Hot off the presses! Jul 31 Mol Cell

The Jul 31 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:

• Related Mechanisms for End Processing at Telomeres and DNA Double-Strand Breaks
  - Mol Cell 35(2):137-138 (2009)
  In a recent issue of Molecular Cell, Bonetti et al. (2009) identify in the yeast Saccharomyces cerevisiae that the molecular activities that generate 3′ overhangs at telomeric DNA ends are the same as those that resect DNA at double-strand breaks.
• MicroRNAs Cross the Line: The Battle for mRNA Stability Enters the Coding Sequence
  - Mol Cell 35(2):139-140 (2009)
  A study in this issue of Molecular Cell (Elcheva et al., 2009) shows the inherent instability of the βTrCP1 mRNA to be caused by microRNA-183 targeting the coding sequence; interestingly, this action is directly opposed by the RNA-binding protein CRD-BP.
• Ras and the FAK Paradox
  - Mol Cell 35(2):141-142 (2009)
  In a recent issue of Molecular Cell, Zheng et al. (2009) describe a surprising set of findings that highlight an unexpected negative regulation of FAK by oncogenic Ras and its consequences for cancer cell migration and invasion.
• A Quorum-Sensing Antagonist Targets Both Membrane-Bound and Cytoplasmic Receptors and Controls Bacterial Pathogenicity
  - Mol Cell 35(2):143-153 (2009)
  Quorum sensing is a process of bacterial communication involving production and detection of secreted molecules called autoinducers. Gram-negative bacteria use acyl-homoserine lactone (AHL) autoinducers, which are detected by one of two receptor types. First, cytoplasmic LuxR-type receptors bind accumulated intracellular AHLs. AHL-LuxR complexes bind DNA and alter gene expression. Second, membrane-bound LuxN-type receptors bind accumulated extracellular AHLs. AHL-LuxN complexes relay information internally by phosphorylation cascades that direct gene expression changes. Here, we show that a small molecule, previously identified as an antagonist of LuxN-type receptors, is also a potent antagonist of the LuxR family, despite differences in receptor structure, localization, AHL specificity, and signaling mechanism. Derivatives were synthesized and optimized for potency, and in each case, we characterized the mode of action of antagonism. The most potent antagonist protect! s Caenorhabditis elegans from quorum-sensing-mediated killing by Chromobacterium violaceum, validating the notion that targeting quorum sensing has potential for antimicrobial drug development.
• Rejuvenation of CcdB-Poisoned Gyrase by an Intrinsically Disordered Protein Domain
  - Mol Cell 35(2):154-163 (2009)
  Toxin-antitoxin modules are small regulatory circuits that ensure survival of bacterial populations under challenging environmental conditions. The ccd toxin-antitoxin module on the F plasmid codes for the toxin CcdB and its antitoxin CcdA. CcdB poisons gyrase while CcdA actively dissociates CcdB:gyrase complexes in a process called rejuvenation. The CcdA:CcdB ratio modulates autorepression of the ccd operon. The mechanisms behind both rejuvenation and regulation of expression are poorly understood. We show that CcdA binds consecutively to two partially overlapping sites on CcdB, which differ in affinity by six orders of magnitude. The first, picomolar affinity interaction triggers a conformational change in CcdB that initiates the dissociation of CcdB:gyrase complexes by an allosteric segmental binding mechanism. The second, micromolar affinity binding event regulates expression of the ccd operon. Both functions of CcdA, rejuvenation and autoregulation, are mechanisti! cally intertwined and depend crucially on the intrinsically disordered nature of the CcdA C-terminal domain.
• Two-Site Phosphorylation of EPRS Coordinates Multimodal Regulation of Noncanonical Translational Control Activity
  - Mol Cell 35(2):164-180 (2009)
  Glutamyl-prolyl tRNA synthetase (EPRS) is a component of the heterotetrameric γ-interferon-activated inhibitor of translation (GAIT) complex that binds 3′UTR GAIT elements in multiple interferon-gamma (IFN-γ)-inducible mRNAs and suppresses their translation. Here, we elucidate the specific EPRS phosphorylation events that regulate GAIT-mediated gene silencing. IFN-γ induces sequential phosphorylation of Ser886 and Ser999 in the noncatalytic linker connecting the synthetase cores. Phosphorylation of both sites is essential for EPRS release from the parent tRNA multisynthetase complex. Ser886 phosphorylation is required for the interaction of NSAP1, which blocks EPRS binding to target mRNAs. The same phosphorylation event induces subsequent binding of ribosomal protein L13a and GAPDH and restores mRNA binding. Finally, Ser999 phosphorylation directs the formation of a functional GAIT complex that binds initiation factor eIF4G and represses translation. Thus, two-sit! e phosphorylation provides structural and functional pliability to EPRS and choreographs the repertoire of activities that regulates inflammatory gene expression.
• Translation Initiation from the Ribosomal A Site or the P Site, Dependent on the Conformation of RNA Pseudoknot I in Dicistrovirus RNAs
  - Mol Cell 35(2):181-190 (2009)
  Translation initiation of the second ORF of insect dicistrovirus RNA depends on an internal ribosomal entry site (IRES) in its intergenic region (IGR) and is exceptional in using a codon other than AUG and in not using the canonical initiator methionine tRNA. Studies in vitro suggest that pseudoknot I (PKI) immediately preceding the initiation codon occupies the ribosomal P site and that an elongator tRNA initiates translation from the ribosomal A site. Using dicistronic reporters carrying mutations in the initiation codon of the second ORF and mutant elongator or initiator tRNAs capable of reading these codons, we provide direct evidence for initiation from the A site in mammalian cells and, under certain conditions, also from the P site. Initiation from the A but not the P site requires PKI. Thus, PKI structure may be dynamic, and optimal IGR IRES-mediated translation of dicistroviral RNAs may require trans-acting factors to stabilize PKI.
• Stability, Flexibility, and Dynamic Interactions of Colliding RNA Polymerase II Elongation Complexes
  - Mol Cell 35(2):191-205 (2009)
  Multiple RNA polymerase II (RNAPII) molecules can transcribe a gene simultaneously, but what happens when such polymerases collide—for example due to polymerase pausing or DNA damage? Here, RNAPII collision was characterized using a reconstituted system for simultaneous transcription by two polymerases. When progression of leading polymerase is obstructed, rear-end collision entails a transient state in which the elongation complexes interact, followed by substantial backtracking of trailing polymerase. Elongation complexes remain stable on DNA, with their activity and the integrity of transcription bubbles remaining intact. Subsequent TFIIS-stimulated transcript cleavage allows resumed forward translocation, resulting in trailing polymerase oscillating at the obstruction. Conversely, if leading polymerase is merely stalled at a pause site, collision and TFIIS cooperate to drive it through. We propose that dynamic interactions between RNAPII elongation complexes help! regulate polymerase traffic and that their conformational flexibility buffers the effect of collisions with objects on DNA, thereby maintaining stability in the face of obstacles to transcription.
• Phosphorylation of Mcm2 by Cdc7 Promotes Pre-replication Complex Assembly during Cell-Cycle Re-entry
  - Mol Cell 35(2):206-216 (2009)
  Cyclin E has been shown to have a role in pre-replication complex (Pre-RC) assembly in cells re-entering the cell cycle from quiescence. The assembly of the pre-RC, which involves the loading of six MCM subunits (Mcm2–7), is a prerequisite for DNA replication. We found that cyclin E, through activation of Cdk2, promotes Mcm2 loading onto chromatin. This function is mediated in part by promoting the accumulation of Cdc7 messenger RNA and protein, which then phosphorylates Mcm2. Consistent with this, a phosphomimetic mutant of Mcm2 can bypass the requirement for Cdc7 in terms of Mcm2 loading. Furthermore, ectopic expression of both Cdc6 and Cdc7 can rescue the MCM loading defect associated with expression of dominant-negative Cdk2. These results are consistent with a role for cyclin E-Cdk2 in promoting the accumulation of Cdc6 and Cdc7, which is required for Mcm2 loading when cells re-enter the cell cycle from quiescence.
• Initial Stages of V(D)J Recombination: The Organization of RAG1/2 and RSS DNA in the Postcleavage Complex
  - Mol Cell 35(2):217-227 (2009)
  To obtain structural information on the early stages of V(D)J recombination, we isolated a complex of the core RAG1 and RAG2 proteins with DNA containing a pair of cleaved recombination signal sequences (RSS). Stoichiometric and molecular mass analysis established that this signal-end complex (SEC) contains two protomers each of RAG1 and RAG2. Visualization of the SEC by negative-staining electron microscopy revealed an anchor-shaped particle with approximate two-fold symmetry. Consistent with a parallel arrangement of DNA and protein subunits, the N termini of RAG1 and RAG2 are positioned at opposing ends of the complex, and the DNA chains beyond the RSS nonamer emerge from the same face of the complex, near the RAG1 N termini. These first images of the V(D)J recombinase in its postcleavage state provide a framework for modeling RAG domains and their interactions with DNA.
• A Genome-wide siRNA Screen Reveals Diverse Cellular Processes and Pathways that Mediate Genome Stability
  - Mol Cell 35(2):228-239 (2009)
  Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer. Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (γH2AX) and revealed links to cellular complexes and to genes with unclassified functions. We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures. Furthermore, we connect increased γH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response. These data indicate that preservation of genome stability is mediated by a larger network of biological proces! ses than previously appreciated.
• CRD-BP Protects the Coding Region of βTrCP1 mRNA from miR-183-Mediated Degradation
  - Mol Cell 35(2):240-246 (2009)
  miRNAs are largely known to base pair with the 3′UTR of target mRNAs, downregulating their stability and translation. mRNA of βTrCP1 ubiquitin ligase is very unstable, but unlike the majority of mRNAs where 3′UTR determines the rate of mRNA turnover, βTrCP1 mRNA contains cis-acting destabilizing elements within its coding region. Here we show that degradation of mRNA of βTrCP1 is miRNA dependent and identify miR-183 as a microRNA that interacts with the coding region of βTrCP1 mRNA. Argonaute2 interacts with the same region of βTrCP1 mRNA in an miR-183-dependent manner. Inhibition of miR-183 function or disruption of the miR-183-binding site stabilizes βTrCP1 mRNA and elevates βTrCP1 levels, resulting in activation of the SCFβTrCP E3 ubiquitin ligase. We previously showed that the RNA-binding protein CRD-BP binds to the coding region of βTrCP1 mRNA and stabilizes it. Here we demonstrate that CRD-BP prevents degradation of βTrCP1 mRNA by attenuating its mi! R-183-dependent interaction with Ago2.
• Protein Occupancy Landscape of a Bacterial Genome
  - Mol Cell 35(2):247-253 (2009)
  Protein-DNA interactions are fundamental to core biological processes, including transcription, DNA replication, and chromosomal organization. We have developed in vivo protein occupancy display (IPOD), a technology that reveals protein occupancy across an entire bacterial chromosome at the resolution of individual binding sites. Application to Escherichia coli reveals thousands of protein occupancy peaks, highly enriched within and in close proximity to noncoding regulatory regions. In addition, we discovered extensive (>1 kilobase) protein occupancy domains (EPODs), some of which are localized to highly expressed genes, enriched in RNA-polymerase occupancy. However, the majority are localized to transcriptionally silent loci dominated by conserved hypothetical ORFs. These regions are highly enriched in both predicted and experimentally determined binding sites of nucleoid proteins and exhibit extreme biophysical characteristics such as high intrinsic curvature. Our o! bservations implicate these transcriptionally silent EPODs as the elusive organizing centers, long proposed to topologically isolate chromosomal domains.

Hot off the presses! Aug 01 Lancet

The Aug 01 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:

• Remaking America's health-care system
  - Lancet 374(9687):357 (2009)
  
• Women's health in rural China
  - Lancet 374(9687):358 (2009)
  
• Supply and safety issues surrounding an H1N1 vaccine
  - Lancet 374(9687):358 (2009)
  
• Surgery in stage III non-small-cell lung cancer
  - Lancet 374(9687):359-360 (2009)
  
• Child survival and IMCI: in need of sustained global support
  - Lancet 374(9687):361-362 (2009)
  
• Cutaneous melanoma in the era of molecular profiling
  - Lancet 374(9687):362-365 (2009)
  
• Clinical staging: a new scenario for the treatment of psychosis
  - Lancet 374(9687):365-367 (2009)
  
• Why multiple sexual partners?
  - Lancet 374(9687):367-369 (2009)
  
• Use of patient-reported outcomes in clinical practice
  - Lancet 374(9687):369-370 (2009)
  
• East African countries struggle with visceral leishmaniasis
  - Lancet 374(9687):371-372 (2009)
  
• Chilling side-effects
  - Lancet 374(9687):373 (2009)
  
• Cecil Gerald Helman
  - Lancet 374(9687):374 (2009)
  
• Elsevier should divest itself of either its medical publishing or pharmaceutical services division
  - Lancet 374(9687):375 (2009)
  
• Elsevier should divest itself of either its medical publishing or pharmaceutical services division
  - Lancet 374(9687):375-376 (2009)
  
• HIV testing in the UK
  - Lancet 374(9687):376 (2009)
  
• HIV testing in the UK
  - Lancet 374(9687):376-377 (2009)
  
• HIV testing in the UK
  - Lancet 374(9687):377 (2009)
  
• HIV testing in the UK
  - Lancet 374(9687):377 (2009)
  
• Could early cord clamping harm neonatal stabilisation?
  - Lancet 374(9687):377-378 (2009)
  
• What is the "primary" prevention of congenital anomalies?
  - Lancet 374(9687):378 (2009)
  
• Department of Error
  - Lancet 374(9687):378 (2009)
  
• Radiotherapy plus chemotherapy with or without surgical resection for stage III non-small-cell lung cancer: a phase III randomised controlled trial
  - Lancet 374(9687):379-386 (2009)
  Background Results from phase II studies in patients with stage IIIA non-small-cell lung cancer with ipsilateral mediastinal nodal metastases (N2) have shown the feasibility of resection after concurrent chemotherapy and radiotherapy with promising rates of survival. We therefore did this phase III trial to compare concurrent chemotherapy and radiotherapy followed by resection with standard concurrent chemotherapy and definitive radiotherapy without resection. Methods Patients with stage T1-3pN2M0 non-small-cell lung cancer were randomly assigned in a 1:1 ratio to concurrent induction chemotherapy (two cycles of cisplatin [50 mg/m2 on days 1, 8, 29, and 36] and etoposide [50 mg/m2 on days 1–5 and 29–33]) plus radiotherapy (45 Gy) in multiple academic and community hospitals. If no progression, patients in group 1 underwent resection and those in group 2 continued radiotherapy uninterrupted up to 61 Gy. Two additional cycles of cisplatin and etoposide were given in both groups. The primary endpoint was overall survival (OS). Analysis was by intention to treat. This study is registered with ClinicalTrials.gov, number NCT00002550. Findings 202 patients (median age 59 years, range 31–77) were assigned to group 1 and 194 (61 years, 32–78) to group 2. Median OS was 23·6 months (IQR 9·0–not reached) in group 1 versus 22·2 months (9·4–52·7) in group 2 (hazard ratio [HR] 0·87 [0·70–1·10]; p=0·24). Number of patients alive at 5 years was 37 (point estimate 27%) in group 1 and 24 (point estimate 20%) in group 2 (odds ratio 0·63 [0·36–1·10]; p=0·10). With N0 status at thoracotomy, the median OS was 34·4 months (IQR 15·7–not reached; 19 [point estimate 41%] patients alive at 5 years). Progression-free survival (PFS) was better in group 1 than in group 2, median 12·8 months (5·3–42·2) vs 10·5 months (4·8–20·6), HR 0·77 [0·62–0·96]; p=0·017); the number of patients without disease progression at 5 years was 32 (point estimate 22%) versus 13 (point estimate 11%), respectively. Neutropenia and oesophagitis were the main grade 3 or 4 toxicities associated with chemotherapy plus ra! diotherapy in group 1 (77 [38%] and 20 [10%], respectively) and group 2 (80 [41%] and 44 [23%], respectively). In group 1, 16 (8%) deaths were treatment related versus four (2%) in group 2. In an exploratory analysis, OS was improved for patients who underwent lobectomy, but not pneumonectomy, versus chemotherapy plus radiotherapy. Interpretation Chemotherapy plus radiotherapy with or without resection (preferably lobectomy) are options for patients with stage IIIA(N2) non-small-cell lung cancer. Funding National Cancer Institute, Canadian Cancer Society, and National Cancer Institute of Canada.
• Late donor cardiectomy after paediatric heterotopic cardiac transplantation
  - Lancet 374(9687):387-392 (2009)
  Background Cardiac transplantation is a life-saving procedure in infants and children with advanced cardiomyopathy. However, it is greatly limited by shortage of paediatric donors and the complications of long-term immunosuppression, including post-transplant lymphoproliferative disorder (PTLD). We report the management of an infant who had heterotopic cardiac transplantation for advanced cardiomyopathy with secondary pulmonary hypertension who developed seemingly incurable PTLD. Methods An 8-month-old girl presented in 1994 with signs of severe heart failure, secondary to dilated cardiomyopathy. At age 11 months, the patient underwent a heterotopic cardiac transplantation. Findings The patient developed many episodes of PTLD associated with Epstein-Barr virus infection that were resistant to several therapies, including reduction of immunosuppression. Native heart recovery enabled removal of the donor heart 10·5 years after the original operation to allow complete cessation of immunosuppression. Her postoperative course was uncomplicated and the outcome was excellent. 3·5 years after surgery, the patient remains well, in complete remission from her PTLD, and has normal cardiac function. Interpretation This case shows several issues relating to the use of heterotopic cardiac transplantation in infants and the capacity of the heart to recover. It also provides new insights into the interaction between the immune system with several aspects of modern management of post-transplantation PTLD. Funding None.
• Effect of the Integrated Management of Childhood Illness strategy on childhood mortality and nutrition in a rural area in Bangladesh: a cluster randomised trial
  - Lancet 374(9687):393-403 (2009)
  Background WHO and UNICEF launched the Integrated Management of Childhood Illness (IMCI) strategy in the mid-1990s to reduce deaths from diarrhoea, pneumonia, malaria, measles, and malnutrition in children younger than 5 years. We assessed the effect of IMCI on health and nutrition of children younger than 5 years in Bangladesh. Methods In this cluster randomised trial, 20 first-level government health facilities in the Matlab subdistrict of Bangladesh and their catchment areas (total population about 350 000) were paired and randomly assigned to either IMCI (intervention; ten clusters) or usual services (comparison; ten clusters). All three components of IMCI—health-worker training, health-systems improvements, and family and community activities—were implemented beginning in February, 2002. Assessment included household and health facility surveys tracking intermediate outputs and outcomes, and nutrition and mortality changes in intervention and comparison areas. Primary endpoint was mortality in children aged between 7 days and 59 months. Analysis was by intention to treat. This study is registered, number ISRCTN52793850. Findings The yearly rate of mortality reduction in children younger than 5 years (excluding deaths in first week of life) was similar in IMCI and comparison areas (8·6% vs 7·8%). In the last 2 years of the study, the mortality rate was 13·4% lower in IMCI than in comparison areas (95% CI −14·2 to 34·3), corresponding to 4·2 fewer deaths per 1000 livebirths (95% CI −4·1 to 12·4; p=0·30). Implementation of IMCI led to improved health-worker skills, health-system support, and family and community practices, translating into increased care-seeking for illnesses. In IMCI areas, more children younger than 6 months were exclusively breastfed (76% vs 65%, difference of differences 10·1%, 95% CI 2·65–17·62), and prevalence of stunting in children aged 24–59 months decreased more rapidly (difference of differences −7·33, 95% CI −13·83 to −0·83) than in comparison areas. Interpretation IMCI was associated with positive changes in all input, output, and outcome indicators, including increased exclusive breastfeeding and decreased stunting. However, IMCI implementation had no effect on mortality within the timeframe of the assessment. Funding Bill & Melinda Gates Foundation, WHO's Department of Child and Adolescent Health and Development, and US Agency for International Development.
• The many faces of tension pneumothoraces
  - Lancet 374(9687):404 (2009)
  
• Blast injuries
  - Lancet 374(9687):405-415 (2009)
  Health-care providers are increasingly faced with the possibility of needing to care for people injured in explosions, but can often, however, feel undertrained for the unique aspects of the patient's presentation and management. Although most blast-related injuries (eg, fragmentation injuries from improvised explosive devices and standard military explosives) can be managed in a similar manner to typical penetrating or blunt traumatic injuries, injuries caused by the blast pressure wave itself cannot. The blast pressure wave exerts forces mainly at air–tissue interfaces within the body, and the pulmonary, gastrointestinal, and auditory systems are at greatest risk. Arterial air emboli arising from severe pulmonary injury can cause ischaemic complications—especially in the brain, heart, and intestinal tract. Attributable, in part, to the scene chaos that undoubtedly exists, poor triage and missed diagnosis of blast injuries are substantial concerns because injuries! can be subtle or their presentation can be delayed. Management of these injuries can be a challenge, compounded by potentially conflicting treatment goals. This Seminar aims to provide a thorough overview of these unique primary blast injuries and their management.
• Men who have sex with men and HIV/AIDS in sub-Saharan Africa
  - Lancet 374(9687):416-422 (2009)
  Globally, men who have sex with men (MSM) continue to bear a high burden of HIV infection. In sub-Saharan Africa, same-sex behaviours have been largely neglected by HIV research up to now. The results from recent studies, however, indicate the widespread existence of MSM groups across Africa, and high rates of HIV infection, HIV risk behaviour, and evidence of behavioural links between MSM and heterosexual networks have been reported. Yet most African MSM have no safe access to relevant HIV/AIDS information and services, and many African states have not begun to recognise or address the needs of these men in the context of national HIV/AIDS prevention and control programmes. The HIV/AIDS community now has considerable challenges in clarifying and addressing the needs of MSM in sub-Saharan Africa; homosexuality is illegal in most countries, and political and social hostility are endemic. An effective response to HIV/AIDS requires improved strategic information about all! risk groups, including MSM. The belated response to MSM with HIV infection needs rapid and sustained national and international commitment to the development of appropriate interventions and action to reduce structural and social barriers to make these accessible.
• The breastmilk brand: promotion of child survival in the face of formula-milk marketing
  - Lancet 374(9687):423-425 (2009)
  
• Chest pain and small red cells: size does matter
  - Lancet 374(9687):426 (2009)
  

Hot off the presses! Aug 01 Nat Methods

The Aug 01 issue of the Nat Methods is now up on Pubget (About Nat Methods): 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:

• Method of the Year 2009 voting begins
  - Nat Methods 6(8):547 (2009)
  We are now accepting nominations and collecting votes for the Method of the Year 2009.
• Software by any name
  - Nat Methods 6(8):547-548 (2009)
  Computational biologists are often tempted to avoid providing a named software implementation of their new algorithm, but resisting this temptation helps avoid difficulties later on and benefits the wider community of biologists.
• MAQGene: software to facilitate C. elegans mutant genome sequence analysis
  - Nat Methods 6(8):549 (2009)
  I want to purchase this article Register now Price: US$18 In order to purchase this article you must be a registered user. I want to subscribe to Nature Methods Select this option to purchase a personal subscription to Nature Methods.
• SHOREmap: simultaneous mapping and mutation identification by deep sequencing
  - Nat Methods 6(8):550-551 (2009)
  I want to purchase this article Register now Price: US$18 In order to purchase this article you must be a registered user. I want to subscribe to Nature Methods Select this option to purchase a personal subscription to Nature Methods.
• Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
  - Nat Methods 6(8):551-552 (2009)
  I want to purchase this article Register now Price: US$18 In order to purchase this article you must be a registered user. I want to subscribe to Nature Methods Select this option to purchase a personal subscription to Nature Methods.
• Mass spectrometers on a chip
  - Nat Methods 6(8):555 (2009)
  A prototype for a mass spectrometer with single-molecule sensitivity has prospects for single-cell proteomics.
• Actions speak louder
  - Nat Methods 6(8):556-557 (2009)
  A fluorescence resonance energy transfer (FRET)-based biosensor helps scientists monitor the activation of an essential signaling protein over the course of embryogenesis in Drosophila melanogaster.
• New shapes of prions
  - Nat Methods 6(8):556-557 (2009)
  Modification of a system for rapid amplification of misfolded prion proteins allows de novo generation of these infectious molecules and provides a glimpse of the diverse range of possible misfolded prion strains.
• News in brief
  - Nat Methods 6(8):557 (2009)
  
• Network countdown
  - Nat Methods 6(8):558 (2009)
  Researchers lay the foundation for networks that will self-destruct after being exposed to a predetermined number of stimuli.
• Clinical proteomics on target
  - Nat Methods 6(8):560 (2009)
  A multilaboratory study designed to assess the reproducibility of multiple reaction monitoring (MRM) mass spectrometry–based proteomics demonstrates the promise of this technology for disease biomarker verification.
• A good nose for stem cells
  - Nat Methods 6(8):562 (2009)
  Cells can be delivered to the rodent brain noninvasively, via the nasal cavity.
• Probing the basis for genotype-phenotype relationships
  - Nat Methods 6(8):565-566 (2009)
  Transposon mutagenesis coupled with microarray analysis helps to rapidly generate information about changing genotype-phenotype relationships in laboratory-evolved bacteria.
• New genetic tools for cell lineage analysis in Drosophila
  - Nat Methods 6(8):566-568 (2009)
  Real-time lineage tracing in flies gets a boost with three techniques to specifically label a progenitor's daughter cells.
• Statistical methods for analysis of high-throughput RNA interference screens
  - Nat Methods 6(8):569-575 (2009)
  RNA interference (RNAi) has become a powerful technique for reverse genetics and drug discovery, and in both of these areas large-scale high-throughput RNAi screens are commonly performed. The statistical techniques used to analyze these screens are frequently borrowed directly from small-molecule screening; however, small-molecule and RNAi data characteristics differ in meaningful ways. We examine the similarities and differences between RNAi and small-molecule screens, highlighting particular characteristics of RNAi screen data that must be addressed during analysis. Additionally, we provide guidance on selection of analysis techniques in the context of a sample workflow.
• Conditional and reversible disruption of essential herpesvirus proteins
  - Nat Methods 6(8):577-579 (2009)
  Elucidating the function of essential proteins of complex pathogenic viruses is impeded by a paucity of complementing systems. By fusing a destabilizing domain of the FK506-binding protein to essential cytomegalovirus proteins, we generated virus mutants in which amounts of fusion proteins and viral growth can be regulated by the synthetic ligand shield-1. This conditional approach will greatly facilitate the analysis of gene functions of herpesviruses and viruses of other families.
• Global discovery of adaptive mutations
  - Nat Methods 6(8):581-583 (2009)
  Although modern DNA sequencing enables rapid identification of genetic variation, characterizing the phenotypic consequences of individual mutations remains a labor-intensive task. Here we describe array-based discovery of adaptive mutations (ADAM), a technology that searches an entire bacterial genome for mutations that contribute to selectable phenotypic variation between an evolved strain and its parent. We found that ADAM identified adaptive mutations in laboratory-evolved Escherichia coli strains with high sensitivity and specificity.
• Mass spectrometry of membrane transporters reveals subunit stoichiometry and interactions
  - Nat Methods 6(8):585-587 (2009)
  We describe a general mass spectrometry approach to determine subunit stoichiometry and lipid binding in intact membrane protein complexes. By exploring conditions for preserving interactions during transmission into the gas phase and for optimally stripping away detergent, by subjecting the complex to multiple collisions, we released the intact complex largely devoid of detergent. This enabled us to characterize both subunit stoichiometry and lipid binding in 4 membrane protein complexes.
• Metabolic network analysis integrated with transcript verification for sequenced genomes
  - Nat Methods 6(8):589-592 (2009)
  With sequencing of thousands of organisms completed or in progress, there is a growing need to integrate gene prediction with metabolic network analysis. Using Chlamydomonas reinhardtii as a model, we describe a systems-level methodology bridging metabolic network reconstruction with experimental verification of enzyme encoding open reading frames. Our quantitative and predictive metabolic model and its associated cloned open reading frames provide useful resources for metabolic engineering.
• Virtual terminator nucleotides for next-generation DNA sequencing
  - Nat Methods 6(8):593-595 (2009)
  We synthesized reversible terminators with tethered inhibitors for next-generation sequencing. These were efficiently incorporated with high fidelity while preventing incorporation of additional nucleotides, and we used them to sequence canine bacterial artificial chromosomes in a single-molecule system that provided even coverage for over 99% of the region sequenced. This single-molecule approach generated high-quality sequence data without the need for target amplification and thus avoided concomitant biases.
• Dereplication and de novo sequencing of nonribosomal peptides
  - Nat Methods 6(8):596-599 (2009)
  Nonribosomal peptides (NRPs) are of great pharmacological importance, but there is currently no technology for high-throughput NRP 'dereplication' and sequencing. We used multistage mass spectrometry followed by spectral alignment algorithms for sequencing of cyclic NRPs. We also developed an algorithm for comparative NRP dereplication that establishes similarities between newly isolated and previously identified similar but nonidentical NRPs, substantially reducing dereplication efforts.
• The twin spot generator for differential Drosophila lineage analysis
  - Nat Methods 6(8):600-602 (2009)
  In Drosophila melanogaster, widely used mitotic recombination–based strategies generate mosaic flies with positive readout for only one daughter cell after division. To differentially label both daughter cells, we developed the twin spot generator (TSG) technique, which through mitotic recombination generates green and red twin spots that are detectable after the first cell division as single cells. We propose wide applications of TSG to lineage and genetic mosaic studies.
• G-TRACE: rapid Gal4-based cell lineage analysis in Drosophila
  - Nat Methods 6(8):603-605 (2009)
  We combined Gal4-UAS and the FLP recombinase–FRT and fluorescent reporters to generate cell clones that provide spatial, temporal and genetic information about the origins of individual cells in Drosophila melanogaster. We named this combination the Gal4 technique for real-time and clonal expression (G-TRACE). The approach should allow for screening and the identification of real-time and lineage-traced expression patterns on a genomic scale.
• Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
  - Nat Methods 6(8):606-612 (2009)
  We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.
• Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
  - Nat Methods 6(8):613-618 (2009)
  We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock-captured single-nucleotide polymorphisms (SNPs) from the transcriptome. We characterized four cell lines established from two human subjects in the Personal Genome Project. Approximately 11–22% of the heterozygous mRNA-associated SNPs showed allele-specific expression in each cell line and 4.3–8.5% were tissue-specific, suggesting the presence of tissue-specific cis regulation. When we applied allelotyping to two pairs of sibling human embryonic stem cell lines, the sibling lines were more similar in allele-specific expression than were the genetically unrelated lines. We found that the variation of allelic ratios in gene expression among different cell lines was primarily explained by genetic variations, much more so than by specific tissue types or growth conditions. Comparison of expressed SNPs on ! the sense and antisense transcripts suggested that allelic ratios are primarily determined by cis-regulatory mechanisms on the sense transcripts.
• Cell culture: building a better matrix
  - Nat Methods 6(8):619-622 (2009)
  With the realization that cells interact extensively with their surrounding microenvironments during growth and development, the challenge for researchers has become designing three-dimensional culture systems that more closely mimic those relationships.

Hot off the presses! Jul 30 Nature

The Jul 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:

• Information overload
  - Nature 460(7255):551 (2009)
  A report released last week by the US National Academies makes recommendations for tackling the issues surrounding the era of petabyte science.
• The shale revolution
  - Nature 460(7255):551-552 (2009)
  The vast reserves of US natural gas must be used judiciously to ease the transition to clean energy.
• Inspiring non-scientists
  - Nature 460(7255):552 (2009)
  Those wishing to reveal scientific ideas should learn from the engaging style of TED conference talks.
• Biology: Chill bill
  - Nature 460(7255):554 (2009)
  
• Phytology: Tree carbon recalibrated?
  - Nature 460(7255):554 (2009)
  
• Nanochemistry: Protein fondue
  - Nature 460(7255):554 (2009)
  
• Cancer biology: Cancer's metabolic roots
  - Nature 460(7255):554 (2009)
  
• Microfluidics: The sounds of science
  - Nature 460(7255):554 (2009)
  
• Earth monitoring: Tsunamis from space
  - Nature 460(7255):555 (2009)
  
• Chemistry: A one-pot shot
  - Nature 460(7255):555 (2009)
  
• Behaviour: Why 'there's never just one'
  - Nature 460(7255):555 (2009)
  
• Physics: A cold shake
  - Nature 460(7255):555 (2009)
  
• Development: Starting from scratch
  - Nature 460(7255):555 (2009)
  
• Journal club
  - Nature 460(7255):555 (2009)
  
• Biodefence lab criticized
  - Nature 460(7255):556-557 (2009)
  The US government's decision to locate a new national biosecurity lab in Manhattan, Kansas, has been called into question by a congressional watchdog. The Government Accountability Office (GAO) concluded that the Department of Homeland Security (DHS) relied on a flawed risk assessment when deciding the location of the US$650-million National Bio and Agro-Defense Facility.
• Physicians fight back against disclosure rules
  - Nature 460(7255):556-557 (2009)
  Even as US legislators work to limit ties between academic physicians and industry, a small group of doctors is calling for greater industry collaboration. On 23 July, they gathered at Brigham and Women's Hospital in Boston to launch a new organization opposed to strict conflict-of-interest rules.
• European body told to cut free
  - Nature 460(7255):557 (2009)
  The European Commission must make "immediate corrections" to the running of the European Research Council (ERC) or risk the body suffering a "deadly blow", an expert review has found. On 23 July, a panel led by the former president of Latvia, Vaira Vike-Freiberga, published a review of the ERC — the first pan-European initiative to fund frontier research solely on the basis of excellence.
• LHC students face data drought
  - Nature 460(7255):558 (2009)
  Computer simulations are the only option when the world's largest particle accelerator isn't working. Last November, Sara Bolognesi stood before a committee at the University of Turin in Italy and defended her PhD thesis in experimental high-energy physics. The 180-page document is a treatise on finding the Higgs boson, part of the mechanism believed to endow all other matter with mass. The pages are crammed with dozens of figures and tables, but something is missing: real data. Sara Bolognesi hopes to move from simulated experiments to real data collection at CERN. That's because the Large Hadron Collider (LHC), the world's largest particle accelerator at CERN, outside Geneva in Switzerland, is broken. The 4.6-billion Swiss franc (US$4.3-billion) collider is designed to accelerate protons to near the speed of light and smash them together in four giant detectors spread around its 27-kilometre circumference. Physicists once hoped that the LHC would start its collisions in late 2006, but last September, after a series of delays and soon after the machine was switched on, an electrical short caused extensive damage along a sector of the machine. Repairs have taken longer than expected, and, as of last week, the LHC was not scheduled to restart before mid-November. The long delays have ended the dreams of a generation of graduate students hoping to use fresh data for their theses. With no machine to deliver results, "people are doing experimental PhDs and effectively doing very little experimenting", says Will Reece, a graduate student at Imperial College London working on a detector known as LHCb. "It's a strange situation." "People are doing experimental PhDs and effectively doing very little experimenting." Strange but not unprecedented, says Rolf-Dieter Heuer, CERN's director-general. During the mid-1980s, physicists were focused on building the Large Electron–Positron collider, the predecessor to the LHC. Over that period, Heuer says, graduate students sometimes wrote theses based on data from detector tests. Today, many of the same physicists work on the LHC project. But although the electron collider took a few years to build, construction of the LHC took more than a decade, and most testing for the current detectors ended years ago. Aside from a trickle of data created by stray cosmic rays hitting the detectors, there will be no data to be analysed until the collider restarts. "It's a mess," says Burton Richter, a Nobel-prizewinning physicist at the SLAC National Accelerator Laboratory in Menlo Park, California. European graduate students such as Bolognesi face strict time constraints for completing their PhDs. Most universities require a thesis to be submitted within three to four years, and that means that students cannot wait for their data. Instead, their analyses are being done with data from 'Monte Carlo' simulations — computer programs that replicate what might come out of real collisions. Not everybody thinks that the simulated data are a problem. "I don't feel that bad about not having data in my thesis," says Carsten Hof, a graduate student at Aachen University in Germany, who is finishing his PhD on software that will automatically analyse real collisions. "All the bugs we found and fixed now will also be fixed for real data." Hof adds that the data drought may actually be an advantage. "You look at everything with no bias," he says. Heuer says that the situation reflects the growing size and sophistication of high-energy physics experiments. Whereas early experiments could be done in days by a handful of people, machines such as the LHC take thousands of researchers years to complete. The current generation of students may not be familiar with real data, he says, but they have extensive experience in building the huge detectors needed to capture them. Future PhD students will work on software without touching the innards of the detectors, he points out. As long as students get a taste of what's involved with each stage of the project, he says, "I don't think that people are losing anything." Others are more worried. Although Monte Carlo simulations can reproduce the uncertainties seen in real data, they will never contain a big surprise. That means simulated data can never be as good as the real thing, says Gustaaf Brooijmans, a physicist at Columbia University in New York. "It's like a badly written murder mystery," he says. "In the first chapter you're given enough information that you know who did it, and then you read the rest of the book, and, lo and behold, you get the right answer." For this reason, Columbia and other US institutions require students to use real data in their PhD theses. That solves the data dilemma, but creates a new problem: US students working on the LHC must move to finish their theses. For students such as Ketino Kaadze of Kansas State University in Manhattan, this meant travelling from Geneva to Batavia, Illinois, the home of the world's other major particle collider, the Tevatron. ADVERTISEMENT Kaadze says that she was initially nervous about the move from one experiment to the other, but she has found it valuable. Although it will take her longer to complete her PhD, she is glad to have made the switch. "I think it's very important to have this experience," she says. Now at CERN for a postdoctoral fellowship, Bolognesi worries that she will be at a disadvantage compared with students like Kaadze. "Two years from now, I will have to search for work," she says. "I hope they will not discriminate against me." By the time she is looking for a job, the LHC should have completed its first run, and Bolognesi will hopefully have completed a first of her own — an analysis of real collisions. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Italy introduces performance-related funding
  - Nature 460(7255):559 (2009)
  Agency to evaluate research is launched. The Italian government has finally given the go-ahead to a national research evaluation agency, ANVUR. But at the same time it published Italy's first university ranking and said performance-related funding would begin immediately. The 24 July announcement of ANVUR was welcomed by many scientists who say that the country has not adequately rewarded best-performing research institutions. A law creating the agency was passed two years ago, but not put into practice until now. ANVUR should start work in about a year, says Mariastella Gelmini, the minister of universities and research. Her ranking of universities caused political outcry however. Up to 7% of the approximately €7-billion (US$10-billion) national university budget will be allocated according to the list. Universities in the centre and north of the country generally did well, but most universities in the poorer south ranked at the bottom. The ranking was based on an internal research evaluation carried out several years ago, combined with other criteria intended to assess teaching quality. Raffaele Lombardo, president of Sicily, denounced the ranking criteria as discriminatory. Poor infrastructure in many southern universities prevents them from attracting independent research funds, he said in newspaper interviews, and high unemployment rates make it hard for graduates to find jobs, a criterion used to measure effectiveness of teaching. Lombardo and others also criticized the use of old bibliometric data. ADVERTISEMENT All universities are concerned that performance-related funding is being introduced in a year when the government plans a 10% cut in the university budget. Davide Bassi, rector of the top-ranking University of Trento, says that this will be a "disaster for all universities, including our own". Details of ANVUR's operation have yet to be set, but it is likely to be responsible for fine-tuning the criteria used in ranking exercises. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Forest growth studies begin to turn up the heat
  - Nature 460(7255):559 (2009)
  Across the United States, researchers are firing up experiments to determine how rising temperatures could reshape the nation's forests. The studies encompass the pines and maples of eastern forests in Massachusetts and North Carolina, the spruce and fir of northern Minnesota, and the alpine tundra ecosystem above the treeline in the Rocky Mountains in Colorado.
• Mice made from induced stem cells
  - Nature 460(7255):560 (2009)
  Two teams of Chinese researchers have created live mice from induced pluripotent stem (iPS) cells, answering a lingering question about the developmental potential of the cells. Since Shinya Yamanaka of Kyoto University in Japan created the first iPS cells1 in 2006, researchers have wondered whether they could generate an entire mammalian body from iPS cells, as they have from true embryonic stem cells.
• Legal battle may reshape nanotechnology firm
  - Nature 460(7255):561 (2009)
  Oxonica, one of the United Kingdom's leading nanotechnology companies (see Nature 446, 963; 2007.
• US puts flu vaccines on trial
  - Nature 460(7255):562 (2009)
  NIAID director Anthony Fauci explains testing strategy. Anthony Fauci.J. Reed/Reuters The US National Institute of Allergy and Infectious Diseases (NIAID) announced last week that it will begin five clinical trials for two pandemic H1N1 influenza vaccines in early August. These trials will help inform a likely US mass-vaccination campaign beginning in September. NIAID director Anthony Fauci talks about what vaccines were chosen, and why. We have planned seven priority trials. The five I announced on 22 July are for non-adjuvanted vaccines, but we also plan two more: testing GlaxoSmithKline's AS03 adjuvant with vaccine from Sanofi Pasteur and from CSL Biotherapies. We prioritized non-adjuvanted vaccines as the US government seems likely to recommend using these for vaccinating the first tier of priority groups — expected to include children and groups at higher risk of severe disease, such as those with certain underlying illnesses and pregnant women. We fully intend to proceed with trials of adjuvanted vaccines. The Europeans have lots of data on the use of adjuvanted flu vaccine in the elderly, but I don't think anybody has really good data on adjuvants in children. The Department of Health and Human Services (DHHS) has therefore decided that we are not going to take the chance, and has made a policy decision that we are not going to give adjuvanted flu vaccines to kids. We don't have the time to collect substantial data. Yes. But, as in other countries, there are many ethical constraints. We are working with both principal investigators and institutional review boards to draw up protocols for such groups. Even if the Food and Drug Administration (FDA) is considering the initial non-adjuvanted vaccines as simply a strain substitution of seasonal vaccine, it's still a new vaccine, so we want to get data from healthy adults before launching into risk groups. We are asking questions that will inform policy decisions likely to affect how we use vaccines, whereas the focus of vaccine makers is generally directed towards studies needed to get a licence for their vaccine. The sort of information that the FDA, DHHS and the vaccine makers told us they needed most included what levels of antigen per dose are essential to getting an adequate immune response, and whether one or two shots of vaccine will be needed. So two trials will test both single and double shots of both 15-microgram [the amount in seasonal H1N1 vaccine] or 30-µg doses of antigen, using antigen from Sanofi Pasteur and from CSL Biotherapies. We will give the first doses in the first week or so of August, and the second dose 21 days later. We will learn very quickly after 21 days, when we draw blood, if one dose of 15 µg is enough. And if it isn't, if 30 µg is any better. And if 15 µg is enough, does 30 µg give an even better response? Shortly after 42 days, we will have data on the second doses. Novartis has quite a sophisticated clinical-trials apparatus. The United States will purchase 45% from Novartis, 26% from Sanofi Pasteur and a little bit less than 19% from CSL Biotherapies. Novartis is able to carry the ball itself, so we made a reasonably well-based decision to fill in the gaps and get information on CSL and Sanofi Pasteur. We don't know. Testing two vaccines against different H1N1s at the same time has never been done. We'll look at three test regimes: giving the pandemic 2009 vaccine before, at the same time as, or after seasonal H1N1 vaccine. ADVERTISEMENT If you give the pandemic H1N1 vaccine first, will subsequently giving the seasonal H1N1 enhance the response to the original dose, or will there be antigenic competition or interference? If you give both at same time, is the body going to have a response that is enhanced against seasonal flu and not do a very good job against the pandemic vaccine, or will it actually amplify the response? And if you give pandemic vaccine after [seasonal vaccine], is that going to have an enhancing or suppressing effect? Immunologically, you can't predict the outcome. You never can predict that, but things look encouraging to me from a molecular-virological standpoint. If you look at the molecular and genetic make-up of the virus from the very first isolates in early April compared to what we are seeing now in late July, it's virtually an identical virus everywhere. So it doesn't look like it is under pressure to mutate to a significant degree. We hope it stays that way for the autumn and winter season. www.nature.com/swineflu Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• German research bodies draft synthetic-biology plan
  - Nature 460(7255):563 (2009)
  
• Step-by-step rating system set to improve African labs
  - Nature 460(7255):563 (2009)
  The number of accredited labs in Africa may rise.AM. SOC. CLIN. PATHOL. An accreditation system that aims to raise the standard of disease diagnosis in African medical laboratories was launched on 27 July in Kigali, Rwanda. The process, developed by the World Health Organization in collaboration with the US government, will mark African pathology labs on an incremental scale, upping the rating as their quality improves rather than using the 'pass or fail' system of many developed countries. The scheme was launched alongside a training programme for African lab workers. The US Centers for Disease Control and Prevention in Atlanta, Georgia, which will implement the step-by-step system, estimates that it could see 60 currently unaccredited African laboratories attain ratings verging on the standard of an average lab in the developed world over the next two years. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• UK government urged to disclose evidence base
  - Nature 460(7255):563 (2009)
  
• Mauna Kea adds to its family of telescopes
  - Nature 460(7255):563 (2009)
  Mauna Kea in Hawaii has beaten off competition from Cerro Armazones, in Chile's Atacama desert, to host the Thirty Meter Telescope. Henry Yang, chancellor of the University of California, Santa Barbara, and chair of the telescope's board of directors, announced the winning site on 21 July. The decision has been two years in the making, he said. Mauna Kea, which already hosts many other telescopes, was picked over its Chilean rival for its superior observing climate. It is higher and drier, has less atmospheric turbulence, and its average temperature fluctuates less through the year and over a day, notes board member Richard Ellis of the California Institute of Technology in Pasadena. Construction of the telescope, which will cost around US$1 billion, is scheduled to begin in 2011 and end in 2018. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Genetic barcode for plants close to agreement
  - Nature 460(7255):563 (2009)
  
• Lucky find of undersea methane bubbles
  - Nature 460(7255):563 (2009)
  NOAA While testing equipment off the Californian coast last month, a newly refitted research vessel stumbled across plumes of methane gas rising 1,400 metres from the sea floor. The Okeanos Explorer, commissioned last year by the US National Oceanic and Atmospheric Administration (NOAA) after a US$20-million refit, was testing a new multi-beam sonar system in the Mendocino fracture zone (see sonar image, above). On 15 July the ship returned to the site to capture plume material for analysis in the coming weeks. The plumes, which measure up to 1 kilometre across, typically dissipate about 600 metres below the surface. Cruise scientist Stephen Hammond of the NOAA office in Newport, Oregon, suspects this is because ice with methane gas trapped in its crystal structure melts at the combination of pressure and temperature at that depth. Similar methane plumes have been discovered from the Oregon coast to the Black Sea, but not this large or numerous. Add your own comment You can be as critical or controversial as you like, but please don't get personal or offensive, and do keep it brief. Remember this is for feedback and discussion - not for publishing papers, press releases or advertisements, for example. If you ramble on in an annoying way too often, we may remove your posting privileges. You need to be registered with Nature to leave a comment. Please log in or register as a new user. You will be re-directed back to this page. * Log in / register
• Wind power: High hopes
  - Nature 460(7255):564-566 (2009)
  A ride on a kite boat might just kill you from fright — if it doesn't crush you first. The vessel is essentially an 8-metre catamaran dragged behind a kite the size of a movie screen — a lot of horsepower for such a small craft.
• Immunology: Lights, camera, infection
  - Nature 460(7255):568-570 (2009)
  Behind the heavy black curtains of his microscopy room, Mark Miller is shooting an action movie. He gives the settings on the multiphoton microscope a once-over while his senior scientist Vjollca Konjufca checks the sedated mouse on the warmed stage.
• Flu: vaccinate to cut risk of chimaeric virus emerging
  - Nature 460(7255):571 (2009)
  The international scientific community and decision-makers on public health are debating how best to manage the anticipated vaccine shortage for the new pandemic strain of influenza A virus, recently emerged from the animal reservoir. Priority distribution of the first product batches must be to individuals at high risk and to crucial employees.
• Flu: weighing up conflicting expert information
  - Nature 460(7255):571 (2009)
  In his Essay 'Pandemics: avoiding the mistakes of 1918' (Nature 459, 324–325; 2009), John M. Barry writes that during an influenza pandemic "telling the public the truth is ... paramount".
• Where will we find the tritium to fuel hybrid reactors?
  - Nature 460(7255):571 (2009)
  In your News Feature 'The hybrid returns' (Nature460, 25–28; 2009), you discuss the feasibility of creating a fusion–fission hybrid reactor to generate greenhouse-gas-free and waste-free nuclear energy. However, there is another challenge to add to the factors to be considered: where would the hundreds of grams of tritium needed daily to fuel the deuterium–tritium fusion reaction be produced?
• The invention of heroes
  - Nature 460(7255):572-573 (2009)
  The Western public's misapprehension that genius in science is always male and caucasian is partly a legacy of Victorian politics, says Christine MacLeod.
• A break from the bench
  - Nature 460(7255):574-577 (2009)
  Nature regulars give their recommendations for relaxed, inspiring holiday reading and viewing — from climate-change history to Isaac Newton the detective.
• Optics: All smoke and metamaterials
  - Nature 460(7255):579-580 (2009)
  An illusion device, placed near but not enclosing an object of arbitrary shape, manipulates and transforms light scattered off the object so as to give it the appearance of a completely different object.
• Structural biology: Trimeric ion-channel design
  - Nature 460(7255):580-581 (2009)
  Cavernous chambers, intricate passages, a gate with a curious lock — the structure of an ATP-activated ion channel reveals its architecture. And this intriguing interior design is found in another type of ion channel too.
• Oceanography: A fishy mix
  - Nature 460(7255):581-582 (2009)
  Ocean life is in almost constant motion, and such activity must surely stir things up. Innovative investigations into this concept of 'biogenic mixing' show a role for jellyfish and their brethren.
• Planetary science: Windy clues to Saturn's spin
  - Nature 460(7255):582-583 (2009)
  Saturn's rotation period has been a mystery. An estimate based on its meteorology comes with implications for our understanding of the planet's atmospheric jet streams and interior structure.
• Earth science: Trickle-down geodynamics
  - Nature 460(7255):583-584 (2009)
  Analysis of the platinum-group elements in a particular type of ancient volcanic rock provides clues about Earth's early history as well as a fresh approach to understanding mantle dynamics.
• Developmental biology: Skeletal muscle comes of age
  - Nature 460(7255):584-585 (2009)
  A regulatory protein thought to be crucial for maintaining the muscle stem-cell pool throughout life is shown to be dispensable in the adult. Muscle biologists are left wondering what fundamental things apply as time goes by.
• Supramolecular chemistry: Phosphorus caged
  - Nature 460(7255):585-586 (2009)
  Violent criminals are imprisoned to keep them under control. Similarly, incarceration in a molecular jail stops white phosphorus from bursting into flames — but on release, it regains its fiery character.
• Recent progress in the biology and physiology of sirtuins
  - Nature 460(7255):587-591 (2009)
  The sirtuins are a highly conserved family of NAD+-dependent enzymes that regulate lifespan in lower organisms. Recently, the mammalian sirtuins have been connected to an ever widening circle of activities that encompass cellular stress resistance, genomic stability, tumorigenesis and energy metabolism. Here we review the recent progress in sirtuin biology, the role these proteins have in various age-related diseases and the tantalizing notion that the activity of this family of enzymes somehow regulates how long we live.
• Biased reptilian palaeothermometer?
  - Nature 460(7255):E1 (2009)
  Arising from: J. J. Head et al.Nature 457, 715–717 (2009); Head et al.reply Palaeotemperatures can be estimated from characteristics of fossils if their living relatives represent the full evolutionary potential of the larger taxon to which the fossil belongs. By drawing on observations1, 2 that the body size of poikilotherms decreases globally with ambient temperature, Head et al.3 used the 13 m length of the newly described fossil boid Titanoboa cerrejonensis to estimate that the Palaeocene neotropical mean annual temperature (MAT) was 30–34 °C. I question the validity of this palaeotemperature estimate by using the same data and approach as Head et al.3 to show that Varanus (Megalania) prisca4, a large extinct lizard that lived in eastern Australia during the Late Pleistocene, was 3–4 times longer than predicted by the largest lizard species in the tropics today. This suggests that the scarcity of large predatory reptiles today may primarily be a function of competition with mammalian carnivores, rather than a function of modern temperatures.
• Re-calibrating the snake palaeothermometer
  - Nature 460(7255):E2 (2009)
  Arising from: J. J. Head et al.Nature 457, 715–717 (2009); Head et al.reply In a recent study1 a new proxy for palaeoclimate reconstructions was proposed on the basis of a theoretical approach linking the largest body sizes to ambient temperature in extant taxa of air-breathing poikilotherms2, 3. The value of the largest fossil snake's body length was used to estimate the mean annual temperature (MAT) for the Palaeocene neotropics of T = 3.8–7.2 °C above the modern value1. Here we argue that the reported temperature difference is a twofold overestimate and obtain a corrected estimate of T = 1.9–3.7 °C using the taxon-specific metabolic scaling exponent = 0.17 for boid snakes. The importance of using relevant taxon-specific information in case of one-taxon-based temperature reconstructions1 while leaving the theoretically derived generic values (such as = 0.33 used by Head et al.1) for broad inter-taxonomic analyses2, 3 is emphasized.
• Can the giant snake predict palaeoclimate?
  - Nature 460(7255):E3 (2009)
  Arising from: J. J. Head et al.Nature 457, 715–717 (2009); Head et al.reply In their report on Titanoboa cerrejonensis, Head et al.1 propose that the great size of this 58 to 60 million-year-old snake (estimated length = 13 m, mass = 1,135 kg) indicates a mean annual neotropical temperature (MAT) of 30–34 °C, substantially higher than previous estimates for that period. They argue that the high MAT was necessary to compensate for the decreased mass-specific metabolic rate intrinsic to a snake of this size. However, the relationship on which Head et al.1 base their conclusion does not account for the scope of behavioural control over body temperature available to Titanoboa due to its huge mass. Our calculations suggest that because of its ability to behaviourally control its body temperature, Titanoboa cannot serve as an accurate palaeothermometer.
• Head et al. reply
  - Nature 460(7255):E4 (2009)
  Replying to: J. M. K. Sniderman Nature 460, 10.1038/nature08222 (2009); A. M. Makarieva, V. G. Gorshkov & B.-L. Li Nature 460, 10.1038/nature08223 (2009); M. W. Denny, B. L. Lockwood & G. N. Somero Nature 460, 10.1038/nature08224 (2009) Denny et al.1 and Sniderman2 question our use of body size in Titanoboa cerrejonensis as an equatorial temperature proxy during the Palaeocene3, and Makarieva et al.4 suggest an adjustment to our temperature estimates. Denny et al.1 misinterpret the physiological model of our study5, 6 and the implications of their body temperature (Tb) estimates relative to the thermal ecology of extant snakes. They assert that our model is inappropriate for large-bodied animals because the relationship between Tb and air temperature (mean annual temperature; MAT3) is not constant across different body sizes in poikilotherms. In fact, the model does not assume constancy of Tb relative to MAT. Changes in Tb (and thus body size) relative to MAT resulting from increasing thermal inertia with size are inherent in the model, as evidenced by the scaling of body length and MAT (see Fig. 3 in ref. 3). The model is accurate for the longest extant snake, Python reticulatus6, with a maximum body lengt! h 70% that of Titanoboa3, indicating that it is appropriate to use with animals approximating the sizes of the largest known snakes.
• Crystal structure of the ATP-gated P2X4 ion channel in the closed state
  - Nature 460(7255):592-598 (2009)
  P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. Here we present crystal structures of the zebrafish P2X4 receptor in its closed, resting state. The chalice-shaped, trimeric receptor is knit together by subunit–subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in -strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an 8 Å slab of protein. We define the location of three non-canonical, intersubunit ATP-binding sites, and suggest that ATP bi! nding promotes subunit rearrangement and ion channel opening.
• Pore architecture and ion sites in acid-sensing ion channels and P2X receptors
  - Nature 460(7255):599-604 (2009)
  Acid-sensing ion channels are proton-activated, sodium-selective channels composed of three subunits, and are members of the superfamily of epithelial sodium channels, mechanosensitive and FMRF-amide peptide-gated ion channels. These ubiquitous eukaryotic ion channels have essential roles in biological activities as diverse as sodium homeostasis, taste and pain. Despite their crucial roles in biology and their unusual trimeric subunit stoichiometry, there is little knowledge of the structural and chemical principles underlying their ion channel architecture and ion-binding sites. Here we present the structure of a functional acid-sensing ion channel in a desensitized state at 3 Å resolution, the location and composition of the 8 Å 'thick' desensitization gate, and the trigonal antiprism coordination of caesium ions bound in the extracellular vestibule. Comparison of the acid-sensing ion channel structure with the ATP-gated P2X4 receptor reveals similarity in pore arc! hitecture and aqueous vestibules, suggesting that there are unanticipated yet common structural and mechanistic principles.
• Resonant stripping as the origin of dwarf spheroidal galaxies
  - Nature 460(7255):605-607 (2009)
  Dwarf spheroidal galaxies are the most dark-matter-dominated systems in the nearby Universe1, 2, 3 and their origin is one of the outstanding puzzles of how galaxies form. Dwarf spheroidals are poor in gas and stars, making them unusually faint4, 5, 6, and those known as ultra-faint dwarfs7, 8 have by far the lowest measured stellar content of any galaxy9, 10. Previous theories11 require that dwarf spheroidals orbit near giant galaxies like the Milky Way, but some dwarfs have been observed in the outskirts of the Local Group12. Here we report simulations of encounters between dwarf disk galaxies and somewhat larger objects. We find that the encounters excite a process, which we term 'resonant stripping', that transforms them into dwarf spheroidals. This effect is distinct from other mechanisms proposed to form dwarf spheroidals, including mergers13, galaxy–galaxy harassment14, or tidal and ram pressure stripping, because it is driven by gravitational resonances. It m! ay account for some of the observed properties of dwarf spheroidals in the Local Group. Within this framework, dwarf spheroidals should form and interact in pairs, leaving detectable long stellar streams and tails.
• Saturn's rotation period from its atmospheric planetary-wave configuration
  - Nature 460(7255):608-610 (2009)
  The rotation period of a gas giant's magnetic field (called the System III reference frame) is commonly used to infer its bulk rotation1. Saturn's dipole magnetic field is not tilted relative to its rotation axis (unlike Jupiter, Uranus and Neptune), so the surrogate measure of its long-wavelength (kilometric) radiation is currently used to fix the System III rotation period2. The period as measured now by the Cassini spacecraft is up to 7 min longer3 than the value of 10 h 39 min 24 s measured 28 years ago by Voyager2. Here we report a determination of Saturn's rotation period based on an analysis of potential vorticity. The resulting reference frame (which we call System IIIw) rotates with a period of 10 h 34 min 13 20 s. This shifted reference frame is consistent with a pattern of alternating jets on Saturn that is more symmetrical between eastward and westward flow. This suggests that Saturn's winds are much more like those of Jupiter than hitherto believed4.
• A 'granocentric' model for random packing of jammed emulsions
  - Nature 460(7255):611-615 (2009)
  Packing problems are ubiquitous1, 2, ranging from oil extraction through porous rocks to grain storage in silos and the compaction of pharmaceutical powders into tablets. At a given density, particulate systems pack into a mechanically stable and amorphous jammed state3, 4. Previous theoretical studies have explored a connection between this jammed state and the glass transition4, 5, 6, 7, 8, the thermodynamics of jamming9, 10, 11, 12 and geometric modelling of random packings13, 14, 15. Nevertheless, a simple underlying mechanism for the random assembly of athermal particles, analogous to crystalline ordering, remains unknown. Here we use three-dimensional measurements of packings of polydisperse emulsion droplets to build a simple statistical model in which the complexity of the global packing is distilled into a local stochastic process. From the perspective of a single particle, the packing problem is reduced to the random formation of nearest neighbours, followed ! by a choice of contacts among them. The two key parameters in the model—the available space around a particle and the ratio of contacts to neighbours—are directly obtained from experiments. We demonstrate that this 'granocentric' view captures the properties of the polydisperse emulsion packing—ranging from the microscopic distributions of nearest neighbours and contacts, to local density fluctuations, to the global packing density. Application of our results to monodisperse and bidisperse systems produces quantitative agreement with previously measured trends in global density16. Our model therefore reveals a general principle of organization for random packing and may provide the foundations for a theory of jammed matter.
• Carbon respiration from subsurface peat accelerated by climate warming in the subarctic
  - Nature 460(7255):616-619 (2009)
  Among the largest uncertainties in current projections of future climate is the feedback between the terrestrial carbon cycle and climate1. Northern peatlands contain one-third of the world's soil organic carbon, equivalent to more than half the amount of carbon in the atmosphere2. Climate-warming-induced acceleration of carbon dioxide (CO2) emissions through enhanced respiration of thick peat deposits, centuries to millennia old, may form a strong positive carbon cycle–climate feedback. The long-term temperature sensitivity of carbon in peatlands, especially at depth, remains uncertain, however, because of the short duration or correlative nature of field studies3, 4, 5 and the disturbance associated with respiration measurements below the surface in situ or during laboratory incubations6, 7. Here we combine non-disturbing in situ measurements of CO2 respiration rates and isotopic (13C) composition of respired CO2 in two whole-ecosystem climate-manipulation experime! nts in a subarctic peatland. We show that approximately 1 °C warming accelerated total ecosystem respiration rates on average by 60% in spring and by 52% in summer and that this effect was sustained for at least eight years. While warming stimulated both short-term (plant-related) and longer-term (peat soil-related) carbon respiration processes, we find that at least 69% of the increase in respiration rate originated from carbon in peat towards the bottom (25–50 cm) of the active layer above the permafrost. Climate warming therefore accelerates respiration of the extensive, subsurface carbon reservoirs in peatlands to a much larger extent than was previously thought6, 7. Assuming that our data from a single site are indicative of the direct response to warming of northern peatland soils on a global scale, we estimate that climate warming of about 1 °C over the next few decades could induce a global increase in heterotrophic respiration of 38–100 megatonnes of C per ye! ar. Our findings suggest a large, long-lasting, positive feedb! ack of carbon stored in northern peatlands to the global climate system.
• Progressive mixing of meteoritic veneer into the early Earth's deep mantle
  - Nature 460(7255):620-623 (2009)
  Komatiites are ancient volcanic rocks, mostly over 2.7 billion years old (from the Archaean era), that formed through high degrees of partial melting of the mantle and therefore provide reliable information on bulk mantle compositions1. In particular, the platinum group element (PGE) contents of komatiites provide a unique source of information on core formation, mantle differentiation and possibly core–mantle interaction2, 3, 4, 5, 6, 7, 8. Most of the available PGE data on komatiites are from late Archaean (2.7–2.9 Gyr old) or early Proterozoic (2.0–2.5 Gyr old) samples. Here we show that most early Archaean (3.5–3.2 Gyr old) komatiites from the Barberton greenstone belt of South Africa and the Pilbara craton of Western Australia are depleted in PGE relative to late Archaean and younger komatiites. Early Archaean komatiites record a signal of PGE depletion in the lower mantle, resulting from core formation. This signal diminishes with time owing to progressiv! e mixing-in to the deep mantle of PGE-enriched cosmic material that the Earth accreted as the 'late veneer' during the Early Archaean (4.5–3.8 Gyr ago) meteorite bombardment.
• A viscosity-enhanced mechanism for biogenic ocean mixing
  - Nature 460(7255):624-626 (2009)
  Recent observations of biologically generated turbulence in the ocean have led to conflicting conclusions regarding the significance of the contribution of animal swimming to ocean mixing. Measurements indicate elevated turbulent dissipation—comparable with levels caused by winds and tides—in the vicinity of large populations of planktonic animals swimming together1. However, it has also been noted that elevated turbulent dissipation is by itself insufficient proof of substantial biogenic mixing, because much of the turbulent kinetic energy of small animals is injected below the Ozmidov buoyancy length scale, where it is primarily dissipated as heat by the fluid viscosity before it can affect ocean mixing2. Ongoing debate regarding biogenic mixing has focused on comparisons between animal wake turbulence and ocean turbulence3, 4. Here, we show that a second, previously neglected mechanism of fluid mixing—first described over 50 years ago by Charles Darwin5— is ! the dominant mechanism of mixing by swimming animals. The efficiency of mixing by Darwin's mechanism is dependent on animal shape rather than fluid length scale and, unlike turbulent wake mixing, is enhanced by fluid viscosity. Therefore, it provides a means of biogenic mixing that can be equally effective in small zooplankton and large mammals. A theoretical model for the relative contributions of Darwinian mixing and turbulent wake mixing is created and validated by in situ field measurements of swimming jellyfish using a newly developed scuba-based laser velocimetry device6. Extrapolation of these results to other animals is straightforward given knowledge of the animal shape and orientation during vertical migration. On the basis of calculations of a broad range of aquatic animal species, we conclude that biogenic mixing via Darwin's mechanism can be a significant contributor to ocean mixing and nutrient transport.
• Adult satellite cells and embryonic muscle progenitors have distinct genetic requirements
  - Nature 460(7255):627-631 (2009)
  Myogenic potential, survival and expansion of mammalian muscle progenitors depend on the myogenic determinants Pax3 and Pax7 embryonically1, and Pax7 alone perinatally2, 3, 4, 5. Several in vitro studies support the critical role of Pax7 in these functions of adult muscle stem cells5, 6, 7, 8 (satellite cells), but a formal demonstration has been lacking in vivo. Here we show, through the application of inducible Cre/loxP lineage tracing9 and conditional gene inactivation to the tibialis anterior muscle regeneration paradigm, that, unexpectedly, when Pax7 is inactivated in adult mice, mutant satellite cells are not compromised in muscle regeneration, they can proliferate and reoccupy the sublaminal satellite niche, and they are able to support further regenerative processes. Dual adult inactivation of Pax3 and Pax7 also results in normal muscle regeneration. Multiple time points of gene inactivation reveal that Pax7 is only required up to the juvenile period when proge! nitor cells make the transition into quiescence. Furthermore, we demonstrate a cell-intrinsic difference between neonatal progenitor and adult satellite cells in their Pax7-dependency. Our finding of an age-dependent change in the genetic requirement for muscle stem cells cautions against inferring adult stem-cell biology from embryonic studies, and has direct implications for the use of stem cells from hosts of different ages in transplantation-based therapy.
• Presenilins are essential for regulating neurotransmitter release
  - Nature 460(7255):632-636 (2009)
  Mutations in the presenilin genes are the main cause of familial Alzheimer's disease. Loss of presenilin activity and/or accumulation of amyloid- peptides have been proposed to mediate the pathogenesis of Alzheimer's disease by impairing synaptic function1, 2, 3, 4, 5. However, the precise site and nature of the synaptic dysfunction remain unknown. Here we use a genetic approach to inactivate presenilins conditionally in either presynaptic (CA3) or postsynaptic (CA1) neurons of the hippocampal Schaeffer-collateral pathway. We show that long-term potentiation induced by theta-burst stimulation is decreased after presynaptic but not postsynaptic deletion of presenilins. Moreover, we found that presynaptic but not postsynaptic inactivation of presenilins alters short-term plasticity and synaptic facilitation. The probability of evoked glutamate release, measured with the open-channel NMDA (N-methyl-d-aspartate) receptor antagonist MK-801, is reduced by presynaptic inactiv! ation of presenilins. Notably, depletion of endoplasmic reticulum Ca2+ stores by thapsigargin, or blockade of Ca2+ release from these stores by ryanodine receptor inhibitors, mimics and occludes the effects of presynaptic presenilin inactivation. Collectively, these results indicate a selective role for presenilins in the activity-dependent regulation of neurotransmitter release and long-term potentiation induction by modulation of intracellular Ca2+ release in presynaptic terminals, and further suggest that presynaptic dysfunction might be an early pathogenic event leading to dementia and neurodegeneration in Alzheimer's disease.
• Macrophage elastase kills bacteria within murine macrophages
  - Nature 460(7255):637-641 (2009)
  Macrophages are aptly positioned to function as the primary line of defence against invading pathogens in many organs, including the lung and peritoneum. Their ability to phagocytose and clear microorganisms has been well documented1, 2. Macrophages possess several substances with which they can kill bacteria, including reactive oxygen species, nitric oxide, and antimicrobial proteins3, 4, 5, 6, 7, 8, 9. We proposed that macrophage-derived proteinases may contribute to the antimicrobial properties of macrophages. Macrophage elastase (also known as matrix metalloproteinase 12 or MMP12) is an enzyme predominantly expressed in mature tissue macrophages10 and is implicated in several disease processes, including emphysema11. Physiological functions for MMP12 have not been described. Here we show that Mmp12-/- mice exhibit impaired bacterial clearance and increased mortality when challenged with both Gram-negative and Gram-positive bacteria at macrophage-rich portals of ent! ry, such as the peritoneum and lung. Intracellular stores of MMP12 are mobilized to macrophage phagolysosomes after the ingestion of bacterial pathogens. Once inside phagolysosomes, MMP12 adheres to bacterial cell walls where it disrupts cellular membranes resulting in bacterial death. The antimicrobial properties of MMP12 do not reside within its catalytic domain, but rather within the carboxy-terminal domain. This domain contains a unique four amino acid sequence on an exposed loop of the protein that is required for the observed antimicrobial activity. The present study represents, to our knowledge, the first report of direct antimicrobial activity by a matrix metallopeptidase, and describes a new antimicrobial peptide that is sequentially and structurally unique in nature.
• MicroRNA-mediated switching of chromatin-remodelling complexes in neural development
  - Nature 460(7255):642-646 (2009)
  One of the most distinctive steps in the development of the vertebrate nervous system occurs at mitotic exit when cells lose multipotency and begin to develop stable connections that will persist for a lifetime1, 2. This transition is accompanied by a switch in ATP-dependent chromatin-remodelling mechanisms that appears to coincide with the final mitotic division of neurons. This switch involves the exchange of the BAF53a (also known as ACTL6a) and BAF45a (PHF10) subunits within Swi/Snf-like neural-progenitor-specific BAF (npBAF) complexes for the homologous BAF53b (ACTL6b) and BAF45b (DPF1) subunits within neuron-specific BAF (nBAF) complexes in post-mitotic neurons. The subunits of the npBAF complex are essential for neural-progenitor proliferation, and mice with reduced dosage for the genes encoding its subunits have defects in neural-tube closure similar to those in human spina bifida3, one of the most serious congenital birth defects. In contrast, BAF53b and the n! BAF complex are essential for an evolutionarily conserved program of post-mitotic neural development and dendritic morphogenesis4, 5. Here we show that this essential transition is mediated by repression of BAF53a by miR-9* and miR-124. We find that BAF53a repression is mediated by sequences in the 3' untranslated region corresponding to the recognition sites for miR-9* and miR-124, which are selectively expressed in post-mitotic neurons. Mutation of these sites led to persistent expression of BAF53a and defective activity-dependent dendritic outgrowth in neurons. In addition, overexpression of miR-9* and miR-124 in neural progenitors caused reduced proliferation. Previous studies have indicated that miR-9* and miR-124 are repressed by the repressor-element-1-silencing transcription factor (REST, also known as NRSF)6. Indeed, expression of REST in post-mitotic neurons led to derepression of BAF53a, indicating that REST-mediated repression of microRNAs directs the essential ! switch of chromatin regulatory complexes.
• Evidence of Xist RNA-independent initiation of mouse imprinted X-chromosome inactivation
  Kalantry S Purushothaman S Bowen RB Starmer J Magnuson T - Nature 460(7255):647-651 (2009)
  XX female mammals undergo transcriptional silencing of most genes on one of their two X chromosomes to equalize X-linked gene dosage with XY males in a process referred to as X-chromosome inactivation (XCI). XCI is an example of epigenetic regulation1. Once enacted in individual cells of the early female embryo, XCI is stably transmitted such that most descendant cells maintain silencing of that X chromosome2. In eutherian mammals, XCI is thought to be triggered by the expression of the non-coding Xist RNA from the future inactive X chromosome (Xi)3, 4, 5; Xist RNA in turn is proposed to recruit protein complexes that bring about heterochromatinization of the Xi6, 7. Here we test whether imprinted XCI, which results in preferential inactivation of the paternal X chromosome (Xp), occurs in mouse embryos inheriting an Xp lacking Xist. We find that silencing of Xp-linked genes can initiate in the absence of paternal Xist; Xist is, however, required to stabilize silencing ! along the Xp. Xp-linked gene silencing associated with mouse imprinted XCI, therefore, can initiate in the embryo independently of Xist RNA.
• Hedgehog signalling is essential for maintenance of cancer stem cells in myeloid leukaemia
  - Nature 460(7255):652 (2009)
  Nature 458, 776–779 (2009) During resubmission of this work, another paper linking CML and Hedgehog signalling was published1. The studies use distinct approaches but come to similar conclusions.
• Hard man to surprise
  - Nature 460(7255):658 (2009)
  A birthday treat.