenhouse-gas emission targets for limiting global warming to 2 °C
    - Nature 458(7242):1158-1162 (2009)
    More than 100 countries have adopted a global warming limit of 2 °C or below (relative to pre-industrial levels) as a guiding principle for mitigation efforts to reduce climate change risks, impacts and damages1, 2. However, the greenhouse gas (GHG) emissions corresponding to a specified maximum warming are poorly known owing to uncertainties in the carbon cycle and the climate response. Here we provide a comprehensive probabilistic analysis aimed at quantifying GHG emission budgets for the 2000–50 period that would limit warming throughout the twenty-first century to below 2 °C, based on a combination of published distributions of climate system properties and observational constraints. We show that, for the chosen class of emission scenarios, both cumulative emissions up to 2050 and emission levels in 2050 are robust indicators of the probability that twenty-first century warming will not exceed 2 °C relative to pre-industrial temperatures. Limiting cumulative C! O2 emissions over 2000–50 to 1,000 Gt CO2 yields a 25% probability of warming exceeding 2 °C—and a limit of 1,440 Gt CO2 yields a 50% probability—given a representative estimate of the distribution of climate system properties. As known 2000–06 CO2 emissions3 were approx234 Gt CO2, less than half the proven economically recoverable oil, gas and coal reserves4, 5, 6 can still be emitted up to 2050 to achieve such a goal. Recent G8 Communiqués7 envisage halved global GHG emissions by 2050, for which we estimate a 12–45% probability of exceeding 2 °C—assuming 1990 as emission base year and a range of published climate sensitivity distributions. Emissions levels in 2020 are a less robust indicator, but for the scenarios considered, the probability of exceeding 2 °C rises to 53–87% if global GHG emissions are still more than 25% above 2000 levels in 2020.
  • Warming caused by cumulative carbon emissions towards the trillionth tonne
    - Nature 458(7242):1163-1166 (2009)
    Global efforts to mitigate climate change are guided by projections of future temperatures1. But the eventual equilibrium global mean temperature associated with a given stabilization level of atmospheric greenhouse gas concentrations remains uncertain1, 2, 3, complicating the setting of stabilization targets to avoid potentially dangerous levels of global warming4, 5, 6, 7, 8. Similar problems apply to the carbon cycle: observations currently provide only a weak constraint on the response to future emissions9, 10, 11. Here we use ensemble simulations of simple climate-carbon-cycle models constrained by observations and projections from more comprehensive models to simulate the temperature response to a broad range of carbon dioxide emission pathways. We find that the peak warming caused by a given cumulative carbon dioxide emission is better constrained than the warming response to a stabilization scenario. Furthermore, the relationship between cumulative emissions an! d peak warming is remarkably insensitive to the emission pathway (timing of emissions or peak emission rate). Hence policy targets based on limiting cumulative emissions of carbon dioxide are likely to be more robust to scientific uncertainty than emission-rate or concentration targets. Total anthropogenic emissions of one trillion tonnes of carbon (3.67 trillion tonnes of CO2), about half of which has already been emitted since industrialization began, results in a most likely peak carbon-dioxide-induced warming of 2 °C above pre-industrial temperatures, with a 5–95% confidence interval of 1.3–3.9 °C.
  • Evolutionary diversification in stickleback affects ecosystem functioning
    - Nature 458(7242):1167-1170 (2009)
    Explaining the ecological causes of evolutionary diversification is a major focus of biology, but surprisingly little has been said about the effects of evolutionary diversification on ecosystems1, 2, 3. The number of species in an ecosystem and their traits are key predictors of many ecosystem-level processes, such as rates of productivity, biomass sequestration and decomposition4, 5. Here we demonstrate short-term ecosystem-level effects of adaptive radiation in the threespine stickleback (Gasterosteus aculeatus) over the past 10,000 years. These fish have undergone recent parallel diversification in several lakes in coastal British Columbia, resulting in the formation of two specialized species (benthic and limnetic) from a generalist ancestor6. Using a mesocosm experiment, we demonstrate that this diversification has strong effects on ecosystems, affecting prey community structure, total primary production, and the nature of dissolved organic materials that regulat! e the spectral properties of light transmission in the system. However, these ecosystem effects do not simply increase in their relative strength with increasing specialization and species richness; instead, they reflect the complex and indirect consequences of ecosystem engineering by sticklebacks. It is well known that ecological factors influence adaptive radiation7, 8. We demonstrate that adaptive radiation, even over short timescales, can have profound effects on ecosystems.
  • A hub-and-spoke circuit drives pheromone attraction and social behaviour in C. elegans
    - Nature 458(7242):1171-1175 (2009)
    Innate social behaviours emerge from neuronal circuits that interpret sensory information on the basis of an individual's own genotype, sex and experience. The regulated aggregation behaviour of the nematode Caenorhabditis elegans, a simple animal with only 302 neurons, is an attractive system to analyse these circuits. Wild social strains of C. elegans aggregate in the presence of specific sensory cues, but solitary strains do not1, 2, 3, 4. Here we identify the RMG inter/motor neuron as the hub of a regulated circuit that controls aggregation and related behaviours. RMG is the central site of action of the neuropeptide receptor gene npr-1, which distinguishes solitary strains (high npr-1 activity) from wild social strains (low npr-1 activity); high RMG activity is essential for all aspects of social behaviour. Anatomical gap junctions connect RMG to several classes of sensory neurons known to promote aggregation, and to ASK sensory neurons, which are implicated in ma! le attraction to hermaphrodite pheromones5. We find that ASK neurons respond directly to pheromones, and that high RMG activity enhances ASK responses in social strains, causing hermaphrodite attraction to pheromones at concentrations that repel solitary hermaphrodites. The coordination of social behaviours by RMG suggests an anatomical hub-and-spoke model for sensory integration in aggregation, and points to functions for related circuit motifs in the C. elegans wiring diagram.
  • Toxin B is essential for virulence of Clostridium difficile
    - Nature 458(7242):1176-1179 (2009)
    Clostridium difficile is the leading cause of infectious diarrhoea in hospitals worldwide, because of its virulence, spore-forming ability and persistence1, 2. C. difficile-associated diseases are induced by antibiotic treatment or disruption of the normal gastrointestinal flora3, 4. Recently, morbidity and mortality resulting from C. difficile-associated diseases have increased significantly due to changes in the virulence of the causative strains and antibiotic usage patterns1, 2, 5, 6. Since 2002, epidemic toxinotype III NAP1/027 strains1, 2, which produce high levels of the major virulence factors, toxin A and toxin B, have emerged. These toxins have 63% amino acid sequence similarity7 and are members of the large clostridial glucosylating toxin family, which are monoglucosyltransferases that are pro-inflammatory, cytotoxic and enterotoxic in the human colon8, 9, 10. Inside host cells, both toxins catalyse the transfer of glucose onto the Rho family of GTPases, lea! ding to cell death8, 11. However, the role of these toxins in the context of a C. difficile infection is unknown. Here we describe the construction of isogenic tcdA and tcdB (encoding toxin A and B, respectively) mutants of a virulent C. difficile strain and their use in the hamster disease model to show that toxin B is a key virulence determinant. Previous studies showed that purified toxin A alone can induce most of the pathology observed after infection of hamsters with C. difficile 8, 9, 12 and that toxin B is not toxic in animals unless it is co-administered with toxin A, suggesting that the toxins act synergistically12. Our work provides evidence that toxin B, not toxin A, is essential for virulence. Furthermore, it is clear that the importance of these toxins in the context of infection cannot be predicted exclusively from studies using purified toxins, reinforcing the importance of using the natural infection process to dissect the role of toxins in disease.
  • Orally delivered siRNA targeting macrophage Map4k4 suppresses systemic inflammation
    - Nature 458(7242):1180-1184 (2009)
    Gene silencing by double-stranded RNA, denoted RNA interference, represents a new paradigm for rational drug design1. However, the transformative therapeutic potential of short interfering RNA (siRNA) has been stymied by a key obstacle—safe delivery to specified target cells in vivo 2. Macrophages are particularly attractive targets for RNA interference therapy because they promote pathogenic inflammatory responses in diseases such as rheumatoid arthritis, atherosclerosis, inflammatory bowel disease and diabetes3. Here we report the engineering of beta1,3-d-glucan-encapsulated siRNA particles (GeRPs) as efficient oral delivery vehicles that potently silence genes in mouse macrophages in vitro and in vivo. Oral gavage of mice with GeRPs containing as little as 20 mug kg-1 siRNA directed against tumour necrosis factor alpha (Tnf-alpha) depleted its messenger RNA in macrophages recovered from the peritoneum, spleen, liver and lung, and lowered serum Tnf-alpha levels. Sc! reening with GeRPs for inflammation genes revealed that the mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4) is a previously unknown mediator of cytokine expression. Importantly, silencing Map4k4 in macrophages in vivo protected mice from lipopolysaccharide-induced lethality by inhibiting Tnf-alpha and interleukin-1beta production. This technology defines a new strategy for oral delivery of siRNA to attenuate inflammatory responses in human disease.
  • Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay
    Matsushita K Takeuchi O Standley DM Kumagai Y Kawagoe T Miyake T Satoh T Kato H Tsujimura T Nakamura H Akira S - Nature 458(7242):1185-1190 (2009)
    Toll-like receptors (TLRs) recognize microbial components, and evoke inflammation and immune responses1, 2, 3. TLR stimulation activates complex gene expression networks that regulate the magnitude and duration of the immune reaction. Here we identify the TLR-inducible gene Zc3h12a as an immune response modifier that has an essential role in preventing immune disorders. Zc3h12a-deficient mice suffered from severe anaemia, and most died within 12 weeks. Zc3h12a -/- mice also showed augmented serum immunoglobulin levels and autoantibody production, together with a greatly increased number of plasma cells, as well as infiltration of plasma cells to the lung. Most Zc3h12a -/- splenic T cells showed effector/memory characteristics and produced interferon-gamma in response to T-cell receptor stimulation. Macrophages from Zc3h12a -/- mice showed highly increased production of interleukin (IL)-6 and IL-12p40 (also known as IL12b), but not TNF, in response to TLR ligands. Altho! ugh the activation of TLR signalling pathways was normal, Il6 messenger RNA decay was severely impaired in Zc3h12a -/- macrophages. Overexpression of Zc3h12a accelerated Il6 mRNA degradation via its 3'-untranslated region (UTR), and destabilized RNAs with 3'-UTRs for genes including Il6, Il12p40 and the calcitonin receptor gene Calcr. Zc3h12a contains a putative amino-terminal nuclease domain, and the expressed protein had RNase activity, consistent with a role in the decay of Il6 mRNA. Together, these results indicate that Zc3h12a is an essential RNase that prevents immune disorders by directly controlling the stability of a set of inflammatory genes.
  • The structural basis of lipopolysaccharide recognition by the TLR4–MD-2 complex
    - Nature 458(7242):1191-1195 (2009)
    The lipopolysaccharide (LPS) of Gram negative bacteria is a well-known inducer of the innate immune response1. Toll-like receptor (TLR) 4 and myeloid differentiation factor 2 (MD-2) form a heterodimer that recognizes a common 'pattern' in structurally diverse LPS molecules. To understand the ligand specificity and receptor activation mechanism of the TLR4–MD-2–LPS complex we determined its crystal structure. LPS binding induced the formation of an m-shaped receptor multimer composed of two copies of the TLR4–MD-2–LPS complex arranged symmetrically. LPS interacts with a large hydrophobic pocket in MD-2 and directly bridges the two components of the multimer. Five of the six lipid chains of LPS are buried deep inside the pocket and the remaining chain is exposed to the surface of MD-2, forming a hydrophobic interaction with the conserved phenylalanines of TLR4. The F126 loop of MD-2 undergoes localized structural change and supports this core hydrophobic interfac! e by making hydrophilic interactions with TLR4. Comparison with the structures of tetra-acylated antagonists bound to MD-2 indicates that two other lipid chains in LPS displace the phosphorylated glucosamine backbone by approx5 Å towards the solvent area2, 3. This structural shift allows phosphate groups of LPS to contribute to receptor multimerization by forming ionic interactions with a cluster of positively charged residues in TLR4 and MD-2. The TLR4–MD-2–LPS structure illustrates the remarkable versatility of the ligand recognition mechanisms employed by the TLR family4, 5, which is essential for defence against diverse microbial infection.
  • A mutation in Ihh that causes digit abnormalities alters its signalling capacity and range
    - Nature 458(7242):1196-1200 (2009)
    Brachydactyly type A1 (BDA1) was the first recorded disorder of the autosomal dominant Mendelian trait in humans, characterized by shortened or absent middle phalanges in digits. It is associated with heterozygous missense mutations in indian hedgehog (IHH)1, 2. Hedgehog proteins are important morphogens for a wide range of developmental processes3, 4. The capacity and range of signalling is thought to be regulated by its interaction with the receptor PTCH1 and antagonist HIP1. Here we show that a BDA1 mutation (E95K) in Ihh impairs the interaction of IHH with PTCH1 and HIP1. This is consistent with a recent paper showing that BDA1 mutations cluster in a calcium-binding site essential for the interaction with its receptor and cell-surface partners5. Furthermore, we show that in a mouse model that recapitulates the E95K mutation, there is a change in the potency and range of signalling. The mice have digit abnormalities consistent with the human disorder.
  • Embryonic stem cells use ZFP809 to silence retroviral DNAs
    - Nature 458(7242):1201-1204 (2009)
    Embryonic stem cells (ESCs) and other primitive stem cells of mice have been known for more than 30 years to potently block retrovirus replication1. Infection of ESCs by the murine leukaemia viruses (MLVs) results in the normal establishment of integrated proviral DNA, but this DNA is then transcriptionally silenced, preventing further viral spread. The repression is largely mediated by trans-acting factors that recognize a conserved sequence element termed the primer binding site, an 18-base pair sequence complementary to the 3' end of a cellular transfer RNA2, 3, 4, 5, 6. A specific tRNA is annealed to the primer binding site sequence of the viral genomic RNA, and is used to prime DNA synthesis7. This same sequence in the context of the integrated proviral DNA is targeted for silencing in ESCs. We have recently shown that a large protein complex binding to the primer binding site in ESCs contains TRIM28 (refs 8, 9), a well-characterized transcriptional co-repressor10! , 11, 12. An important question remains as to the identity of the factor that directly recognizes integrated retroviral DNAs and recruits TRIM28 to mediate their specific silencing. Here we identify the zinc finger protein ZFP809 as the recognition molecule that bridges the integrated proviral DNA and TRIM28. We show that expression of ZFP809 is sufficient to render even differentiated cells highly resistant to MLV infection. Furthermore, we demonstrate that ZFP809 is able to potently block transcription from DNA constructs of human T-cell lymphotropic virus-1 (HTLV-1), which use the same primer tRNA. These results identify ZFP809 as a DNA-binding factor that specifically recognizes a large subset of mammalian retroviruses and retroelements, targeting them for transcriptional silencing. We propose that ZFP809 evolved as a stem-cell-specific retroviral restriction factor, and therefore constitutes a new component of the intrinsic immune system of stem cells.
  • En passant
    - Nature 458(7242):1212 (2009)
    Family ties.
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