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1.  Structure and inhibition of EV-D68, a virus that causes respiratory illness in children 
Science (New York, N.Y.)  2015;347(6217):71-74.
Enterovirus D68 (EV-D68) is a member of Picornaviridae and is a causative agent of recent outbreaks in the USA of respiratory illness in children. We report here the crystal structures of EV-D68 and its complex with pleconaril, a capsid binding compound that had been developed as an anti-rhinovirus drug. The hydrophobic drug binding pocket in viral protein 1 contained density that is consistent with a fatty acid of about 10 carbon atoms. This density could be displaced by pleconaril. We also showed that pleconaril inhibits EV-D68 at a half maximal effective concentration (EC50) of 430 nM and might, therefore, be a possible drug candidate to alleviate EV-D68 outbreaks.
PMCID: PMC4307789  PMID: 25554786
2.  Caffeine in floral nectar enhances a pollinator’s memory of reward 
Science (New York, N.Y.)  2013;339(6124):1202-1204.
Plant defence compounds occur in floral nectar, but their ecological role is not well-understood. We provide the first evidence that plant compounds pharmacologically alter pollinator behaviour by enhancing their memory of reward. Honeybees rewarded with caffeine, which occurs naturally in nectar of Coffea and Citrus species, were three times more likely to remember a learned floral scent than those rewarded with sucrose alone. Caffeine potentiated responses of mushroom body neurons involved in olfactory learning and memory by acting as an adenosine receptor antagonist. Caffeine concentrations in nectar never exceeded the bees’ bitter taste threshold, implying that pollinators impose selection for nectar that is pharmacologically active but not repellent. By using a drug to enhance memories of reward, plants secure pollinator fidelity and improve reproductive success.
PMCID: PMC4521368  PMID: 23471406
3.  Expansion Microscopy 
Science (New York, N.Y.)  2015;347(6221):543-548.
In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. Here we report the discovery that, by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification. By covalently anchoring specific labels located within the specimen directly to the polymer network, labels spaced closer than the optical diffraction limit can be isotropically separated and optically resolved, a process we call expansion microscopy (ExM). Thus, this process can be used to perform scalable super-resolution microscopy with diffraction-limited microscopes. We demonstrate ExM with effective ~70 nm lateral resolution in both cultured cells and brain tissue, performing three-color super-resolution imaging of ~107 μm3 of the mouse hippocampus with a conventional confocal microscope.
PMCID: PMC4312537  PMID: 25592419
4.  Dynamic signaling by T follicular helper cells during germinal center B cell selection 
Science (New York, N.Y.)  2014;345(6200):1058-1062.
T follicular helper (TFH) cells select high-affinity, antibody-producing B cells for clonal expansion in germinal centers (GCs), but the nature of their interaction is not well defined. Using intravital imaging, we found that selection is mediated by large but transient contacts between TFH and GC B cells presenting the highest levels of cognate peptide bound to major histocompatibility complex II. These interactions elicited transient and sustained increases in TFH intracellular free calcium (Ca2+) that were associated with TFH cell coexpression of the cytokines interleukin-4 and -21. However, increased intracellular Ca2+ did not arrest TFH cell migration. Instead, TFH cells remained motile and continually scanned the surface of many GC B cells, forming short-lived contacts that induced selection through further repeated transient elevations in intracellular Ca2+.
PMCID: PMC4519234  PMID: 25170154
5.  Mutations in FUS, an RNA Processing Protein, Cause Familial Amyotrophic Lateral Sclerosis Type 6 
Science (New York, N.Y.)  2009;323(5918):1208-1211.
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that is familial in 10% of cases. We have identified a missense mutation in the gene encoding fused in sarcoma (FUS) in a British kindred, linked to ALS6. In a survey of 197 familial ALS index cases, we identified two further missense mutations in eight families. Postmortem analysis of three cases with FUS mutations showed FUS-immunoreactive cytoplasmic inclusions and predominantly lower motor neuron degeneration. Cellular expression studies revealed aberrant localization of mutant FUS protein. FUS is involved in the regulation of transcription and RNA splicing and transport, and it has functional homology to another ALS gene, TARDBP, which suggests that a common mechanism may underlie motor neuron degeneration.
PMCID: PMC4516382  PMID: 19251628
6.  Beyond Access vs. Protection in Trials of Innovative Therapies 
Science (New York, N.Y.)  2010;328(5980):829-830.
Review of first-in-human trials should aim to safeguard the integrity of the scientific enterprise through a focus on pre-clinical and clinical study quality.
PMCID: PMC4516403  PMID: 20466907 CAMSID: cams4899
7.  Rethinking Research Ethics: The Case of Postmarketing Trials 
Science (New York, N.Y.)  2012;336(6081):544-545.
Phase IV studies are often criticized for poor scientific standards. Yet they provide an important resource for addressing evidence shortfalls in drug safety, comparative effectiveness, and real-world utility. Current research ethics policies, and contemplated revisions to them, do not provide an adequate framework for preventing social harms that result from poor post-marketing research practice. Rather than focus exclusively on the welfare and interests of human volunteers, research policies and ethics should also safeguard the integrity of the research enterprise as a system for producing reliable medical evidence. We close by briefly describing how an integrity framework might be implemented for phase IV studies.
PMCID: PMC4516406  PMID: 22556237 CAMSID: cams4900
8.  SARM1 activation triggers axon degeneration locally via NAD+ destruction 
Science (New York, N.Y.)  2015;348(6233):453-457.
Axon degeneration is an intrinsic self-destruction program that underlies axon loss during injury and disease. Sterile alpha and TIR motif containing 1 (SARM1) protein is an essential mediator of axon degeneration. We report that SARM1 initiates a local destruction program involving rapid breakdown of NAD+ after injury. We used an engineered protease-sensitized SARM1 to demonstrate that SARM1 activity is required after axon injury to induce axon degeneration. Dimerization of the Toll-Interleukin Receptor (TIR) domain of SARM1 alone was sufficient to induce locally-mediated axon degeneration. Formation of the SARM1 TIR dimer triggered rapid breakdown of NAD+, whereas SARM1-induced axon destruction could be counteracted by increased NAD+ synthesis. SARM1-induced depletion of NAD+ may explain the potent axon protection in Wallerian Degeneration slow (Wlds) mutant mice.
PMCID: PMC4513950  PMID: 25908823
9.  The HydG Enzyme Generates an Fe(CO)2(CN) Synthon in Assembly of the FeFe Hydrogenase H-Cluster 
Science (New York, N.Y.)  2014;343(6169):424-427.
Three iron-sulfur proteins–HydE, HydF, and HydG–play a key role in the synthesis of the [2Fe]H component of the catalytic H-cluster of FeFe hydrogenase. The radical S-adenosyl-l-methionine enzyme HydG lyses free tyrosine to produce p-cresol and the CO and CN− ligands of the [2Fe]H cluster. Here, we applied stopped-flow Fourier transform infrared and electron-nuclear double resonance spectroscopies to probe the formation of HydG-bound Fe-containing species bearing CO and CN− ligands with spectroscopic signatures that evolve on the 1- to 1000-second time scale. Through study of the 13C, 15N, and 57Fe isotopologs of these intermediates and products, we identify the final HydG-bound species as an organometallic Fe(CO)2(CN) synthon that is ultimately transferred to apohydrogenase to form the [2Fe]H component of the H-cluster.
PMCID: PMC4514031  PMID: 24458644
10.  The in vivo dynamics of antigenic variation in Trypanosoma brucei 
Science (New York, N.Y.)  2015;347(6229):1470-1473.
Trypanosoma brucei, a causative agent of African Sleeping Sickness, constantly changes its dense variant surface glycoprotein (VSG) coat to avoid elimination by the immune system of its mammalian host, using an extensive repertoire of dedicated genes. However, the dynamics of VSG expression in T. brucei during an infection are poorly understood. We have developed a method, based on de novo assembly of VSGs, for quantitatively examining the diversity of expressed VSGs in any population of trypanosomes, and thereby monitored VSG population dynamics in vivo. Our experiments revealed unexpected diversity within parasite populations, and a mechanism for diversifying the genome-encoded VSG repertoire. The interaction between T. brucei and its host is substantially more dynamic and nuanced than previously expected.
PMCID: PMC4514441  PMID: 25814582
11.  Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling 
Science (New York, N.Y.)  2014;345(6200):1065-1070.
Histone H3 lysine27-to-methionine (H3K27M) gain-of-function mutations occur in highly aggressive pediatric gliomas. Here, we establish a Drosophila animal model for the pathogenic histone H3K27M mutation and show that its overexpression resembles Polycomb repressive complex 2 (PRC2) loss-of-function phenotypes, causing de-repression of PRC2 target genes and developmental perturbations. Similarly, a H3K9M mutant depletes H3K9 methylation levels and suppresses position-effect variegation in various Drosophila tissues. The histone H3K9 demethylase KDM3B/JHDM2 associates with H3K9M nucleosomes and its overexpression in Drosophila results in loss of H3K9 methylation levels and heterochromatic silencing defects. Here we establish histone lysine-to-methionine mutants as robust in vivo tools for inhibiting methylation pathways that also function as biochemical reagents for capturing site-specific histone-modifying enzymes, thus providing molecular insight into chromatin-signaling pathways.
PMCID: PMC4508193  PMID: 25170156
12.  A Memory of Errors in Sensorimotor Learning 
Science (New York, N.Y.)  2014;345(6202):1349-1353.
The current view of motor learning suggests that when we revisit a task, the brain recalls the motor commands it previously learned. In this view, motor memory is a memory of motor commands, acquired through trial-and-error and reinforcement. Here we show that the brain controls how much it is willing to learn from the current error through a principled mechanism that depends on the history of past errors. This suggests that the brain stores a previously unknown form of memory, a memory of errors. A mathematical formulation of this idea provides insights into a host of puzzling experimental data, including savings and meta-learning, demonstrating that when we are better at a motor task, it is partly because the brain recognizes the errors it experienced before.
PMCID: PMC4506639  PMID: 25123484
13.  Interferon λ cures persistent murine norovirus infection in the absence of adaptive immunity 
Science (New York, N.Y.)  2014;347(6219):269-273.
Norovirus gastroenteritis is a major public health burden worldwide. Although fecal shedding is important for transmission of enteric viruses, little is known about the immune factors that restrict persistent enteric infection. We report here that while the cytokines interferon-α (IFN-α) and IFN-β prevented the systemic spread of murine norovirus (MNoV), only IFN-λ controlled persistent enteric infection. Infection-dependent induction of IFN-λ was governed by the MNoV capsid protein and correlated with diminished enteric persistence. Treatment of established infection with IFN-λ cured mice in a manner requiring non-hematopoietic cell expression of the IFN-λ receptor, Ifnlr1, and independent of adaptive immunity. These results suggest the therapeutic potential of IFN-λ for curing virus infections in the gastrointestinal tract.
PMCID: PMC4398891  PMID: 25431489
14.  Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection 
Science (New York, N.Y.)  2014;347(6219):266-269.
The capacity of human norovirus (NoV), which causes >90% of global epidemic nonbacterial gastroenteritis, to infect a subset of people persistently may contribute to its spread. How such enteric viruses establish persistent infections is not well understood. We found that antibiotics prevented persistent murine norovirus (MNoV) infection, an effect that was reversed by replenishment of the bacterial microbiota. Antibiotics did not prevent tissue infection or affect systemic viral replication but acted specifically in the intestine. The receptor for the antiviral cytokine interferon-λ, Ifnlr1, as well as the transcription factors Stat1 and Irf3, were required for antibiotics to prevent viral persistence. Thus, the bacterial microbiome fosters enteric viral persistence in a manner counteracted by specific components of the innate immune system.
PMCID: PMC4409937  PMID: 25431490
15.  GWAS to Therapy by Genome Edits? 
Science (New York, N.Y.)  2013;342(6155):206-207.
PMCID: PMC4500047  PMID: 24115432
16.  C57BL/6N mutation in Cytoplasmic FMR interacting protein 2 regulates cocaine response 
Science (New York, N.Y.)  2013;342(6165):1508-1512.
The inbred mouse C57BL/6J is the reference strain for genome sequence and for most behavioral and physiological phenotypes. However the International Knockout Mouse Consortium uses an embryonic stem cell line derived from a related C57BL/6N substrain. We found that C57BL/6N has lower acute and sensitized response to cocaine and methamphetamine. We mapped a single causative locus and identified a non-synonymous mutation of serine to phenylalanine (S968F) in Cytoplasmic FMR interacting protein 2 (Cyfip2) as the causative variant. The S968F mutation destabilizes CYFIP2 and deletion of the C57BL/6N mutant allele leads to acute and sensitized cocaine response phenotypes. We propose CYFIP2 is a key regulator of cocaine response in mammals and present a framework to utilize mouse substrains to discover novel genes and alleles regulating behavior.
PMCID: PMC4500108  PMID: 24357318
17.  Specific HIV integration sites are linked to clonal expansion and persistence of infected cells 
Science (New York, N.Y.)  2014;345(6193):179-183.
The persistence of HIV-Infected cells in individuals on suppressive combination antiretroviral therapy (cART) presents a major barrier for curing HIV infections. HIV integrates its DNA into many sites in the host genome; we identified 2410 integration sites in peripheral blood lymphocytes of five infected individuals on cART. About 40% of the integrations were in clonally expanded cells. Approximately 50% of the infected cells in one patient were from a single clone and some clones persisted for many years. There were multiple independent integrations in several genes, including MKL2 and BACH2; many of these integrations were in clonally expanded cells. Our findings show that HIV integration sites can play a critical role in expansion and persistence of HIV infected cells.
PMCID: PMC4262401  PMID: 24968937
18.  PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair** 
Science (New York, N.Y.)  2015;347(6218):185-188.
XRCC4 and XLF are two structurally-related proteins that function in DNA double-strand break (DSB) repair. Here, we identify human PAXX (PAralog of XRCC4 and XLF; also called C9orf142) as a new XRCC4-superfamily member, and show that its crystal structure resembles that of XRCC4. PAXX interacts directly with the DSB-repair protein Ku and is recruited to DNA-damage sites in cells. Using RNA interference and CRISPR-Cas9 to generate PAXX−/− cells, we demonstrate that PAXX functions with XRCC4 and XLF to mediate DSB repair and cell survival in response to DSB-inducing agents. Finally, we reveal that PAXX promotes Ku-dependent DNA ligation in vitro, and assembly of core non-homologous end-joining (NHEJ) factors on damaged chromatin in cells. These findings identify PAXX as a new component of the NHEJ machinery.
PMCID: PMC4338599  PMID: 25574025
19.  Division of Labor in Transhydrogenase by alternating proton translocation and hydride transfer 
Science (New York, N.Y.)  2015;347(6218):178-181.
NADPH/NADP+ homeostasis is critical for countering oxidative stress in cells. Nicotinamide nucleotide transhydrogenase (TH), a membrane enzyme present in both bacteria and mitochondria, couples the proton motive force to the generation of NADPH. We present the 2.8 Å crystal structure of the transmembrane proton channel domain of TH from Thermus thermophilus and the 6.9 Å crystal structure of the entire enzyme (holo-TH). The membrane domain crystallized as a symmetric dimer, with each protomer containing a putative proton channel. The holo-TH is a highly asymmetric dimer with the NADP(H)-binding domain (dIII) in two different orientations. This unusual arrangement suggests a catalytic mechanism in which the two copies of dIII alternatively function in proton translocation and hydride transfer.
PMCID: PMC4479213  PMID: 25574024
20.  Controlled-release mitochondrial protonophore reverses diabetes and steatohepatitis in rats 
Science (New York, N.Y.)  2015;347(6227):1253-1256.
Nonalcoholic fatty liver disease (NAFLD) is a major factor in the pathogenesis of type 2 diabetes (T2D) and nonalcoholic steatohepatitis (NASH). The mitochondrial protonophore 2,4 dinitrophenol (DNP) has beneficial effects on NAFLD, insulin resistance, and obesity in preclinical models but is too toxic for clinical use. We developed a controlled-release oral formulation of DNP, called CRMP (controlled-release mitochondrial protonophore), that produces mild hepatic mitochondrial uncoupling. In rat models, CRMP reduced hypertriglyceridemia, insulin resistance, hepatic steatosis, and diabetes. It also normalized plasma transaminase concentrations, ameliorated liver fibrosis, and improved hepatic protein synthetic function in a methionine/choline–deficient rat model of NASH. Chronic treatment with CRMP was not associated with any systemic toxicity. These data offer proof of concept that mild hepatic mitochondrial uncoupling may be a safe and effective therapy for the related epidemics of metabolic syndrome, T2D, and NASH.
PMCID: PMC4495920  PMID: 25721504
21.  SIRT7 and Stem Cell Aging: Holding Your Breath for Longevity 
Science (New York, N.Y.)  2015;347(6228):1319-1320.
PMCID: PMC4494667  PMID: 25792319
22.  A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging 
Science (New York, N.Y.)  2015;348(6239):1160-1163.
Werner syndrome (WS) is a premature aging disorder caused by WRN protein deficiency. Here, we report on the generation of a human WS model in human embryonic stem cells (ESCs). Differentiation of WRN-null ESCs to mesenchymal stem cells (MSCs) recapitulates features of premature cellular aging, a global loss of H3K9me3, and changes in heterochromatin architecture. We show that WRN associates with heterochromatin proteins SUV39H1 and HP1α and nuclear lamina-heterochromatin anchoring protein LAP2β. Targeted knock-in of catalytically inactive SUV39H1 in wild-type MSCs recapitulates accelerated cellular senescence, resembling WRN-deficient MSCs. Moreover, decrease in WRN and heterochromatin marks are detected in MSCs from older individuals. Our observations uncover a role for WRN in maintaining heterochromatin stability and highlight heterochromatin disorganization as a potential determinant of human aging.
PMCID: PMC4494668  PMID: 25931448
23.  Structure of the HIV-1 RNA Packaging Signal 
Science (New York, N.Y.)  2015;348(6237):917-921.
The 5′-leader of the HIV-1 genome contains conserved elements that direct selective packaging of the unspliced, dimeric viral RNA into assembling particles. Using a 2H-edited NMR approach, we determined the structure of a 155-nucleotide region of the leader that is independently capable of directing packaging (Core Encapsidation Signal; ΨCES). The RNA adopts an unexpected tandem three-way junction structure, in which residues of the major splice donor and translation initiation sites are sequestered by long-range base pairing, and guanosines essential for both packaging and high-affinity binding to the cognate Gag protein are exposed in helical junctions. The structure reveals how translation is attenuated, Gag binding promoted, and unspliced dimeric genomes selected, by the RNA conformer that directs packaging.
PMCID: PMC4492308  PMID: 25999508
24.  De Novo Formation of a Distinct Coronary Vascular Population in Neonatal Heart 
Science (New York, N.Y.)  2014;345(6192):90-94.
The postnatal coronary vessels have been viewed as developing through expansion of vessels formed during the fetal period. Using genetic lineage tracing, we found that a substantial portion of postnatal coronary vessels arise de novo in the neonatal mouse heart, rather than expanding from pre-existing embryonic vasculature. Our data show that lineage conversion of neonatal endocardial cells during trabecular compaction generates a distinct compartment of the coronary circulation located within the inner half of the ventricular wall. This lineage conversion occurs within a brief period after birth and provides an efficient means of rapidly augmenting the coronary vasculature. This mechanism of postnatal coronary vascular growth provides avenues for understanding and stimulating cardiovascular regeneration following injury and disease.
PMCID: PMC4275002  PMID: 24994653
25.  Smoking Is Associated with Mosaic Loss of Chromosome Y 
Science (New York, N.Y.)  2014;347(6217):81-83.
Tobacco smoking is a risk factor for numerous disorders, including cancers affecting organs outside the respiratory tract. Epidemiological data suggest that smoking is a greater risk factor for these cancers in males compared to females. This observation, together with the fact that males have a higher incidence of, and mortality from, most non-sex-specific cancers, remain unexplained. Loss of chromosome Y (LOY) in blood cells is associated with increased risk of non-hematological tumors. We demonstrate here that smoking is associated with LOY in blood cells in three independent cohorts (TwinGene: odds ratio [OR]=4.3, 95% CI =2.8-6.7; ULSAM: OR=2.4, 95% CI=1.6-3.6; and PIVUS: OR=3.5, 95% CI=1.4-8.4) encompassing a total of 6014 men. The data also suggest that smoking has a transient and dose-dependent mutagenic effect on LOY-status. The finding that smoking induces LOY thus links a preventable risk factor with the most common acquired human mutation.
PMCID: PMC4356728  PMID: 25477213

Results 1-25 (2332)