Hot off the presses! Jul 15 N Engl J Med

The Jul 15 issue of the N Engl J Med is now up on Pubget (About N Engl J Med): 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:

• Buying Health Care, the Individual Mandate, and the Constitution
  Rosenbaum S Gruber J - N Engl J Med 363(5) (2010)
  In Rashomon, a classic film that explores the concept of truth, director Akira Kurosawa presents a story about a single incident retold by four narrators, leaving the audience to figure out what is real. Litigation has a Rashomon-like quality to it: two sides meet in a courtroom and each presents its case, arguing not only that abstract legal principles favor its cause, but equally important, that its version of the event that gave rise to the dispute should be the filter through which the court decides the matter. Three separate cases raising constitutional challenges to the Affordable Care Act .
• The SGR for Physician Payment â€" An Indispensable Abomination
  Aaron HJ - N Engl J Med 363(5) (2010)
  Congress has just extended the life of the sustainable growth rate (SGR) â€" the formula that Medicare uses to calculate physicians' fees â€" for 6 more months. The SGR was enacted in 1998 to hold down the growth of these fees. It replaced a formula with the same objective that wasn't working. It ties the annual growth of Medicare fees to growth of the real gross domestic product, Medicare caseloads, and practice costs. But it ignores the principal reason that health care spending outpaces income growth: the increasing number and complexity of medical interventions. The SGR purports to control total .
• Geographic Variation in Medicare Drug Spending
  Zhang Y Baicker K Newhouse JP - N Engl J Med 363(5) (2010)
  The widespread geographic variation in Medicare spending has garnered a great deal of attention in the health care reform debate, both as a marker of inefficient resource use and as a window into potential strategies for improving the quality and value of U.S. health care. Analyses to date, however, have focused solely on inpatient and outpatient spending (Parts A and B) and have lacked information on pharmaceutical spending (Part D). With drug spending accounting for a rising share of total health care spending, these data limitations hinder interpretation of the variation in spending: do Medicare patients who spend more on .
• The Renaissance in HIV Vaccine Development â€" Future Directions
  Koff WC Berkley SF - N Engl J Med 363(5) (2010)
  From July 18 through July 23, 2010, delegates from around the globe will convene for the biennial International AIDS Conference in Vienna. They will discuss our current risk of losing the war against the human immunodeficiency virus (HIV). Despite an unprecedented outpouring of resources and proliferation of programs, today, for every two patients who begin receiving treatment for HIV, five people are newly infected. Furthermore, new guidelines from the World Health Organization recommending that infected persons begin receiving treatment earlier will significantly increase the number of patients targeted for therapy. If we are to control this pandemic, we must recognize .
• Sipuleucel-T Immunotherapy for Castration-Resistant Prostate Cancer
  - N Engl J Med 363(5):411-422 (2010)
  Prostate cancer is the most common noncutaneous cancer among men in the United States and is the second leading cause of death from cancer in men.1 Localized prostate cancer may be cured with surgery or radiation therapy, but the disease recurs in approximately 20 to 30% of patients. Androgen-deprivation therapy, the most common treatment after recurrence, is effective, but the disease eventually progresses in most patients who receive such treatment.2 For men with metastatic castration-resistant prostate cancer, the median survival in recent phase 3 studies has ranged from 12.2 to 21.7 months.3â€"9 A chemotherapeutic agent, docetaxel, is the only .
• CPR with Chest Compression Alone or with Rescue Breathing
  - N Engl J Med 363(5):423-433 (2010)
  Out-of-hospital cardiac arrest claims hundreds of thousands of lives each year worldwide.1,2 Successful resuscitation is challenging but achievable, requiring an interdependent set of actions that consist of early arrest recognition, early cardiopulmonary resuscitation (CPR), early defibrillation, expert advanced life support, and timely postresuscitation care.3 Early initiation of CPR by a layperson can increase the patient's chances of surviving and having a favorable long-term neurologic recovery.4,5 CPR performed by a layperson has traditionally consisted of chest compressions interspersed with rescue breathing, which allows some measure of both circulation and oxygenation.6 Interest in CPR that focuses on chest compressions and .
• Compression-Only CPR or Standard CPR in Out-of-Hospital Cardiac Arrest
  - N Engl J Med 363(5):434-442 (2010)
  Emergency medical dispatch centers are crucial in supporting and giving instructions to witnesses or bystanders who call for help for patients with cardiac arrest before the arrival of emergency medical services (EMS) personnel.1 Telephone instructions given for cardiopulmonary resuscitation (CPR) seem to be given predominantly for CPR involving chest compression.2 Using an animal model, Berg and colleagues3 found that compression-only CPR and standard CPR (i.e., CPR involving both compression and ventilation) have similar efficacy. In a clinical study in which dispatchers gave randomly assigned instructions to callers for aid to patients with cardiac arrest â€" to attempt resuscitation with the .
• A School-Based Intervention for Diabetes Risk Reduction
  The HEALTHY Study Group - N Engl J Med 363(5) (2010)
  Recent data indicate that 16% of children 6 to 19 years of age in the United States are overweight, and 19% are obese.1 Rates are even higher in economically disadvantaged ethnic minority groups.2 Of all the consequences of childhood obesity,3â€"5 the most serious is the development of type 2 diabetes. Children in whom type 2 diabetes develops are at risk for complications from the disease, including retinopathy, neuropathy, and cardiovascular and renal disease, that can be manifested when they are adults, if not earlier. Schools present opportunities for reducing the risk of diabetes, since no other institution has as .
• Acupuncture for Chronic Low Back Pain
  - N Engl J Med 363(5):454-461 (2010)
  Foreword This Journal feature begins with a case vignette that includes a therapeutic recommendation. A discussion of the clinical problem and the mechanism of benefit of this form of therapy follows. Major clinical studies, the clinical use of this therapy, and potential adverse effects are reviewed. Relevant formal guidelines, if they exist, are presented. The article ends with the authors' clinical recommendations. Stage A 45-year-old construction worker with a 7-year history of intermittent low back pain is seen by his family physician. The pain has gradually increased over the past 4 months, despite pain medications, physical therapy, and two epidural corticosteroid injections. The pain is described as a dull ache in the lumbosacral area with episodic aching in the posterior aspect of both thighs; it worsens with prolonged standing and sitting. He is concerned about losing his job, while at the same time worried that continuing to work could cause further pain. The results of a neurologic examination and a straight-legâ€"raising test .
• Pneumothorax â€" An Uncommon Complication of a Common Procedure
  - N Engl J Med 363(5):462-462 (2010)
  A 92-year-old woman was admitted to the hospital with a severe left-sided ischemic stroke causing altered mental status (i.e., a score of 9 on the Glasgow Coma Scale, on which scores range from 3 to 15, with higher scores indicating increased consciousness), weakness on the right side, and dysphagia. An initial attempt to insert a small-caliber nasogastric tube for feeding was unsuccessful, with coiling of the tube in the mouth. A subsequent attempt with a stiff stylet resulted in easy insertion, without cough or respiratory distress. While awaiting radiography to confirm positioning of the tube, the patient had shortness of .
• Serpentine Supravenous Hyperpigmentation
  - N Engl J Med 363(5) (2010)
  A 61-year-old man with recently diagnosed, inoperable esophageal squamous-cell carcinoma was treated with induction chemotherapy combining cisplatin and fluorouracil and concurrent radiotherapy. Because of worsening renal function, the use of cisplatin was suspended, and the chemotherapy was shifted to weekly high-dose fluorouracil and leucovorin. After the seventh infusion of fluorouracilâ€"leucovorin, thrombosis developed in the right jugular and subclavian veins. This venous thrombosis prohibited further use of the permanent tunneled central-infusion catheter. The eighth infusion of fluorouracilâ€"leucovorin was administered continuously over a 24-hour period by means of a peripheral catheter in the left forearm. A day later, the patient noticed a .
• Case 23-2010
  - N Engl J Med 363(5):463-475 (2010)
  Presentation of Case Dr. David B. Sykes (Hematologyâ€"Oncology): A 49-year-old man was admitted to this hospital because of erythrocytosis, perinephric collections of fluid, and acute renal failure. The patient had been well until 7 years earlier, when routine testing at another facility revealed a hematocrit of 58.1%; the level of erythropoietin was 16.2 mIU per milliliter (reference range, 4.1 to 19.5). Ultrasonography of the abdomen reportedly revealed normal-size kidneys, with no hydronephrosis or cysts, and several hepatic lesions (approximately 1 cm in diameter) that were consistent with hemangiomas. A presumptive diagnosis of polycythemia vera was made, and therapeutic phlebotomy was .
• Don't Mess with the DSMB
  Drazen JM Wood AJ - N Engl J Med 363(5) (2010)
  If the lyrics of the popular Jim Croce song from the early 1970s were adapted for a clinical trialist anthem, the refrain would likely be You don't tug on Superman's cape You don't spit into the wind You don't pull the mask off that old Lone Ranger And you don't mess around with the DSMB. Since the DSMB (data and safety monitoring board) is charged with ensuring that clinical equipoise is maintained as trial data are accrued, it is considered very bad, even self-destructive, behavior for people who are involved with the study to interact with DSMB members on trial-related .
• New Therapies for Castration-Resistant Prostate Cancer
  - N Engl J Med 363(5):479-481 (2010)
  On April 29, 2010, the Food and Drug Administration (FDA) approved a new immunotherapy, sipuleucel-T, for the treatment of patients with asymptomatic or minimally symptomatic castration-resistant prostate cancer. Traditionally, immune-based therapies have been categorized according to whether the agent has direct antitumor effects (so-called passive immunotherapy) or stimulates a host antitumor response (active immunotherapy) and whether the agent elicits a general increase in immune activation (nonspecific) or an immune response based on tumor recognition (specific). Sipuleucel-T is a form of active specific immunotherapy. The sipuleucel-T intervention involves harvesting the patient's peripheral-blood mononuclear cells (PBMCs), culturing them with a chimeric protein .
• In CPR, Less May Be Better
  - N Engl J Med 363(5):481-483 (2010)
  Fifty years have passed since Kouwenhoven, Jude, and Knickerbocker1 proposed external chest compression to provide circulation of blood to the brain and heart after cardiac arrest. Shortly thereafter, mouth-to-mouth rescue breathing was adopted as an essential addition to this lifesaving procedure. Since that time, there has been very little fundamental change in the method or manner of cardiopulmonary resuscitation (CPR). Decades of observational studies have shown that survival is improved if CPR is performed by bystanders rather than being provided only when emergency medical services (EMS) staff arrives. The use of automated external defibrillators by bystanders and the use of .
• Response to Dengue Fever â€" The Good, the Bad, and the Ugly?
  - N Engl J Med 363(5):484-487 (2010)
  Dengue may be the most widespread arboviral illness worldwide. Most patients with dengue infection have only mild disease or classic dengue fever, with influenza-like symptoms, severe headache, and aching joints and muscles. However, in a small percentage of patients â€" maybe half a million people every year â€" potentially lethal forms of dengue called dengue hemorrhagic fever and dengue shock syndrome develop. It has been known for many years that antibodies directed against either of the two surface proteins of the dengue virus (the precursor membrane protein and the envelope protein) can neutralize infectivity and confer protection, although envelope protein .
• Duration of Clopidogrel Therapy with Drug-Eluting Stents
  - N Engl J Med 363(5):488-490 (2010)
  To the Editor: In their article about the duration of dual antiplatelet therapy after implantation of drug-eluting stents, Park and colleagues (April 15 issue)1 report that the use of extended dual antiplatelet therapy in patients who had received drug-eluting stents was not significantly more effective than aspirin monotherapy in reducing the rate of myocardial infarction or death from cardiac causes. Yet the rate of a composite of myocardial infarction, stroke, or death from any cause was nearly significantly higher in patients receiving extended dual antiplatelet therapy than in those receiving aspirin alone. These results are unpredictable and thus are difficult .
• Physician Cost Profiling
  - N Engl J Med 363(5):491-493 (2010)
  To the Editor: Adams et al. (March 18 issue)1 highlight problems in the use of claims data to profile physicians. We agree caution is necessary, but not all “profiling” is problematic. Three modifications can improve estimates: excluding infrequent and expensive items outside the physician's control, focusing on the primary care physician, and being condition-specific. For the profiling of resource use (i.e., cost) related to specific chronic illnesses, we recommend setting aside inpatient care. We evaluated data on 20,073 year-long episodes of care for patients with diabetes (excluding inpatient costs) in a large medical group in 2006, 2007, and 2008. Costs .
• Outpatient Management of Severe COPD
  - N Engl J Med 363(5):493-495 (2010)
  To the Editor: Niewoehner (April 15 issue)1 reports that there are no serious safety problems associated with inhaled bronchodilators. We disagree. First, the Towards a Revolution in COPD Health trial (TORCH; ClinicalTrials.gov number, NCT00268216) showed a significantly increased risk of serious pneumonia with the use of long-acting beta-agonist combinations (relative risk with inhaled corticosteroids plus long-acting beta-agonists vs. long-acting beta-agonists, 1.58; 95% confidence interval [CI], 1.24 to 2.01).2 Second, there was a significantly increased risk of intestinal obstruction (reported as adverse events) with the use of tiotropium (relative risk, 5.55; 95% CI, 1.24 to 24.8) in the Understanding Potential Long-Term .
• What's Keeping Us So Busy in Primary Care?
  - N Engl J Med 363(5):495-496 (2010)
  To the Editor: The article by Baron (April 29 issue)1 paints a fascinating picture of the reality of a five-member single-specialty primary care group practice. One interesting aspect of that practice is that although it employed four medical assistants, five front-desk staff, one business manager, and one billing manager, it did not have any nurse or midlevel practitioners on board at the time of the study. After the study, they hired a registered nurse (RN) to take on “information triage” to reduce some of the physicians' workload. This is a good example of the value of an electronic health record, .
• PLA2R Autoantibodies and Recurrent Membranous Nephropathy after Transplantation
  - N Engl J Med 363(5):496-498 (2010)
  To the Editor: Membranous nephropathy is a leading cause of the nephrotic syndrome in adults. One third of patients have a progressive loss of renal function and reach end-stage renal disease.1 Membranous nephropathy recurs in up to 40% of patients after renal transplantation.2 Recently, Beck et al.3 found that patients with membranous nephropathy had circulating autoantibodies against M-type phospholipase A2 receptor (PLA2R), which in the kidney is exclusively expressed on glomerular podocytes. Binding of PLA2R autoantibodies to this receptor is responsible for the induction of idiopathic membranous nephropathy.4 We report findings regarding a 56-year-old female patient with biopsy-proven membranous .
• Pay-for-Performance System for English Physicians
  - N Engl J Med 363(5):498-498 (2010)
  Pay-for-Performance System for English Physicians Correspondence, N Engl J Med 2008:359;2176-2177. In Table 1 (page 2177), the Exception rate should have been equal to “n2/Ntotal, n3/Ntotal,” rather than “n1/Ntotal, n3/Ntotal.” We regret the error. The article has been corrected at NEJM.org.
• Low Diagnostic Yield of Elective Coronary Angiography
  - N Engl J Med 363(5):498-498 (2010)
  Low Diagnostic Yield of Elective Coronary Angiography Original Article, N Engl J Med 2010:362;886-895. In Table 2 (page 892), the value of the Adjusted Odds Ratio in the “Not requiring dialysis” row under “Renal failure” should have been “1.15,” rather than “1.45.” The article has been corrected at NEJM.org.
• Stenting versus Endarterectomy for Treatment of Carotid-Artery Stenosis
  - N Engl J Med 363(5):498-498 (2010)
  Stenting versus Endarterectomy for Treatment of Carotid-Artery Stenosis Original Article, N Engl J Med 2010:363;11-23. In the third paragraph of the Discussion section (page 21), the third sentence should have ended “.

Hot off the presses! Jul 01 Nat Meth

The Jul 01 issue of the Nat Meth is now up on Pubget (About Nat Meth): 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:

• Bioclouds
  - Nat Meth 7(7):481 (2010)
  Understanding how cloud computing can serve the scientific community is a research question in its own right and one that researchers—with the help of funders—should address.
• The author file: Vivek Jayaraman
  - Nat Meth 7(7):483 (2010)
  Fly brains light the way for neurobehavioral circuits.
• Primer-initiated sequence synthesis to detect and assemble structural variants
  Massouras A Hens K Gubelmann C Uplekar S Decouttere F Rougemont J Cole ST Deplancke B - Nat Meth 7(7):485-486 (2010)
  To the Editor: Structural variants constitute the largest portion of nucleotide variation in genomes, yet their comprehensive characterization based on high-throughput sequencing technologies is still challenging. Here we present primer-initiated sequence synthesis for genomes (PrInSeS-G), a software tool that detects and assembles sequence variants (1 base pair (bp) to |[sim]|10 kilobases (kb)) from single- or paired-end short reads.
• Nano-imaging of membrane topography affects interpretations in cell biology
  Jalink K van Rheenen J - Nat Meth 7(7):486 (2010)
  To the Editor: In their correspondence in Nature Methods, Adler et al. claim to present the first high-resolution topography of plasma membranes in living cells. Using hopping-probe ion conductance microscopy (HPICM), they show that the plasma membrane contains many subresolution membrane folds and point out serious implications for single-particle tracking studies.
• Advent of synthetic life
  - Nat Meth 7(7):487 (2010)
  Researchers synthesized the first functional synthetic bacterial genome; repeating this feat with different bacteria will require further methodological development.
• A toolset for the proficient geneticist
  - Nat Meth 7(7):488-489 (2010)
  New strategies expand the genetic toolkit for transgene expression, lineage tracing and mosaic analysis of gene function in flies and mammalian cells.
• Where do you come from?
  - Nat Meth 7(7):488-489 (2010)
  Live-cell time-lapse imaging of somatic cells undergoing reprogramming raises interesting questions about the mechanism of the process.
• News in brief
  - Nat Meth 7(7):489 (2010)
  Genomics The splicing code, decoded For many years, researchers have attempted to define the combinatorial rules that control alternative splicing. Barash et al. now report a code, implemented in a web tool, that predicts tissue-specific alternative splicing with high accuracy.
• Robotics on the nanoscale
  - Nat Meth 7(7):490 (2010)
  Nanoscale robots can be programmed to walk a DNA origami track.
• Searching for mismatches in a vast genomic landscape
  - Nat Meth 7(7):492 (2010)
  Raw data of millions of sequences used to assemble the reference genomes of ten organisms are analyzed in search of mismatches indicative of editing events. Findings include candidate sites for in vivo DNA and RNA editing, and a common sequencing error.
• Faster, sharper electron microscopy
  - Nat Meth 7(7):494 (2010)
  A technique combining laser and electron pulses is used to achieve nanometer and femtosecond resolution in biological imaging.
• Next-generation sequencing: adjusting to data overload
  Baker M - Nat Meth 7(7):495-499 (2010)
  To keep pace with accelerating sequencing machines, genomics researchers clean house and move toward the cloud.
• Illuminating eukaryotic transcription start sites
  Stamatoyannopoulos JA - Nat Meth 7(7):501-503 (2010)
  The initiation of transcription by RNA polymerase II is a defining event in eukaryotic gene regulation and represents the convergence of multiple cis- and trans-acting regulatory mechanisms. Genes are conventionally held to have a single canonical promoter, which in some cases may be accompanied by alternative promoters located at some distance (typically >500 base pairs (bp)) from the canonical promoter and one another.
• Watching the fly brain in action
  Clark DA de Vries SE Clandinin TR - Nat Meth 7(7):505-506 (2010)
  How does the brain transform sensory input into behavioral output? A strong approach to answering this question is to monitor activity from neurons in awake, behaving animals responding to sensory stimuli. Most of these experiments have been done in primates and rodents, and have identified brain regions and neural pathways involved in perception, sensorimotor integration and decision-making, among others.
• The inside view on plant growth
  Spalding EP - Nat Meth 7(7):506-507 (2010)
  Plant growth is a fine example of how a system in flux, such as a river, nonetheless presents a constant structure. From one day to the next, a plant meristem looks more or less the same despite being the site of prodigious cell division.
• Proteome-wide analysis of protein carboxy termini: C terminomics
  Schilling O Barré O Huesgen PF Overall CM - Nat Meth 7(7):508-511 (2010)
  As proteome-wide C-terminal sequence analysis has been largely intractable, we developed a polymer-based enrichment approach to profile protein C-terminal peptides by mass spectrometry and identified hundreds of C-terminal peptides in the Escherichia coli proteome. We isotopically labeled GluC protease–digested and undigested samples and identified GluC substrates and their cleavage sites by quantification of neo–C-terminal peptides. Our method thus enables global annotation of protein C-terminal posttranslational modifications, including proteolytic truncations.
• Complementary positional proteomics for screening substrates of endo- and exoproteases
  Van Damme P Staes A Bronsoms S Helsens K Colaert N Timmerman E Aviles FX Vandekerckhove J Gevaert K - Nat Meth 7(7):512-515 (2010)
  We describe a positional proteomics approach to simultaneously analyze N- and C-terminal peptides and used it to screen for human protein substrates of granzyme B and carboxypeptidase A4 in human cell lysates. This approach allowed comprehensive proteome studies, and we report the identification of 965 database-annotated protein C termini, 334 neo–C termini resulting from granzyme B processing and 16 neo–C termini resulting from carboxypeptidase A4 processing.
• Simultaneous intracellular chloride and pH measurements using a GFP-based sensor
  Arosio D Ricci F Marchetti L Gualdani R Albertazzi L Beltram F - Nat Meth 7(7):516-518 (2010)
  Chloride and protons perform important closely related roles in many cellular responses. Here we developed a ratiometric biosensor, ClopHensor, based on a highly chloride-sensitive Aequorea victoria GFP variant that is suited for the combined real-time optical detection of pH changes and chloride fluxes in live cells. We detected high chloride concentration in large dense-core exocytosis granules by targeting ClopHensor to these intracellular compartments.
• Estimating prion concentration in fluids and tissues by quantitative PMCA
  Chen B Morales R Barria MA Soto C - Nat Meth 7(7):519-520 (2010)
  Prions, the proteinaceous infectious agent responsible for prion diseases, can be detected with high sensitivity by protein misfolding cyclic amplification (PMCA) technology. Here we describe a quantitative PMCA procedure to calculate the concentration of very low levels of prions in biological samples. Using this procedure, we determined the quantities of misfolded prion protein (PrPSc) in brain, spleen, blood and urine of scrapie-affected hamsters.
• A paired-end sequencing strategy to map the complex landscape of transcription initiation
  - Nat Meth 7(7):521-527 (2010)
  Recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by RNA polymerase II, helping to define several initiation patterns in which transcription start sites (TSSs) cluster in both narrow and broad genomic windows. Here we describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. We used this strategy to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly promoters exhibited distinct initiation patterns, which were linked to specific promoter sequence motifs. Furthermore, we identified many 5′ capped transcripts originating from coding exons; our analyses support that they are unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications. We demonstrated paired-end TSS analysis to be a powerful method to uncover ! the transcriptional complexity of eukaryotic genomes.
• Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan
  Plessy C Bertin N Takahashi H Simone R Salimullah M Lassmann T Vitezic M Severin J Olivarius S Lazarevic D Hornig N Orlando V Bell I Gao H Dumais J Kapranov P Wang H Davis CA Gingeras TR Kawai J Daub CO Hayashizaki Y Gustincich S Carninci P - Nat Meth 7(7):528-534 (2010)
  Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and noncoding RNAs with capped 5′ ends that vary in size. Methods to identify the 5′ ends of transcripts will facilitate the discovery of new promoters and 5′ ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we developed nano–cap analysis of gene expression (nanoCAGE), a method that captures the 5′ ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5′ ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.
• Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior
  Seelig JD Chiappe ME Lott GK Dutta A Osborne JE Reiser MB Jayaraman V - Nat Meth 7(7):535-540 (2010)
  Drosophila melanogaster is a model organism rich in genetic tools to manipulate and identify neural circuits involved in specific behaviors. Here we present a technique for two-photon calcium imaging in the central brain of head-fixed Drosophila walking on an air-supported ball. The ball's motion is tracked at high resolution and can be treated as a proxy for the fly's own movements. We used the genetically encoded calcium sensor, GCaMP3.0, to record from important elements of the motion-processing pathway, the horizontal-system lobula plate tangential cells (LPTCs) in the fly optic lobe. We presented motion stimuli to the tethered fly and found that calcium transients in horizontal-system neurons correlated with robust optomotor behavior during walking. Our technique allows both behavior and physiology in identified neurons to be monitored in a genetic model organism with an extensive repertoire of walking behaviors.
• cnvHap: an integrative population and haplotype–based multiplatform model of SNPs and CNVs
  Coin LJ Asher JE Walters RG El-Sayed Moustafa JS de Smith AJ Sladek R Balding DJ Froguel P Blakemore AI - Nat Meth 7(7):541-546 (2010)
  Although genome-wide association studies have uncovered single-nucleotide polymorphisms (SNPs) associated with complex disease, these variants account for a small portion of heritability. Some contribution to this 'missing heritability' may come from copy-number variants (CNVs), in particular rare CNVs; but assessment of this contribution remains challenging because of the difficulty in accurately genotyping CNVs, particularly small variants. We report a population-based approach for the identification of CNVs that integrates data from multiple samples and platforms. Our algorithm, cnvHap, jointly learns a chromosome-wide haplotype model of CNVs and cluster-based models of allele intensity at each probe. Using data for 50 French individuals assayed on four separate platforms, we found that cnvHap correctly detected at least 14% more deleted and 50% more amplified genotypes than PennCNV or QuantiSNP, with an 82% and 115% improvement for aberrations containing <10 probes! . Combining data from multiple platforms additionally improved sensitivity.
• Imaging plant growth in 4D: robust tissue reconstruction and lineaging at cell resolution
  Fernandez R Das P Mirabet V Moscardi E Traas J Verdeil JL Malandain G Godin C - Nat Meth 7(7):547-553 (2010)
  Quantitative information on growing organs is required to better understand morphogenesis in both plants and animals. However, detailed analyses of growth patterns at cellular resolution have remained elusive. We developed an approach, multiangle image acquisition, three-dimensional reconstruction and cell segmentation–automated lineage tracking (MARS-ALT), in which we imaged whole organs from multiple angles, computationally merged and segmented these images to provide accurate cell identification in three dimensions and automatically tracked cell lineages through multiple rounds of cell division during development. Using these methods, we quantitatively analyzed Arabidopsis thaliana flower development at cell resolution, which revealed differential growth patterns of key regions during early stages of floral morphogenesis. Lastly, using rice roots, we demonstrated that this approach is both generic and scalable.
• Enhanced neuronal RNAi in C. elegans using SID-1
  Calixto A Chelur D Topalidou I Chen X Chalfie M - Nat Meth 7(7):554-559 (2010)
  We expressed SID-1, a transmembrane protein from Caenorhabditis elegans that is required for systemic RNA interference (RNAi), in C. elegans neurons. This expression increased the response of neurons to double-stranded (ds)RNA delivered by feeding. Mutations in the lin-15b and lin-35 genes enhanced this effect. Worms expressing neuronal SID-1 showed RNAi phenotypes when fed with bacteria expressing dsRNA for known neuronal genes and for uncharacterized genes with no previously known neuronal phenotypes. Neuronal expression of sid-1 decreased nonneuronal RNAi, suggesting that neurons expressing transgenic sid-1(+) served as a sink for dsRNA. This effect, or a sid-1(–) background, can be used to uncover neuronal defects for lethal genes. Expression of sid-1(+) from cell-specific promoters in sid-1 mutants results in cell-specific feeding RNAi. We used these strains to identify a role for integrin signaling genes in mechanosensation.
• Probabilistic density maps to study global endomembrane organization
  Schauer K Duong T Bleakley K Bardin S Bornens M Goud B - Nat Meth 7(7):560-566 (2010)
  We developed a computational imaging approach that describes the three-dimensional spatial organization of endomembranes from micromanipulation-normalized mammalian cells with probabilistic density maps. Applied to several well-known marker proteins, this approach revealed the average steady-state organization of early endosomes, multivesicular bodies or lysosomes, endoplasmic reticulum exit sites, the Golgi apparatus and Golgi-derived transport carriers in crossbow-shaped cells. The steady-state organization of each tested endomembranous population was well-defined, unique and in some cases depended on the cellular adhesion geometry. Density maps of all endomembrane populations became stable when pooling several tens of cells only and were reproducible in independent experiments, allowing construction of a standardized cell model. We detected subtle changes in steady-state organization induced by disruption of the cellular cytoskeleton, with statistical significance o! bserved for just 20 cells. Thus, combining micropatterning with construction of endomembrane density maps allows the systematic study of intracellular trafficking determinants.
• Corrigendum: A photoconvertible reporter of the ubiquitin-proteasome system in vivo
  - Nat Meth 7(7):567 (2010)
  Introduction Nat. Methods 7, 473–478 (2010); published online 9 May 2010; corrected after print 17 June 2010. ADVERTISEMENT In the version of this paper originally published, a reference to previous work on the use of Dendra2 as a reporter for protein stability in cultured cells should have been included (ref. 35). The error has been corrected in the PDF and HTML versions of the article.

Hot off the presses! Jul 01 Nat Rev Immunol

The Jul 01 issue of the Nat Rev Immunol is now up on Pubget (About Nat Rev Immunol): 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:

• From the editors
  - Nat Rev Immunol 10(7):461 (2010)
  For goalkeepers playing in this month's World Cup, quick reactions are essential for stopping that ball from reaching the back of the net. Similarly, a rapid response by the innate immune system is crucial for protecting the body against incoming threats.
• T cell memory: DCs gather crumbs to feed memory
  - Nat Rev Immunol 10(7):462 (2010)
  Acute viral infections are rapidly cleared by the host immune system, but there is evidence that depots of viral antigen can persist after the resolution of infection and sustain memory T cells. Previous studies suggested that these reservoirs are located in lymph nodes draining the site of infection; Kim et al.
• T cell responses: Vesicle fusion keeps cells moving
  - Nat Rev Immunol 10(7):463 (2010)
  Migrating cells adopt a polarized morphology, characterized by a leading-edge lamellipodia and a trailing-edge uropod, and move through tissues by sequential adhesion and release steps. Understanding the molecular mechanisms by which chemoattractants promote such migration is an important goal for immunologists and cell biologists.
• In brief: Autoimmunity, Tumour immunology, T cells
  - Nat Rev Immunol 10(7):463 (2010)
  Functionally defective germline variants of sialic acid acetylesterase in autoimmunity Surolia, I.et al. Nature16 Jun 2010 (doi:10.1038/nature09115)
• Autoimmunity: New players in lupus nephritis
  - Nat Rev Immunol 10(7):464 (2010)
  Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody (IgM, IgG and IgA)-containing immune complexes that are deposited in, and cause damage to, numerous organs — including the kidneys (lupus nephritis). In addition to B cells, T helper 1 (TH1) cells, TH17 cells, macrophages and dendritic cells have all been shown to have a role in SLE.
• Inflammation: Hope for sepsis treatment
  - Nat Rev Immunol 10(7):464 (2010)
  The incidence of sepsis (and death from septic shock) is increasing, and treatments are still inadequate. Now a study in Science offers promise for a new treatment option involving blockade of sphingosine kinase 1 (SPHK1), which protected mice from lethal and uncontrolled systemic inflammation induced by bacterial products or polymicrobial sepsis.
• Antiviral immunity: Speed and endurance required
  - Nat Rev Immunol 10(7):465 (2010)
  New research shows that the innate immune response to cytosolic viruses through retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) must be both rapid and sustained and that these properties are mediated by different signalling pathways. Sustained antiviral signalling at mitochondrial membranes is supported and preceded by the rapid response of peroxisome-based antiviral pathways.
• Tumour immunology: Run and hide
  - Nat Rev Immunol 10(7):466 (2010)
  Metastasis is the main cause of cancer-associated death and, therefore, it is important to determine when and how tumour cells disseminate from the primary tumour. It was previously thought that metastasis occurs late in cancer development, but more recent evidence suggests that it occurs early during tumour progression.
• Regulatory T cells: Nurtured by TGFβ
  - Nat Rev Immunol 10(7):466 (2010)
  Transforming growth factor-β (TGFβ) is an important regulator of T cell tolerance, in part through the induction of regulatory T (TReg) cells in the periphery. Now, a new study shows that it also functions in the thymus where it protects thymocytes from deletion and promotes natural TReg cell development and homeostasis.
• γδ T cell effector functions: a blend of innate programming and acquired plasticity
  Bonneville M O'Brien RL Born WK - Nat Rev Immunol 10(7):467 (2010)
  γδ T cells have several innate cell-like features that allow their early activation following recognition of conserved stress-induced ligands. Here we review recent observations revealing the ability of γδ T cells to rapidly produce cytokines that regulate pathogen clearance, inflammation and tissue homeostasis in response to tissue stress. These studies provide insights into how they acquire these properties, through both developmental programming in the thymus and functional polarization in the periphery. Innate features of γδ T cells underlie their non-redundant role in several physiopathological contexts and are therefore being exploited in the design of new immunotherapeutic approaches.
• Innate IL-17-producing cells: the sentinels of the immune system
  Cua DJ Tato CM - Nat Rev Immunol 10(7):479 (2010)
  The cytokine interleukin-17 (IL-17) has received considerable attention since the discovery of a distinct CD4+ T helper (TH) cell subset that produces it, known as the TH17 cell subset. Despite the fact that most of the recent literature describes IL-17 as a T cell-secreted cytokine, much of the IL-17 released during an inflammatory response is produced by innate immune cells. In this Review, we explore the many innate immune cell populations that are an early source of IL-17 in response to stress, injury or pathogens. These early sources have been shown to have a central role in the initiation of IL-17-dependent immune responses, even before the first CD4+T cell sees its cognate antigen and initiates the TH17 cell developmental programme.
• FOXP3+ regulatory T cells in the human immune system
  Sakaguchi S Miyara M Costantino CM Hafler DA - Nat Rev Immunol 10(7):490 (2010)
  Forkhead box P3 (FOXP3)+ regulatory T (TReg) cells are potent mediators of dominant self tolerance in the periphery. But confusion as to the identity, stability and suppressive function of human TReg cells has, to date, impeded the general therapeutic use of these cells. Recent studies have suggested that human TReg cells are functionally and phenotypically diverse. Here we discuss recent findings regarding human TReg cells, including the ontogeny and development of TReg cell subsets that have naive or memory phenotypes, the unique mechanisms of suppression mediated by TReg cell subsets and factors that regulate TReg cell lineage commitment. We discuss future studies that are needed for the successful therapeutic use of human TReg cells.
• Immune cell crosstalk in type 1 diabetes
  Lehuen A Diana J Zaccone P Cooke A - Nat Rev Immunol 10(7):501 (2010)
  The development of type 1 diabetes involves a complex interaction between pancreatic β-cells and cells of both the innate and adaptive immune systems. Analyses of the interactions between natural killer (NK) cells, NKT cells, different dendritic cell populations and T cells have highlighted how these different cell populations can influence the onset of autoimmunity. There is evidence that infection can have either a potentiating or inhibitory role in the development of type 1 diabetes. Interactions between pathogens and cells of the innate immune system, and how this can influence whether T cell activation or tolerance occurs, have been under close scrutiny in recent years. This Review focuses on the nature of this crosstalk between the innate and the adaptive immune responses and how pathogens influence the process.
• Immunity and immunopathology to viruses: what decides the outcome?
  Rouse BT Sehrawat S - Nat Rev Immunol 10(7):514 (2010)
  Many viruses infect humans and most are controlled satisfactorily by the immune system with limited damage to host tissues. Some viruses, however, do cause overt damage to the host, either in isolated cases or as a reaction that commonly occurs after infection. The outcome is influenced by properties of the infecting virus, the circumstances of infection and several factors controlled by the host. In this Review, we focus on host factors that influence the outcome of viral infection, including genetic susceptibility, the age of the host when infected, the dose and route of infection, the induction of anti-inflammatory cells and proteins, as well as the presence of concurrent infections and past exposure to cross-reactive agents.
• Structure–function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design
  Zolla-Pazner S Cardozo T - Nat Rev Immunol 10(7):527 (2010)
  One of the main challenges of developing an HIV-1 vaccine lies in eliciting immune responses that can overcome the antigenic variability exhibited by HIV. Most HIV-1 vaccine development has focused on inducing immunity to conserved regions of the HIV-1 envelope. However, new studies of the sequence-variable regions of the HIV-1 gp120 envelope glycoprotein have shown that there are conserved immunological and structural features in these regions. Recombinant immunogens that include these features may provide the means to address the antigenic diversity of HIV-1 and induce protective antibodies that can prevent infection with HIV-1.

Hot off the presses! Jul 01 Nat Rev Cancer

The Jul 01 issue of the Nat Rev Cancer is now up on Pubget (About Nat Rev Cancer): 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:

• From the editors
  - Nat Rev Cancer 10(7):449 (2010)
  The American Society of Clinical Oncology held its annual meeting at the start of June and reported several findings from a number of clinical trials investigating new targeted agents. Among these was a Phase III trial of an antibody, ipilimumab, which inhibits cytotoxic T lymphocyte antigen 4 (CTLA4).
• Tumorigenesis: Hormonally driven
  - Nat Rev Cancer 10(7):451 (2010)
  The ovarian hormones oestrogen and progesterone are inextricably linked to breast cancer. Not only do their levels influence disease risk and prognosis, but manipulating their activity also forms the basis for gold standard treatments.
• Metastasis: Pushing on through
  - Nat Rev Cancer 10(7):452 (2010)
  Metastasis is a complex process of which we still understand little, but the parallels between metastasis and cell invasion during development can give us some clues. During the development of a connection between uterine cells and vulval cells in the nematode Caenorhabditis elegans, one cell, the anchor cell (AC), has to invade through a basement membrane.
• Melanoma: Don't let sleeping cells lie
  - Nat Rev Cancer 10(7):452 (2010)
  Melanomas are heterogenous tumours that are highly metastastic, but patients with this disease can be cured if they are treated at an early stage before tumour cells colonize distant organs. Therefore, keeping the growth of primary tumours and metastases under control is one possible route to successful therapy.
• Therapy: An unhelpful hand
  - Nat Rev Cancer 10(7):453 (2010)
  Increased signalling through the insulin-like growth factor (IGF) pathway has been implicated in the progression of several types of human cancer. The IGF2 ligand is frequently overexpressed in colon and breast cancers, and inhibitors of one its receptors, IGF1 receptor (IGF1R), are in clinical trials.
• Transcription: We bonded — now make a decision
  - Nat Rev Cancer 10(7):454 (2010)
  p53 regulates the expression of genes involved in cell cycle arrest and apoptosis by binding to a DNA consensus sequence. Two recent papers by the groups of Thorsten Stiewe and Joaquín Espinosa provide insight into the mechanisms that influence the decision making between these two events.
• Mutation: It's the CpG content that counts
  - Nat Rev Cancer 10(7):454 (2010)
  The rate of neutral mutations — those that are not subject to natural selection — shows substantial variation, but the factors contributing to mutational rate have remained elusive. Now, new evidence indicates that the CpG content of DNA can influence the mutation rate of non-CpG-containing sequences, suggesting that the intrinsic properties of DNA sequences may be more important than the chromosomal environment in determining mutation rates and genome integrity.
• Oncogenes: Adding more to the Myc story
  - Nat Rev Cancer 10(7):455 (2010)
  The Myc family of transcription factors are well-known oncoproteins and three new studies contribute important insights into mechanisms of MYC regulation and the roles of MYCN in tumorigenesis and progression.Richard Young and colleagues demonstrate that MYC plays a key part in regulating transcriptional elongation by RNA polymerase II (Pol II).
• Covalent histone modifications — miswritten, misinterpreted and mis-erased in human cancers
  - Nat Rev Cancer 10(7):457 (2010)
  Post-translational modification of histones provides an important regulatory platform for processes such as gene transcription and DNA damage repair. It has become increasingly apparent that the misregulation of histone modification, which is caused by the deregulation of factors that mediate the modification installation, removal and/or interpretation, actively contributes to human cancer. In this Review, we summarize recent advances in understanding the interpretation of certain histone methylations by plant homeodomain finger-containing proteins, and how misreading, miswriting and mis-erasing of histone methylation marks can be associated with oncogenesis and progression. These observations provide us with a greater mechanistic understanding of epigenetic alterations in human cancers and might also help direct new therapeutic interventions in the future.
• Non-germline genetically engineered mouse models for translational cancer research
  - Nat Rev Cancer 10(7):470 (2010)
  Genetically engineered mouse models (GEMMs) of cancer have affected virtually all areas of cancer research. However, the accelerated discovery of new cancer genes emerging from large-scale cancer genomics and new chemical entities pouring from the drug discovery pipeline have strained the capacity of traditional germline mouse models to provide crucial insights. This Review introduces new approaches to modelling cancer, with emphasis on a growing collection of non-germline GEMMs (nGEMMs). These offer flexibility, speed and uniformity at reduced costs, thus paving the way for much needed throughput and practical preclinical therapeutic testing models.
• Cartilage tumours and bone development: molecular pathology and possible therapeutic targets
  Bovée JV Hogendoorn PC Wunder JS Alman BA - Nat Rev Cancer 10(7):481 (2010)
  As a group, cartilage tumours are the most common primary bone lesions. They range from benign lesions, such as enchondromas and osteochondromas, to malignant chondrosarcoma. The benign lesions result from the deregulation of the hedgehog signalling pathway, which is involved in normal bone development. These lesions can be the precursors of malignant chondrosarcomas, which are notoriously resistant to conventional chemotherapy and radiotherapy. Cytogenetic studies and mouse models are beginning to identify genes and signalling pathways that have roles in tumour progression, such as hedgehog, p53, insulin-like growth factor, cyclin-dependent kinase 4, hypoxia-inducible factor, matrix metalloproteinases, SRC and AKT, suggesting potential new therapeutic approaches.
• Sphingosine 1-phosphate and cancer
  Pyne NJ Pyne S - Nat Rev Cancer 10(7):489 (2010)
  There is substantial evidence that sphingosine 1-phosphate (S1P) is involved in cancer. S1P regulates processes such as inflammation, which can drive tumorigenesis; neovascularization, which provides cancer cells with nutrients and oxygen; and cell growth and survival. This occurs at multiple levels and involves S1P receptors, sphingosine kinases, S1P phosphatases and S1P lyase. This Review summarizes current research findings and examines the potential for new therapeutics designed to alter S1P signalling and function in cancer.
• Targeting the tumour vasculature: insights from physiological angiogenesis
  - Nat Rev Cancer 10(7):505 (2010)
  The cardiovascular system ensures the delivery of nutrients, oxygen, and blood and immune cells to all organs and tissues: it is also responsible for the removal of waste metabolites. The vascular system develops and matures through two tightly regulated processes: vasculogenesis and angiogenesis. Angiogenesis is active only under specific physiological conditions in healthy adults but the vasculature can be aberrantly activated to generate new blood vessels during pathological conditions such as cancer and chronic inflammation. In this Opinion article we discuss the parallels and differences in the angiogenic process under either a physiological or a pathological state, especially tumorigenesis.
• Envisioning the future of early anticancer drug development
  Yap TA Sandhu SK Workman P de Bono JS - Nat Rev Cancer 10(7):514 (2010)
  The development of novel molecularly targeted cancer therapeutics remains slow and expensive with many late-stage failures. There is an urgent need to accelerate this process by improving early clinical anticancer drug evaluation through modern and rational trial designs that incorporate predictive, pharmacokinetic, pharmacodynamic, pharmacogenomic and intermediate end-point biomarkers. In this article, we discuss current approaches and propose strategies that will potentially maximize benefit to patients and expedite the regulatory approvals of new anticancer drugs.
• Correspondence: The ABC of glycosylation
  Perego P Gatti L Beretta GL - Nat Rev Cancer 10(7):523 (2010)
  We read with great interest the Opinion article by Jamie Fletcher and colleagues, ABC transporters in cancer: more than just drug efflux pumps. Nature Rev. Cancer. 10, 147–156 (2010)
• Correspondence: Breast and prostate cancer: familial associations
  - Nat Rev Cancer 10(7):523 (2010)
  In a recent Opinion article by Gail Risbridger and colleagues, Breast and prostate cancer: more similar than different (Nature Rev. Cancer 10, 205–212 (2010)), the extensive biological similarities of the hormone-dependant pathways of breast and prostate cancers were discussed1.
• Corrigendum: Genetic variation in microRNA networks: the implications for cancer research
  - Nat Rev Cancer 10(7):523 (2010)
  There were several mistakes in TABLES 1–3 of this article. In TABLE 1 on page 385, for rs2910164 in hepatocelluar carcinoma the odds ratio data refer to males only. For rs11614913 in lung cancer the odds ratio is for both sexes and not for males only. For rs11614913 in oesophageal cancer the reference genotype should be CC/CT and the analysed genotype should be TT. For rs11614913 in breast cancer the reference genotype should be CC and the analysed genotypes should be CT and then TT. For rs895819 in breast cancer the reference genotype should be CT. In TABLE 2 on page 396, for the SEDT8 alleles, the miRNA binds the derived alleles and not the ancestral alleles. For the BCTRP allele, the miRNA binds deletion alleles that are derived and not insertion alleles that are ancestral. For the BMPR1B allele, the miRNA binds the C allele and not the derived allele. For the CD86 allele, the miRNA binds the ancestral allele and not the derived allele. In TABLE 3 on page 398, the! odds ratio given for GEMIN4 rs7813 is for all cases of renal cell carcinoma, not just clear cell carcinoma as indicated. For GEMIN3 rs197414 the cancer site should be bladder and not renal cell carcinoma and the reference is 35 and not 111. This has been corrected online.