Hot off the presses! Sep 28 PLoS Biol

The Sep 28 issue of the PLoS Biol is now up on Pubget (About PLoS 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:

• The Upside of Slackers
  Meadows R - PLoS Biol 8(9):e1000487 (2010)
  
• NOX4: A Guilty Party in Stroke Damage
  - PLoS Biol 8(9):e1000478 (2010)
  
• Quiet Down Now: How Excitatory Neurons Inhibit One Another
  Robinson R - PLoS Biol 8(9):e1000474 (2010)
  
• Clever Cattle Parasite Captures Cell Division Machinery
  - PLoS Biol 8(9):e1000498 (2010)
  
• Arms and the Man: The Problem of Symmetric Growth
  Wolpert L - PLoS Biol 8(9):e1000477 (2010)
  
• Bringing the Tiger Back from the Brink—The Six Percent Solution
  Walston J Robinson JG Bennett EL Breitenmoser U da Fonseca GA Goodrich J Gumal M Hunter L Johnson A Karanth KU Leader-Williams N Mackinnon K Miquelle D Pattanavibool A Poole C Rabinowitz A Smith JL Stokes EJ Stuart SN Vongkhamheng C Wibisono H - PLoS Biol 8(9):e1000485 (2010)
  
• Primed for Reading
  - PLoS Biol 8(9):e1000424 (2010)
  
• The Goldilocks Model for TCR—Too Much Attraction Might Not Be Best for Vaccine Design
  Slansky JE Jordan KR - PLoS Biol 8(9):e1000482 (2010)
  Recent research on T cell-antigen interactions suggests that tighter binding is not always better at eliciting an effective immune response.
• How and Why Chromosome Inversions Evolve
  - PLoS Biol 8(9):e1000501 (2010)
  
• Creative Research Science Experiences for High School Students
  - PLoS Biol 8(9):e1000447 (2010)
  
• Inferring the Dynamics of Diversification: A Coalescent Approach
  - PLoS Biol 8(9):e1000493 (2010)
  Recent analyses of the fossil record and molecular phylogenies suggest that there are fundamental limits to biodiversity, possibly arising from constraints in the availability of space, resources, or ecological niches. Under this hypothesis, speciation rates decay over time and biodiversity eventually saturates, with new species emerging only when others are driven to extinction. This view of macro-evolution contradicts an alternative hypothesis that biodiversity is unbounded, with species ever accumulating as they find new niches to occupy. These contrasting theories of biodiversity dynamics yield fundamentally different explanations for the disparity in species richness across taxa and regions. Here, we test whether speciation rates have decayed or remained constant over time, and whether biodiversity is saturated or still expanding. We first derive a general likelihood expression for internode distances in a phylogeny, based on the well-known coalescent process from! population genetics. This expression accounts for either time-constant or time-variable rates, time-constant or time-variable diversity, and completely or incompletely sampled phylogenies. We then compare the performance of different diversification scenarios in explaining a set of 289 phylogenies representing amphibians, arthropods, birds, mammals, mollusks, and flowering plants. Our results indicate that speciation rates typically decay over time, but that diversity is still expanding at present. The evidence for expanding-diversity models suggests that an upper limit to biodiversity has not yet been reached, or that no such limit exists.
• Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses
  - PLoS Biol 8(9):e1000495 (2010)
  Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host's cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host's germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologo! us insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10−8 substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolutio! n on a deep time scale.
• A Mixture of "Cheats" and "Co-Operators" Can Enable Maximal Group Benefit
  Maclean RC Fuentes-Hernandez A Greig D Hurst LD Gudelj I - PLoS Biol 8(9):e1000486 (2010)
  Is a group best off if everyone co-operates? Theory often considers this to be so (e.g. the "conspiracy of doves"), this understanding underpinning social and economic policy. We observe, however, that after competition between "cheat" and "co-operator" strains of yeast, population fitness is maximized under co-existence. To address whether this might just be a peculiarity of our experimental system or a result with broader applicability, we assemble, benchmark, dissect, and test a systems model. This reveals the conditions necessary to recover the unexpected result. These are 3-fold: (a) that resources are used inefficiently when they are abundant, (b) that the amount of co-operation needed cannot be accurately assessed, and (c) the population is structured, such that co-operators receive more of the resource than the cheats. Relaxing any of the assumptions can lead to population fitness being maximized when cheats are absent, which we experimentally demon! strate. These three conditions will often be relevant, and hence in order to understand the trajectory of social interactions, understanding the dynamics of the efficiency of resource utilization and accuracy of information will be necessary.
• Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping
  - PLoS Biol 8(9):e1000489 (2010)
  There is a considerable contrast between the various functions assigned to Broca's region and its relatively simple subdivision into two cytoarchitectonic areas (44 and 45). Since the regional distribution of transmitter receptors in the cerebral cortex has been proven a powerful indicator of functional diversity, the subdivision of Broca's region was analyzed here using a multireceptor approach. The distribution patterns of six receptor types using in vitro receptor autoradiography revealed previously unknown areas: a ventral precentral transitional cortex 6r1, dorsal and ventral areas 44d and 44v, anterior and posterior areas 45a and 45p, and areas op8 and op9 in the frontal operculum. A significant lateralization of receptors was demonstrated with respect to the cholinergic M2 receptor, particularly in area 44v+d. We propose a new concept of the anterior language region, which elucidates the relation between premotor cortex, prefrontal cortex, and Broca's region. It! offers human brain homologues to the recently described subdivision of area 45, and the segregation of the ventral premotor cortex in macaque brains. The results provide a novel structural basis of the organization of language regions in the brain.
• Post-Stroke Inhibition of Induced NADPH Oxidase Type 4 Prevents Oxidative Stress and Neurodegeneration
  - PLoS Biol 8(9):e1000479 (2010)
  Ischemic stroke is the second leading cause of death worldwide. Only one moderately effective therapy exists, albeit with contraindications that exclude 90% of the patients. This medical need contrasts with a high failure rate of more than 1,000 pre-clinical drug candidates for stroke therapies. Thus, there is a need for translatable mechanisms of neuroprotection and more rigid thresholds of relevance in pre-clinical stroke models. One such candidate mechanism is oxidative stress. However, antioxidant approaches have failed in clinical trials, and the significant sources of oxidative stress in stroke are unknown. We here identify NADPH oxidase type 4 (NOX4) as a major source of oxidative stress and an effective therapeutic target in acute stroke. Upon ischemia, NOX4 was induced in human and mouse brain. Mice deficient in NOX4 (Nox4−/−) of either sex, but not those deficient for NOX1 or NOX2, were largely protected from oxidative stress, blood-brain-barrier leakage,! and neuronal apoptosis, after both transient and permanent cerebral ischemia. This effect was independent of age, as elderly mice were equally protected. Restoration of oxidative stress reversed the stroke-protective phenotype in Nox4−/− mice. Application of the only validated low-molecular-weight pharmacological NADPH oxidase inhibitor, VAS2870, several hours after ischemia was as protective as deleting NOX4. The extent of neuroprotection was exceptional, resulting in significantly improved long-term neurological functions and reduced mortality. NOX4 therefore represents a major source of oxidative stress and novel class of drug target for stroke therapy.
• Desynchronization of Neocortical Networks by Asynchronous Release of GABA at Autaptic and Synaptic Contacts from Fast-Spiking Interneurons
  - PLoS Biol 8(9):e1000492 (2010)
  Networks of specific inhibitory interneurons regulate principal cell firing in several forms of neocortical activity. Fast-spiking (FS) interneurons are potently self-inhibited by GABAergic autaptic transmission, allowing them to precisely control their own firing dynamics and timing. Here we show that in FS interneurons, high-frequency trains of action potentials can generate a delayed and prolonged GABAergic self-inhibition due to sustained asynchronous release at FS-cell autapses. Asynchronous release of GABA is simultaneously recorded in connected pyramidal (P) neurons. Asynchronous and synchronous autaptic release show differential presynaptic Ca2+ sensitivity, suggesting that they rely on different Ca2+ sensors and/or involve distinct pools of vesicles. In addition, asynchronous release is modulated by the endogenous Ca2+ buffer parvalbumin. Functionally, asynchronous release decreases FS-cell spike reliability and reduces the ability of P neurons to integrate in! coming stimuli into precise firing. Since each FS cell contacts many P neurons, asynchronous release from a single interneuron may desynchronize a large portion of the local network and disrupt cortical information processing.
• Brief Bursts Self-Inhibit and Correlate the Pyramidal Network
  Berger TK Silberberg G Perin R Markram H - PLoS Biol 8(9):e1000473 (2010)
  Inhibitory pathways are an essential component in the function of the neocortical microcircuitry. Despite the relatively small fraction of inhibitory neurons in the neocortex, these neurons are strongly activated due to their high connectivity rate and the intricate manner in which they interconnect with pyramidal cells (PCs). One prominent pathway is the frequency-dependent disynaptic inhibition (FDDI) formed between layer 5 PCs and mediated by Martinotti cells (MCs). Here, we show that simultaneous short bursts in four PCs are sufficient to exert FDDI in all neighboring PCs within the dimensions of a cortical column. This powerful inhibition is mediated by few interneurons, leading to strongly correlated membrane fluctuations and synchronous spiking between PCs simultaneously receiving FDDI. Somatic integration of such inhibition is independent and electrically isolated from monosynaptic excitation formed between the same PCs. FDDI is strongly shaped by I(h) in PC de! ndrites, which determines the effective integration time window for inhibitory and excitatory inputs. We propose a key disynaptic mechanism by which brief bursts generated by a few PCs can synchronize the activity in the pyramidal network.
• A Key Commitment Step in Erythropoiesis Is Synchronized with the Cell Cycle Clock through Mutual Inhibition between PU.1 and S-Phase Progression
  - PLoS Biol 8(9):e1000484 (2010)
  Hematopoietic progenitors undergo differentiation while navigating several cell division cycles, but it is unknown whether these two processes are coupled. We addressed this question by studying erythropoiesis in mouse fetal liver in vivo. We found that the initial upregulation of cell surface CD71 identifies developmentally matched erythroblasts that are tightly synchronized in S-phase. We show that DNA replication within this but not subsequent cycles is required for a differentiation switch comprising rapid and simultaneous committal transitions whose precise timing was previously unknown. These include the onset of erythropoietin dependence, activation of the erythroid master transcriptional regulator GATA-1, and a switch to an active chromatin conformation at the β-globin locus. Specifically, S-phase progression is required for the formation of DNase I hypersensitive sites and for DNA demethylation at this locus. Mechanistically, we show that S-phase progression ! during this key committal step is dependent on downregulation of the cyclin-dependent kinase p57KIP2 and in turn causes the downregulation of PU.1, an antagonist of GATA-1 function. These findings therefore highlight a novel role for a cyclin-dependent kinase inhibitor in differentiation, distinct to their known function in cell cycle exit. Furthermore, we show that a novel, mutual inhibition between PU.1 expression and S-phase progression provides a "synchromesh" mechanism that "locks" the erythroid differentiation program to the cell cycle clock, ensuring precise coordination of critical differentiation events.
• A Senescence-Like Cell-Cycle Arrest Occurs During Megakaryocytic Maturation: Implications for Physiological and Pathological Megakaryocytic Proliferation
  Besancenot R Chaligné R Tonetti C Pasquier F Marty C Lécluse Y Vainchenker W Constantinescu SN Giraudier S - PLoS Biol 8(9):e1000476 (2010)
  Thrombopoietin (TPO) via signaling through its cognate receptor MPL is a key cytokine involved in the regulation of megakaryocyte differentiation leading to platelet production. Mature megakaryocytes are polyploid cells that have arrested DNA replication and cellular proliferation but continue sustained protein synthesis. Here, we show that TPO induces cell-cycle arrest in the megakaryocytic UT7-MPL cell line by the activation of the ERK/MAPK pathway, induction of p21CIP transcription, and senescence markers through EGR1 activation. A similar senescence-like process was also detected in normal primary postmitotic megakaryocytes. In contrast, senescence was not observed in malignant megakaryocytes derived from primary myelofibrosis patients (a form of chronic myeloid hemopathy). Our data indicate that polyploid mature megakaryocytes receive signals from TPO to arrest cell proliferation and enter a senescent-like state. An escape from this physiological process may be as! sociated with certain myeloproliferative neoplasms leading to abnormal megakaryocytic proliferation.
• Attenuated T Cell Responses to a High-Potency Ligand In Vivo
  Corse E Gottschalk RA Krogsgaard M Allison JP - PLoS Biol 8(9):e1000481 (2010)
  αβ T cell receptor (TCR) recognition of foreign peptides bound to major histocompatibility complex (pMHC) molecules on the surface of antigen presenting cells is a key event in the initiation of adaptive cellular immunity. In vitro, high-affinity binding and/or long-lived interactions between TCRs and pMHC correlate with high-potency T cell activation. However, less is known about the influence of TCR/pMHC interaction parameters on T cell responses in vivo. We studied the influence of TCR/pMHC binding characteristics on in vivo T cell immunity by tracking CD4+ T cell activation, effector, and memory responses to immunization with peptides exhibiting a range of TCR/pMHC half-lives and in vitro T cell activation potencies. Contrary to predictions from in vitro studies, we found that optimal in vivo T cell responses occur to ligands with intermediate TCR/pMHC half-lives. The diminished in vivo responses we observed to the ligand exhibiting the longest TCR/pMHC half-life! were associated with attenuation of intracellular signaling, expansion, and function over a broad range of time points. Our results reveal a level of control over T cell activation in vivo not recapitulated in in vitro assays and highlight the importance of considering in vivo efficacy of TCR ligands as part of vaccine design.
• The Transforming Parasite Theileria Co-opts Host Cell Mitotic and Central Spindles to Persist in Continuously Dividing Cells
  - PLoS Biol 8(9):e1000499 (2010)
  The protozoan parasite Theileria inhabits the host cell cytoplasm and possesses the unique capacity to transform the cells it infects, inducing continuous proliferation and protection against apoptosis. The transforming schizont is a multinucleated syncytium that resides free in the host cell cytoplasm and is strictly intracellular. To maintain transformation, it is crucial that this syncytium is divided over the two daughter cells at each host cell cytokinesis. This process was dissected using different cell cycle synchronization methods in combination with the targeted application of specific inhibitors. We found that Theileria schizonts associate with newly formed host cell microtubules that emanate from the spindle poles, positioning the parasite at the equatorial region of the mitotic cell where host cell chromosomes assemble during metaphase. During anaphase, the schizont interacts closely with host cell central spindle. As part of this process, the schizont recr! uits a host cell mitotic kinase, Polo-like kinase 1, and we established that parasite association with host cell central spindles requires Polo-like kinase 1 catalytic activity. Blocking the interaction between the schizont and astral as well as central spindle microtubules prevented parasite segregation between the daughter cells during cytokinesis. Our findings provide a striking example of how an intracellular eukaryotic pathogen that evolved ways to induce the uncontrolled proliferation of the cells it infects usurps the host cell mitotic machinery, including Polo-like kinase 1, one of the pivotal mitotic kinases, to ensure its own persistence and survival.
• Stochastic E2F Activation and Reconciliation of Phenomenological Cell-Cycle Models
  - PLoS Biol 8(9):e1000488 (2010)
  The transition of the mammalian cell from quiescence to proliferation is a highly variable process. Over the last four decades, two lines of apparently contradictory, phenomenological models have been proposed to account for such temporal variability. These include various forms of the transition probability (TP) model and the growth control (GC) model, which lack mechanistic details. The GC model was further proposed as an alternative explanation for the concept of the restriction point, which we recently demonstrated as being controlled by a bistable Rb-E2F switch. Here, through a combination of modeling and experiments, we show that these different lines of models in essence reflect different aspects of stochastic dynamics in cell cycle entry. In particular, we show that the variable activation of E2F can be described by stochastic activation of the bistable Rb-E2F switch, which in turn may account for the temporal variability in cell cycle entry. Moreover, we show ! that temporal dynamics of E2F activation can be recast into the frameworks of both the TP model and the GC model via parameter mapping. This mapping suggests that the two lines of phenomenological models can be reconciled through the stochastic dynamics of the Rb-E2F switch. It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states.
• Polymorphic Cis- and Trans-Regulation of Human Gene Expression
  Cheung VG Nayak RR Wang IX Elwyn S Cousins SM Morley M Spielman RS - PLoS Biol 8(9):e1000480 (2010)
  Expression levels of human genes vary extensively among individuals. This variation facilitates analyses of expression levels as quantitative phenotypes in genetic studies where the entire genome can be scanned for regulators without prior knowledge of the regulatory mechanisms, thus enabling the identification of unknown regulatory relationships. Here, we carried out such genetic analyses with a large sample size and identified cis- and trans-acting polymorphic regulators for about 1,000 human genes. We validated the cis-acting regulators by demonstrating differential allelic expression with sequencing of transcriptomes (RNA-Seq) and the trans-regulators by gene knockdown, metabolic assays, and chromosome conformation capture analysis. The majority of the regulators act in trans to the target (regulated) genes. Most of these trans-regulators were not known to play a role in gene expression regulation. The identification of these regulators enabled the characterization! of polymorphic regulation of human gene expression at a resolution that was unattainable in the past.
• A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation
  - PLoS Biol 8(9):e1000500 (2010)
  The role of chromosomal inversions in adaptation and speciation is controversial. Historically, inversions were thought to contribute to these processes either by directly causing hybrid sterility or by facilitating the maintenance of co-adapted gene complexes. Because inversions suppress recombination when heterozygous, a recently proposed local adaptation mechanism predicts that they will spread if they capture alleles at multiple loci involved in divergent adaptation to contrasting environments. Many empirical studies have found inversion polymorphisms linked to putatively adaptive phenotypes or distributed along environmental clines. However, direct involvement of an inversion in local adaptation and consequent ecological reproductive isolation has not to our knowledge been demonstrated in nature. In this study, we discovered that a chromosomal inversion polymorphism is geographically widespread, and we test the extent to which it contributes to adaptation and repr! oductive isolation under natural field conditions. Replicated crosses between the prezygotically reproductively isolated annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus, revealed that alternative chromosomal inversion arrangements are associated with life-history divergence over thousands of kilometers across North America. The inversion polymorphism affected adaptive flowering time divergence and other morphological traits in all replicated crosses between four pairs of annual and perennial populations. To determine if the inversion contributes to adaptation and reproductive isolation in natural populations, we conducted a novel reciprocal transplant experiment involving outbred lines, where alternative arrangements of the inversion were reciprocally introgressed into the genetic backgrounds of each ecotype. Our results demonstrate for the first time in nature the contribution of an inversion to adaptation, an annual/perennial life-history shift,! and multiple reproductive isolating barriers. These results a! re consistent with the local adaptation mechanism being responsible for the distribution of the two inversion arrangements across the geographic range of M. guttatus and that locally adaptive inversion effects contribute directly to reproductive isolation. Such a mechanism may be partially responsible for the observation that closely related species often differ by multiple chromosomal rearrangements.
• Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
  Dalloul RA Long JA Zimin AV Aslam L Beal K Ann Blomberg L Bouffard P Burt DW Crasta O Crooijmans RP Cooper K Coulombe RA De S Delany ME Dodgson JB Dong JJ Evans C Frederickson KM Flicek P Florea L Folkerts O Groenen MA Harkins TT Herrero J Hoffmann S Megens HJ Jiang A de Jong P Kaiser P Kim H Kim KW Kim S Langenberger D Lee MK Lee T Mane S Marcais G Marz M McElroy AP Modise T Nefedov M Notredame C Paton IR Payne WS Pertea G Prickett D Puiu D Qioa D Raineri E Ruffier M Salzberg SL Schatz MC Scheuring C Schmidt CJ Schroeder S Searle SM Smith EJ Smith J Sonstegard TS Stadler PF Tafer H Tu ZJ Van Tassell CP Vilella AJ Williams KP Yorke JA Zhang L Zhang HB Zhang X Zhang Y Reed KM - PLoS Biol 8(9):e1000475 (2010)
  A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene l! oss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
• A Global Census of Fission Yeast Deubiquitinating Enzyme Localization and Interaction Networks Reveals Distinct Compartmentalization Profiles and Overlapping Functions in Endocytosis and Polarity
  Kouranti I McLean JR Feoktistova A Liang P Johnson AE Roberts-Galbraith RH Gould KL - PLoS Biol 8(9):e1000471 (2010)
  Ubiquitination and deubiquitination are reciprocal processes that tune protein stability, function, and/or localization. The removal of ubiquitin and remodeling of ubiquitin chains is catalyzed by deubiquitinating enzymes (DUBs), which are cysteine proteases or metalloproteases. Although ubiquitination has been extensively studied for decades, the complexity of cellular roles for deubiquitinating enzymes has only recently been explored, and there are still several gaps in our understanding of when, where, and how these enzymes function to modulate the fate of polypeptides. To address these questions we performed a systematic analysis of the 20 Schizosaccharomyces pombe DUBs using confocal microscopy, proteomics, and enzymatic activity assays. Our results reveal that S. pombe DUBs are present in almost all cell compartments, and the majority are part of stable protein complexes essential for their function. Interestingly, DUB partners identified by our study include the! homolog of a putative tumor suppressor gene not previously linked to the ubiquitin pathway, and two conserved tryptophan-aspartate (WD) repeat proteins that regulate Ubp9, a DUB that we show participates in endocytosis, actin dynamics, and cell polarity. In order to understand how DUB activity affects these processes we constructed multiple DUB mutants and find that a quintuple deletion of ubp4 ubp5 ubp9 ubp15 sst2/amsh displays severe growth, polarity, and endocytosis defects. This mutant allowed the identification of two common substrates for five cytoplasmic DUBs. Through these studies, a common regulatory theme emerged in which DUB localization and/or activity is modulated by interacting partners. Despite apparently distinct cytoplasmic localization patterns, several DUBs cooperate in regulating endocytosis and cell polarity. These studies provide a framework for dissecting DUB signaling pathways in S. pombe and may shed light on DUB functions in metazoans.
• Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach
  Opalka N Brown J Lane WJ Twist KA Landick R Asturias FJ Darst SA - PLoS Biol 8(9):e1000483 (2010)
  The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role i! n the E. coli transcription program.

Hot off the presses! Sep 24 mol cell

The Sep 24 issue of the mol cell is now up on Pubget (About mol 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:

• A Mitotic Beacon Reveals Its Nucleosome Anchor
  - mol cell 39(6):829-830 (2010)
  Mitosis, nuclear envelope formation, and nucleocytoplasmic transport require chromosomes to identify themselves by enriching Ran-GTP around the chromatin fiber. In a recent Nature report, Makde et al. (2010) describe the structure of the Ran activator RCC1 anchored onto nucleosomes.
• The End of the Circle for Yeast Mitochondrial DNA
  - mol cell 39(6):831-832 (2010)
  In this issue of Molecular Cell, Gerhold et al. (2010) find no circular DNA during mitochondrial DNA (mtDNA) replication in the aerobic yeast Candida albicans, a result with important implications for mtDNA replication in Saccharomyces cerevisiae.
• Long Noncoding RNAs Add Another Layer to Pre-mRNA Splicing Regulation
  - mol cell 39(6):833-834 (2010)
  In this issue of Molecular Cell, Tripathi and coworkers (Tripathi et al., 2010) decode some of the functions of a long noncoding RNA MALAT1. They provide evidence that MALAT1 regulates alternative splicing by controlling the activity of the SR protein family of splicing factors.
• aMAGEing New Players Enter the RING to Promote Ubiquitylation
  - mol cell 39(6):835-837 (2010)
  The MAGE proteins are best known as curious tumor-specific antigens. However, Doyle et al. (2010) reveal that MAGE proteins interact with RING proteins to promote ubiquitylation which provides important new insights into the physiological and pathological functions of this enigmatic family of proteins.
• CK2 Phospho-Dependent Binding of R2TP Complex to TEL2 Is Essential for mTOR and SMG1 Stability
  - mol cell 39(6):839-850 (2010)
  TEL2 interacts with and is essential for the stability of all phosphatidylinositol 3-kinase-related kinases (PIKKs), but its mechanism of action remains unclear. Here, we show that TEL2 is constitutively phosphorylated on conserved serines 487 and 491 by casein kinase 2 (CK2). Proteomic analyses establish that the CK2 phosphosite of TEL2 confers binding to the R2TP/prefoldin-like complex, which possesses chaperon/prefoldin activities required during protein complex assembly. The PIH1D1 subunit of the R2TP complex binds directly to the CK2 phosphosite of TEL2 in vitro and is required for the TEL2-R2TP/prefoldin-like complex interaction in vivo. Although the CK2 phosphosite mutant of TEL2 retains association with the PIKKs and HSP90 in cells, failure to interact with the R2TP/prefoldin-like complex results in instability of the PIKKs, principally mTOR and SMG1. We propose that TEL2 acts as a scaffold to coordinate the activities of R2TP/prefoldin-like and HSP90 chaperone! complexes during the assembly of the PIKKs.
• Strand Invasion Structures in the Inverted Repeat of Candida albicans Mitochondrial DNA Reveal a Role for Homologous Recombination in Replication
  - mol cell 39(6):851-861 (2010)
  Molecular recombination and transcription are proposed mechanisms to initiate mitochondrial DNA (mtDNA) replication in yeast. We conducted a comprehensive analysis of mtDNA from the yeast Candida albicans. Two-dimensional agarose gel electrophoresis of mtDNA intermediates reveals no bubble structures diagnostic of specific replication origins, but rather supports recombination-driven replication initiation of mtDNA in yeast. Specific species of Y structures together with DNA copy number analyses of a C. albicans mutant strain provide evidence that a region in a mainly noncoding inverted repeat is predominantly involved in replication initiation via homologous recombination. Our further findings show that the C. albicans mtDNA forms a complex branched network that does not contain detectable amounts of circular molecules. We provide topological evidence for recombination-driven mtDNA replication initiation and introduce C. albicans as a suitable model organism to study ! wild-type mtDNA maintenance in yeast.
• Swi2/Snf2-Related Translocases Prevent Accumulation of Toxic Rad51 Complexes during Mitotic Growth
  - mol cell 39(6):862-872 (2010)
  Purified DNA translocases Rdh54 and Rad54 can dissociate complexes formed by eukaryotic RecA-like recombinases on double-stranded DNA. Here, we show that Rad51 complexes are dissociated by these translocases in mitotic cells. Rad51 overexpression blocked growth of cells deficient in Rdh54 activity. This toxicity was associated with accumulation of Rad51 foci on undamaged chromatin. At normal Rad51 levels, rdh54 deficiency resulted in slight elevation of Rad51 foci. A triple mutant lacking Rdh54, Rad54, and a third Swi2/Snf2 homolog Uls1 accumulated Rad51 foci, grew slowly, and suffered chromosome loss. Thus, Uls1 and Rad54 can partially substitute for Rdh54 in the removal of toxic, nondamage-associated Rad51-DNA complexes. Additional data suggest that the function of Rdh54 and Rad54 in removal of Rad51 foci is significantly specialized; Rad54 predominates for removal of damage-associated foci, and Rdh54 predominates for removal of nondamage-associated foci.
• AID-Induced Genotoxic Stress Promotes B Cell Differentiation in the Germinal Center via ATM and LKB1 Signaling
  - mol cell 39(6):873-885 (2010)
  During an immune response, B cells undergo rapid proliferation and activation-induced cytidine deaminase (AID)-dependent remodeling of immunoglobulin (IG) genes within germinal centers (GCs) to generate memory B and plasma cells. Unfortunately, the genotoxic stress associated with the GC reaction also promotes most B cell malignancies. Here, we report that exogenous and intrinsic AID-induced DNA strand breaks activate ATM, which signals through an LKB1 intermediate to inactivate CRTC2, a transcriptional coactivator of CREB. Using genome-wide location analysis, we determined that CRTC2 inactivation unexpectedly represses a genetic program that controls GC B cell proliferation, self-renewal, and differentiation while opposing lymphomagenesis. Inhibition of this pathway results in increased GC B cell proliferation, reduced antibody secretion, and impaired terminal differentiation. Multiple distinct pathway disruptions were also identified in human GC B cell lymphoma patie! nt samples. Combined, our data show that CRTC2 inactivation, via physiologic DNA damage response signaling, promotes B cell differentiation in response to genotoxic stress.
• Polycomb Group Protein Displacement and Gene Activation through MSK-Dependent H3K27me3S28 Phosphorylation
  - mol cell 39(6):886-900 (2010)
  Epigenetic regulation of chromatin structure is essential for the expression of genes determining cellular specification and function. The Polycomb repressive complex 2 (PRC2) di- and trimethylates histone H3 on lysine 27 (H3K27me2/me3) to establish repression of specific genes in embryonic stem cells and during differentiation. How the Polycomb group (PcG) target genes are regulated by environmental cues and signaling pathways is quite unexplored. Here, we show that the mitogen- and stress-activated kinases (MSK), through a mechanism that involves promoter recruitment, histone H3K27me3S28 phosphorylation, and displacement of PcG proteins, lead to gene activation. We present evidence that the H3K27me3S28 phosphorylation is functioning in response to stress signaling, mitogenic signaling, and retinoic acid (RA)-induced neuronal differentiation. We propose that MSK-mediated H3K27me3S28 phosphorylation serves as a mechanism to activate a subset of PcG target genes determi! ned by the biological stimuli and thereby modulate the gene expression program determining cell fate.
• H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes
  - mol cell 39(6):901-911 (2010)
  Profound chromatin changes occur during mitosis to allow for gene silencing and chromosome segregation followed by reactivation of memorized transcription states in daughter cells. Using genome-wide sequencing, we found H2A.Z-containing +1 nucleosomes of active genes shift upstream to occupy TSSs during mitosis, significantly reducing nucleosome-depleted regions. Single-molecule analysis confirmed nucleosome shifting and demonstrated that mitotic shifting is specific to active genes that are silenced during mitosis and, thus, is not seen on promoters, which are silenced by methylation or mitotically expressed genes. Using the GRP78 promoter as a model, we found H3K4 trimethylation is also maintained while other indicators of active chromatin are lost and expression is decreased. These key changes provide a potential mechanism for rapid silencing and reactivation of genes during the cell cycle.
• HSP90 and Its R2TP/Prefoldin-like Cochaperone Are Involved in the Cytoplasmic Assembly of RNA Polymerase II
  - mol cell 39(6):912-924 (2010)
  RNA polymerases are key multisubunit cellular enzymes. Microscopy studies indicated that RNA polymerase I assembles near its promoter. However, the mechanism by which RNA polymerase II is assembled from its 12 subunits remains unclear. We show here that RNA polymerase II subunits Rpb1 and Rpb3 accumulate in the cytoplasm when assembly is prevented and that nuclear import of Rpb1 requires the presence of all subunits. Using MS-based quantitative proteomics, we characterized assembly intermediates. These included a cytoplasmic complex containing subunits Rpb1 and Rpb8 associated with the HSP90 cochaperone hSpagh (RPAP3) and the R2TP/Prefoldin-like complex. Remarkably, HSP90 activity stabilized incompletely assembled Rpb1 in the cytoplasm. Our data indicate that RNA polymerase II is built in the cytoplasm and reveal quality-control mechanisms that link HSP90 to the nuclear import of fully assembled enzymes. hSpagh also bound the free RPA194 subunit of RNA polymerase I, su! ggesting a general role in assembling RNA polymerases.
• The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation
  - mol cell 39(6):925-938 (2010)
  Alternative splicing (AS) of pre-mRNA is utilized by higher eukaryotes to achieve increased transcriptome and proteomic complexity. The serine/arginine (SR) splicing factors regulate tissue- or cell-type-specific AS in a concentration- and phosphorylation-dependent manner. However, the mechanisms that modulate the cellular levels of active SR proteins remain to be elucidated. In the present study, we provide evidence for a role for the long nuclear-retained regulatory RNA (nrRNA), MALAT1 in AS regulation. MALAT1 interacts with SR proteins and influences the distribution of these and other splicing factors in nuclear speckle domains. Depletion of MALAT1 or overexpression of an SR protein changes the AS of a similar set of endogenous pre-mRNAs. Furthermore, MALAT1 regulates cellular levels of phosphorylated forms of SR proteins. Taken together, our results suggest that MALAT1 regulates AS by modulating the levels of active SR proteins. Our results further highlight the r! ole for an nrRNA in the regulation of gene expression.
• Structural Basis for Substrate Placement by an Archaeal Box C/D Ribonucleoprotein Particle
  - mol cell 39(6):939-949 (2010)
  Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2′-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide ! RNA and large ribosomal and spliceosomal substrate RNAs.
• The 5′-7-Methylguanosine Cap on Eukaryotic mRNAs Serves Both to Stimulate Canonical Translation Initiation and to Block an Alternative Pathway
  - mol cell 39(6):950-962 (2010)
  Translational control is frequently exerted at the stage of mRNA recruitment to the initiating ribosome. We have reconstituted mRNA recruitment to the 43S preinitiation complex (PIC) using purified S. cerevisiae components. We show that eIF3 and the eIF4 factors not only stabilize binding of mRNA to the PIC, they also dramatically increase the rate of recruitment. Although capped mRNAs require eIF3 and the eIF4 factors for efficient recruitment to the PIC, uncapped mRNAs can be recruited in the presence of eIF3 alone. The cap strongly inhibits this alternative recruitment pathway, imposing a requirement for the eIF4 factors for rapid and stable binding of natural mRNA. Our data suggest that the 5′ cap serves as both a positive and negative element in mRNA recruitment, promoting initiation in the presence of the canonical group of mRNA handling factors while preventing binding to the ribosome via an aberrant, alternative pathway requiring only eIF3.
• MAGE-RING Protein Complexes Comprise a Family of E3 Ubiquitin Ligases
  - mol cell 39(6):963-974 (2010)
  The melanoma antigen (MAGE) family consists of more than 60 genes, many of which are cancer-testis antigens that are highly expressed in cancer and play a critical role in tumorigenesis. However, the biochemical and cellular functions of this enigmatic family of proteins have remained elusive. Here, we identify really interesting new gene (RING) domain proteins as binding partners for MAGE family proteins. Multiple MAGE family proteins bind E3 RING ubiquitin ligases with specificity. The crystal structure of one of these MAGE-RING complexes, MAGE-G1-NSE1, reveals structural insights into MAGE family proteins and their interaction with E3 RING ubiquitin ligases. Biochemical and cellular assays demonstrate that MAGE proteins enhance the ubiquitin ligase activity of RING domain proteins. For example, MAGE-C2-TRIM28 is shown to target p53 for degradation in a proteasome-dependent manner, consistent with its tumorigenic functions. These findings define a biochemical and cel! lular function for the MAGE protein family.
• Imaging-Based Identification of a Critical Regulator of FtsZ Protofilament Curvature in Caulobacter
  - mol cell 39(6):975-987 (2010)
  FtsZ is an essential bacterial GTPase that polymerizes at midcell, recruits the division machinery, and may generate constrictive forces necessary for cytokinesis. However, many of the mechanistic details underlying these functions are unknown. We sought to identify FtsZ-binding proteins that influence FtsZ function in Caulobacter crescentus. Here, we present a microscopy-based screen through which we discovered two FtsZ-binding proteins, FzlA and FzlC. FzlA is conserved in α-proteobacteria and was found to be functionally critical for cell division in Caulobacter. FzlA altered FtsZ structure both in vivo and in vitro, forming stable higher-order structures that were resistant to depolymerization by MipZ, a spatial determinant of FtsZ assembly. Electron microscopy revealed that FzlA organizes FtsZ protofilaments into striking helical bundles. The degree of curvature induced by FzlA depended on the nucleotide bound to FtsZ. Induction of FtsZ curvature by FzlA carries i! mplications for regulating FtsZ function by modulating its superstructure.

Hot off the presses! Oct 01 Trends in Ecology & Evolution

The Oct 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): 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:

• Editorial Board
  - Trends in Ecology and Evolution 25(10):i (2010)
  
• Monitoring does not always count
  McDonald-Madden E Baxter PW Fuller RA Martin TG Game ET Montambault J Possingham HP - Trends in Ecology and Evolution 25(10):547-550 (2010)
  The gross under-resourcing of conservation endeavours has placed an increasing emphasis on spending accountability. Increased accountability has led to monitoring forming a central element of conservation programs. Although there is little doubt that information obtained from monitoring can improve management of biodiversity, the cost (in time and/or money) of gaining this knowledge is rarely considered when making decisions about allocation of resources to monitoring. We present a simple framework allowing managers and policy advisors to make decisions about when to invest in monitoring to improve management.
• Uniting marine and terrestrial modelling of biodiversity under climate change
  Mokany K Richardson AJ Poloczanska ES Ferrier S The CSIRO CAF Biodiversity Working Group - Trends in Ecology and Evolution 25(10):550-551 (2010)
  
• "Awkward wording. Rephrase": linguistic injustice in ecological journals
  Clavero M - Trends in Ecology and Evolution 25(10):552-553 (2010)
  
• The balancing act of conservation
  - Trends in Ecology and Evolution 25(10):553-554 (2010)
  
• Landscapes of hope, oceans of promise: trophic cascades
  - Trends in Ecology and Evolution 25(10):554-555 (2010)
  
• Environmental myopia: a diagnosis and a remedy
  Silvertown J Tallowin J Stevens C Power SA Morgan V Emmett B Hester A Grime PJ Morecroft M Buxton R Poulton P Jinks R Bardgett R - Trends in Ecology and Evolution 25(10):556-561 (2010)
  Long-term ecological observation affords a picture of the past that uniquely informs our understanding of present and future ecological communities and processes. Without a long-term perspective, our vision is prone to environmental myopia. Long-term experiments (LTEs) in particular can reveal the mechanisms that underlie change in communities and ecosystem functioning in a way that cannot be understood by long-term monitoring alone. Despite the urgent need to know more about how climate change will affect ecosystems and their functioning, the continued existence of LTEs is extremely precarious and we believe that dedicated funds are needed to support them. A new non-profit organization called the Ecological Continuity Trust seeks to provide a solution to this problem by establishing an endowment that will be specifically earmarked to sustain LTEs as a scientific tool for the benefit of future generations.
• Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology
  Clutton-Brock T Sheldon BC - Trends in Ecology and Evolution 25(10):562-573 (2010)
  Many important questions in ecology and evolutionary biology can only be answered with data that extend over several decades and answering a substantial proportion of questions requires records of the life histories of recognisable individuals. We identify six advantages that long-term, individual based studies afford in ecology and evolution: (i) analysis of age structure; (ii) linkage between life history stages; (iii) quantification of social structure; (iv) derivation of lifetime fitness measures; (v) replication of estimates of selection; (vi) linkage between generations, and we review their impact on studies in six key areas of evolution and ecology. Our review emphasises the unusual opportunities and productivity of long-term, individual-based studies and documents the important role that they play in research on ecology and evolutionary biology as well as the difficulties they face.
• Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time
  Magurran AE Baillie SR Buckland ST Dick JM Elston DA Scott EM Smith RI Somerfield PJ Watt AD - Trends in Ecology and Evolution 25(10):574-582 (2010)
  The growing need for baseline data against which efforts to reduce the rate of biodiversity loss can be judged highlights the importance of long-term datasets, some of which are as old as ecology itself. We review methods of evaluating change in biodiversity at the community level using these datasets, and contrast whole-community approaches with those that combine information from different species and habitats. As all communities experience temporal turnover, one of the biggest challenges is distinguishing change that can be attributed to external factors, such as anthropogenic activities, from underlying natural change. We also discuss methodological issues, such as false alerts and modifications in design, of which users of these data sets need to be aware.
• Biodiversity baselines, thresholds and resilience: testing predictions and assumptions using palaeoecological data
  Willis KJ Bailey RM Bhagwat SA Birks HJ - Trends in Ecology and Evolution 25(10):583-591 (2010)
  Fossil records are replete with examples of long-term biotic responses to past climate change. One particularly useful set of records are those preserved in lake and marine sediments, recording both climate changes and corresponding biotic responses. Recently there has been increasing focus on the need for conservation of ecological and evolutionary processes in the face of climate change. We review key areas where palaeoecological archives contribute to this conservation goal, namely: (i) determination of rates and nature of biodiversity response to climate change; (ii) climate processes responsible for ecological thresholds; (iii) identification of ecological resilience to climate change; and (iv) management of novel ecosystems. We stress the importance of long-term palaeoecological data in fully understanding contemporary and future biotic responses.
• Accessible ecology: synthesis of the long, deep, and broad
  Peters DP - Trends in Ecology and Evolution 25(10):592-601 (2010)
  Large volumes of data have been collected to document the many ways that ecological systems are responding to changing environmental drivers. A general buy-in on solutions to these problems can be reached only if these and future data are made easily accessible to and understood by a broad audience that includes the public, decision-makers, and other scientists. A developing framework for synthesis is reviewed that integrates three main strategies of ecological research (long-term studies; short-term, process-based studies; and broad-scale observations) with derived data products and additional sources of knowledge. This framework focuses on making data from multiple sources and disciplines easily understood by many, a prerequisite for finding synthetic solutions and predicting future dynamics in a changing world.
• Multi-decadal oceanic ecological datasets and their application in marine policy and management
  Edwards M Beaugrand G Hays GC Koslow JA Richardson AJ - Trends in Ecology and Evolution 25(10):602-610 (2010)
  Long-term biological time-series in the oceans are relatively rare. Using the two longest of these we show how the information value of such ecological time-series increases through space and time in terms of their potential policy value. We also explore the co-evolution of these oceanic biological time-series with changing marine management drivers. Lessons learnt from reviewing these sequences of observations provide valuable context for the continuation of existing time-series and perspective for the initiation of new time-series in response to rapid global change. Concluding sections call for a more integrated approach to marine observation systems and highlight the future role of ocean observations in adaptive marine management.
• Never mind the length, feel the quality: the impact of long-term epidemiological data sets on theory, application and policy
  Rohani P King AA - Trends in Ecology and Evolution 25(10):611-618 (2010)
  Infectious diseases have been a prime testing ground for ecological theory. However, the ecological perspective is increasingly recognized as essential in epidemiology. Long-term, spatially resolved reliable data on disease incidence and the ability to test them using mechanistic models have been critical in this cross-fertilization. Here, we review some of the key intellectual developments in epidemiology facilitated by long-term data. We identify research frontiers at the interface of ecology and epidemiology and their associated data needs.

Hot off the presses! Oct 01 TRENDS GENET

The Oct 01 issue of the TRENDS GENET is now up on Pubget (About TRENDS GENET): 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:

• Editorial Board
  - TRENDS GENET 26(10):i (2010)
  
• Maintenance of duplicate genes and their functional redundancy by reduced expression
  Qian W Liao BY Chang AY Zhang J - TRENDS GENET 26(10):425-430 (2010)
  Although evolutionary theories predict functional divergence between duplicate genes, many old duplicates still maintain a high degree of functional similarity and are synthetically lethal or sick, an observation that has puzzled many geneticists. We propose that expression reduction, a special type of subfunctionalization, facilitates the retention of duplicates and the conservation of their ancestral functions. Consistent with this hypothesis, gene expression data from both yeasts and mammals show a substantial decrease in the level of gene expression after duplication. Whereas the majority of the expression reductions are likely to be neutral, some are apparently beneficial to rebalancing gene dosage after duplication.
• Mimivirus: the emerging paradox of quasi-autonomous viruses
  Claverie JM Abergel C - TRENDS GENET 26(10):431-437 (2010)
  What is a virus? Are viruses alive? Should they be classified among microorganisms? One would expect these simple questions to have been settled a century after the discovery of the first viral disease. For years, modern virology successfully unravelled the huge diversity of viruses in terms of genetic material, replication mechanism, pathogenicity, host infection, and more recently particle structure, planet-wide distribution and ecological significance. Yet, little progress was made in understanding their evolutionary origin(s), as well as the fundamental nature of their relationship with the cellular world. Thanks to the recent studies on Mimivirus and other large DNA viruses, we are now entering a new era where the most basic concepts about viruses are revisited, including their true nature, how fundamentally different they are from cellular microorganisms, and how essential they might have been in the major innovations that punctuated the evolution of life.
• Towards a complete resolution of the genetic architecture of disease
  Singleton AB Hardy J Traynor BJ Houlden H - TRENDS GENET 26(10):438-442 (2010)
  After years of linear gains in the genetic dissection of human disease we are now in a period of exponential discovery. This is particularly apparent for complex disease. Genome-wide association studies (GWAS) have provided myriad associations between common variability and disease, and have shown that common genetic variability is unlikely to explain the entire genetic predisposition to disease. Here we detail how one can expand on this success and systematically identify genetic risks that lead or predispose to disease using next-generation sequencing. Geneticists have had for many years a protocol to identify Mendelian disease. A similar set of tools is now available for the identification of rare moderate-risk loci and common low-risk variants. Whereas major challenges undoubtedly remain, particularly regarding data handling and the functional classification of variants, we suggest that these will be largely practical and not conceptual.
• Crosstalk between genetic and epigenetic information through cytosine deamination
  Chahwan R Wontakal SN Roa S - TRENDS GENET 26(10):443-448 (2010)
  Decades of work have elucidated the existence of two forms of heritable information, namely genetic and epigenetic, which are collectively referred to as the 'dual inheritance'. The underlying mechanisms behind these two modes of inheritance have so far remained distinct. Cytosine deaminases, such as activation-induced cytidine deaminase (AID) and other members of the APOBEC family, have been implicated both in genetic variation of somatic cells and in epigenetic remodeling of germ and pluripotent cells. We hereby synthesize these seemingly dissociated functions into one coherent model, and further suggest that cytosine deaminases, particularly AID, might have a broader influence by modulating epigenetic information in somatic or cancer cells, as well as by triggering genetic variation in germ and pluripotent cells through mutation followed by natural selection. We therefore propose that the AID/APOBEC family of deaminases are likely to have acted as drivers throug! hout vertebrate evolution.
• Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation
  Osbourn A - TRENDS GENET 26(10):449-457 (2010)
  Microbes and plants produce a huge array of secondary metabolites that have important ecological functions. These molecules have long been exploited in medicine as antibiotics, anticancer and anti-infective agents and for a wide range of other applications. Gene clusters for secondary metabolic pathways are common in bacteria and filamentous fungi, and examples have now been discovered in plants. Here, current knowledge of gene clusters across the kingdoms is evaluated with the aim of trying to understand the rules behind cluster existence and evolution. Such knowledge will be crucial in learning how to activate the enormous number of 'silent' gene clusters being revealed by whole-genome sequencing and hence in making available a wealth of novel compounds for evaluation as drug leads and other bioactives. It could also facilitate the development of crop plants with enhanced pest or disease resistance, improved nutritional qualities and/or elevated levels of high-va! lue products.