bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural basis for cooperativity of CRM1 export complex formation
Authors: Monecke Thomas , Haselbach David , Voß Béla , Russek Andreas , Neumann Piotr , Thomson Emma , Hurt Ed , Zachariae Ulrich , Stark Holger , Grubmüller Helmut , Dickmanns Achim , Ficner Ralf
Published: January 2013

In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-β superfamily termed importins and exportins. The highly versatile exportin chromosome region maintenance 1 (CRM1) is essential for nuclear depletion of numerous structurally and functionally unrelated protein and ribonucleoprotein cargoes. CRM1 has been shown to adopt a toroidal structure in several functional transport complexes and was thought to maintain this conformation throughout the entire nucleocytoplasmic transport cycle. We solved crystal structures of free CRM1 from the thermophilic eukaryote
Chaetomium thermophilum
. Surprisingly, unbound CRM1 exhibits an overall extended and pitched superhelical conformation. The two regulatory regions, namely the acidic loop and the C-terminal α-helix, are dramatically repositioned in free CRM1 in comparison with the ternary CRM1–Ran–Snurportin1 export complex. Single-particle EM analysis demonstrates that, in a noncrystalline environment, free CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations. Molecular dynamics simulations show that the C-terminal helix plays an important role in regulating the transition from an extended to a compact conformation and reveal how the binding site for nuclear export signals of cargoes is modulated by different CRM1 conformations. Combining these results, we propose a model for the cooperativity of CRM1 export complex assembly involving the long-range allosteric communication between the distant binding sites of GTP-bound Ran and cargo.
Navigating the protein fitness landscape with Gaussian processes
Authors: Romero Philip A. , Krause Andreas , Arnold Frances H.
Published: January 2013

Knowing how protein sequence maps to function (the “fitness landscape”) is critical for understanding protein evolution as well as for engineering proteins with new and useful properties. We demonstrate that the protein fitness landscape can be inferred from experimental data, using Gaussian processes, a Bayesian learning technique. Gaussian process landscapes can model various protein sequence properties, including functional status, thermostability, enzyme activity, and ligand binding affinity. Trained on experimental data, these models achieve unrivaled quantitative accuracy. Furthermore, the explicit representation of model uncertainty allows for efficient searches through the vast space of possible sequences. We develop and test two protein sequence design algorithms motivated by Bayesian decision theory. The first one identifies small sets of sequences that are informative about the landscape; the second one identifies optimized sequences by iteratively improving the Gaussian process model in regions of the landscape that are predicted to be optimized. We demonstrate the ability of Gaussian processes to guide the search through protein sequence space by designing, constructing, and testing chimeric cytochrome P450s. These algorithms allowed us to engineer active P450 enzymes that are more thermostable than any previously made by chimeragenesis, rational design, or directed evolution.
Smg1 haploinsufficiency predisposes to tumor formation and inflammation
Authors: Roberts Tara L. , Ho Uda , Luff John , Lee C. Soon , Apte Simon H. , MacDonald Kelli P. A. , Raggat Liza J. , Pettit Allison R. , Morrow Carl A. , Waters Michael J. , Chen Phil , Woods Rick G. , Thomas Gethin P. , St. Pierre Liam , Farah Camile S. , Clarke Raymond A. , Brown James A. L. , Lavin Martin F.
Published: January 2013

SMG1 is a member of the phosphoinositide kinase-like kinase family of proteins that includes ATM, ATR, and DNA-PK, proteins with known roles in DNA damage and cellular stress responses. SMG1 has a well-characterized role in nonsense-mediated decay as well as suggested roles in the DNA damage response, resistance to oxidative stress, regulation of hypoxic responses, and apoptosis. To understand the roles of SMG1 further, we generated a Genetrap
Smg1
mouse model.
Smg1
homozygous KO mice were early embryonic lethal, but
Smg1
heterozygous mice showed a predisposition to a range of cancers, particularly lung and hematopoietic malignancies, as well as development of chronic inflammation. These mice did not display deficiencies in known roles of SMG1, including nonsense-mediated decay. However, they showed elevated basal tissue and serum cytokine levels, indicating low-level inflammation before the development of tumors.
Smg1
heterozygous mice also showed evidence of oxidative damage in tissues. These data suggest that the inflammation observed in
Smg1
haploinsufficiency contributes to susceptibility to cancer and that
Smg1
-deficient animals represent a model of inflammation-enhanced cancer development.
Relationship between sea level and climate forcing by CO
2
on geological timescales
Authors: Foster Gavin L. , Rohling Eelco J.
Published: January 2013

On 10
3
- to 10
6
-year timescales, global sea level is determined largely by the volume of ice stored on land, which in turn largely reflects the thermal state of the Earth system. Here we use observations from five well-studied time slices covering the last 40 My to identify a well-defined and clearly sigmoidal relationship between atmospheric CO
2
and sea level on geological (near-equilibrium) timescales. This strongly supports the dominant role of CO
2
in determining Earth’s climate on these timescales and suggests that other variables that influence long-term global climate (e.g., topography, ocean circulation) play a secondary role. The relationship between CO
2
and sea level we describe portrays the “likely” (68% probability) long-term sea-level response after Earth system adjustment over many centuries. Because it appears largely independent of other boundary condition changes, it also may provide useful long-range predictions of future sea level. For instance, with CO
2
stabilized at 400–450 ppm (as required for the frequently quoted “acceptable warming” of 2 °C), or even at AD 2011 levels of 392 ppm, we infer a likely (68% confidence) long-term sea-level rise of more than 9 m above the present. Therefore, our results imply that to avoid significantly elevated sea level in the long term, atmospheric CO
2
should be reduced to levels similar to those of preindustrial times.
Impact of seawater acidification on pH at the tissue–skeleton interface and calcification in reef corals
Authors: Venn Alexander A. , Tambutté Eric , Holcomb Michael , Laurent Julien , Allemand Denis , Tambutté Sylvie
Published: January 2013

Insight into the response of reef corals and other major marine calcifiers to ocean acidification is limited by a lack of knowledge about how seawater pH and carbonate chemistry impact the physiological processes that drive biomineralization. Ocean acidification is proposed to reduce calcification rates in corals by causing declines in internal pH at the calcifying tissue–skeleton interface where biomineralization takes place. Here, we performed an in vivo study on how partial-pressure CO
2
-driven seawater acidification impacts intracellular pH in coral calcifying cells and extracellular pH in the fluid at the tissue–skeleton interface [subcalicoblastic medium (SCM)] in the coral
Stylophora pistillata
. We also measured calcification in corals grown under the same conditions of seawater acidification by measuring lateral growth of colonies and growth of aragonite crystals under the calcifying tissue. Our findings confirm that seawater acidification decreases pH of the SCM, but this decrease is gradual relative to the surrounding seawater, leading to an increasing pH gradient between the SCM and seawater. Reductions in calcification rate, both at the level of crystals and whole colonies, were only observed in our lowest pH treatment when pH was significantly depressed in the calcifying cells in addition to the SCM. Overall, our findings suggest that reef corals may mitigate the effects of seawater acidification by regulating pH in the SCM, but they also highlight the role of calcifying cell pH homeostasis in determining the response of reef corals to changes in external seawater pH and carbonate chemistry.
Temperature-driven range expansion of an irruptive insect heightened by weakly coevolved plant defenses
Authors: Raffa Kenneth F. , Powell Erinn N. , Townsend Philip A.
Published: January 2013

Warming climate has increased access of native bark beetles to high-elevation pines that historically received only intermittent exposure to these tree-killing herbivores. Here we show that a dominant, relatively naïve, high-elevation species, whitebark pine, has inferior defenses against mountain pine beetle compared with its historical lower-elevation host, lodgepole pine. Lodgepole pines respond by exuding more resin and accumulating higher concentrations of toxic monoterpenes than whitebark pine, where they co-occur. Furthermore, the chemical composition of whitebark pine appears less able to inhibit the pheromonal communication beetles use to jointly overcome tree defenses. Despite whitebark pine’s inferior defenses, beetles were more likely to attack their historical host in mixed stands. This finding suggests there has been insufficient sustained contact for beetles to alter their complex behavioral mechanisms driving host preference. In no-choice assays, however, beetles readily entered and tunneled in both hosts equally, and in stands containing less lodgepole pine, attacks on whitebark pines increased. High-elevation trees in pure stands may thus be particularly vulnerable to temperature-driven range expansions. Predators and competitors were more attracted to volatiles from herbivores attacking their historical host, further increasing risk in less coevolved systems. Our results suggest cold temperatures provided a sufficient barrier against herbivores for high-elevation trees to allocate resources to other physiological processes besides defense. Changing climate may reduce the viability of that evolutionary strategy, and the life histories of high-elevation trees seem unlikely to foster rapid counter adaptation. Consequences extend from reduced food supplies for endangered grizzly bears to altered landscape and hydrological processes.
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
Authors: Shih Patrick M. , Wu Dongying , Latifi Amel , Axen Seth D. , Fewer David P. , Talla Emmanuel , Calteau Alexandra , Cai Fei , Tandeau de Marsac Nicole , Rippka Rosmarie , Herdman Michael , Sivonen Kaarina , Coursin Therese , Laurent Thierry , Goodwin Lynne , Nolan Matt , Davenport Karen W. , Han Cliff S. , Rubin Edward M. , Eisen Jonathan A. , Woyke Tanja , Gugger Muriel , Kerfeld Cheryl A.
Published: January 2013

The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for “green” biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.
Cadherin-based intercellular adhesions organize epithelial cell–matrix traction forces
Authors: Mertz Aaron F. , Che Yonglu , Banerjee Shiladitya , Goldstein Jill M. , Rosowski Kathryn A. , Revilla Stephen F. , Niessen Carien M. , Marchetti M. Cristina , Dufresne Eric R. , Horsley Valerie
Published: January 2013

Cell–cell and cell–matrix adhesions play essential roles in the function of tissues. There is growing evidence for the importance of cross talk between these two adhesion types, yet little is known about the impact of these interactions on the mechanical coupling of cells to the extracellular matrix (ECM). Here, we combine experiment and theory to reveal how intercellular adhesions modulate forces transmitted to the ECM. In the absence of cadherin-based adhesions, primary mouse keratinocytes within a colony appear to act independently, with significant traction forces extending throughout the colony. In contrast, with strong cadherin-based adhesions, keratinocytes in a cohesive colony localize traction forces to the colony periphery. Through genetic or antibody-mediated loss of cadherin expression or function, we show that cadherin-based adhesions are essential for this mechanical cooperativity. A minimal physical model in which cell–cell adhesions modulate the physical cohesion between contractile cells is sufficient to recreate the spatial rearrangement of traction forces observed experimentally with varying strength of cadherin-based adhesions. This work defines the importance of cadherin-based cell–cell adhesions in coordinating mechanical activity of epithelial cells and has implications for the mechanical regulation of epithelial tissues during development, homeostasis, and disease.
Deterministic matrices matching the compressed sensing phase transitions of Gaussian random matrices
Authors: Monajemi Hatef , Jafarpour Sina , Gavish Matan ,   Stat 330/CME 362 Collaboration, Donoho David L. , Ambikasaran Sivaram , Bacallado Sergio , Bharadia Dinesh , Chen Yuxin , Choi Young , Chowdhury Mainak , Chowdhury Soham , Damle Anil , Fithian Will , Goetz Georges , Grosenick Logan , Gross Sam , Hills Gage , Hornstein Michael , Lakkam Milinda , Lee Jason , Li Jian , Liu Linxi , Sing-Long Carlos , Marx Mike , Mittal Akshay , Monajemi Hatef , No Albert , Omrani Reza , Pekelis Leonid , Qin Junjie , Raines Kevin , Ryu Ernest , Saxe Andrew , Shi Dai , Siilats Keith , Strauss David , Tang Gary , Wang Chaojun , Zhou Zoey , Zhu Zhen
Published: January 2013

In compressed sensing, one takes

samples of an
N
-dimensional vector

using an

matrix
A
, obtaining undersampled measurements

. For random matrices with independent standard Gaussian entries, it is known that, when

is
k
-sparse, there is a precisely determined phase transition: for a certain region in the (

,

)-phase diagram, convex optimization

typically finds the sparsest solution, whereas outside that region, it typically fails. It has been shown empirically that the same property—with the same phase transition location—holds for a wide range of non-Gaussian random matrix ensembles. We report extensive experiments showing that the Gaussian phase transition also describes numerous deterministic matrices, including Spikes and Sines, Spikes and Noiselets, Paley Frames, Delsarte-Goethals Frames, Chirp Sensing Matrices, and Grassmannian Frames. Namely, for each of these deterministic matrices in turn, for a typical
k
-sparse object, we observe that convex optimization is successful over a region of the phase diagram that coincides with the region known for Gaussian random matrices. Our experiments considered coefficients constrained to

for four different sets

, and the results establish our finding for each of the four associated phase transitions.
Analysis of natural variation reveals neurogenetic networks forDrosophilaolfactory behavior
Authors: Swarup Shilpa , Huang Wen , Mackay Trudy F. C. , Anholt Robert R. H.
Published: January 2013

Understanding the relationship between genetic variation and phenotypic variation for quantitative traits is necessary for predicting responses to natural and artificial selection and disease risk in human populations, but is challenging because of large sample sizes required to detect and validate loci with small effects. Here, we used the inbred, sequenced, wild-derived lines of theDrosophila melanogasterGenetic Reference Panel (DGRP) to perform three complementary genome-wide association (GWA) studies for natural variation in olfactory behavior. The first GWA focused on single nucleotide polymorphisms (SNPs) associated with mean differences in olfactory behavior in the DGRP, the second was an extreme quantitative trait locus GWA on an outbred advanced intercross population derived from extreme DGRP lines, and the third was for SNPs affecting the variance among DGRP lines. No individual SNP in any analysis was associated with variation in olfactory behavior by using a strict threshold accounting for multiple tests, and no SNP overlapped among the analyses. However, combining the top SNPs from all three analyses revealed a statistically enriched network of genes involved in cellular signaling and neural development. We used mutational and gene expression analyses to validate both candidate genes and network connectivity at a high rate. The lack of replication between the GWA analyses, small marginal SNP effects, and convergence on common cellular networks were likely attributable to epistasis. These results suggest that fully understanding the genotype–phenotype relationship requires a paradigm shift from a focus on single SNPs to pathway associations.
Protective role of brain water channel AQP4 in murine cerebral malaria
Authors: Promeneur Dominique , Lunde Lisa Kristina , Amiry-Moghaddam Mahmood , Agre Peter
Published: January 2013

Tragically common among children in sub-Saharan Africa, cerebral malaria is characterized by rapid progression to coma and death. In this study, we used a model of cerebral malaria appearing in C57BL/6 WT mice after infection with the rodent malaria parasite
Plasmodium berghei
ANKA. Expression and cellular localization of the brain water channel aquaporin-4 (AQP4) was investigated during the neurological syndrome. Semiquantitative real-time PCR comparing uninfected and infected mice showed a reduction of brain AQP4 transcript in cerebral malaria, and immunoblots revealed reduction of brain AQP4 protein. Reduction of brain AQP4 protein was confirmed in cerebral malaria by quantitative immunogold EM; however, polarized distribution of AQP4 at the perivascular and subpial astrocyte membranes was not altered. To further examine the role of AQP4 in cerebral malaria, WT mice and littermates genetically deficient in AQP4 were infected with
P. berghei
. Upon development of cerebral malaria, WT and AQP4-null mice exhibited similar increases in width of perivascular astroglial end-feet in brain. Nevertheless, the AQP4-null mice exhibited more severe signs of cerebral malaria with greater brain edema, although disruption of the blood–brain barrier was similar in both groups. In longitudinal studies, cerebral malaria appeared nearly 1 d earlier in the AQP4-null mice, and reduced survival was noted when chloroquine rescue was attempted. We conclude that the water channel AQP4 confers partial protection against cerebral malaria.
Convergent and divergent effects of costimulatory molecules in conventional and regulatory CD4
+
T cells
Authors: Wakamatsu Ei , Mathis Diane , Benoist Christophe
Published: January 2013

Costimulatory molecules of the CD28 family on T lymphocytes integrate cues from innate immune system sensors and modulate activation responses in conventional CD4
+
T cells (Tconv) and their FoxP3
+
regulatory counterparts (Treg). To better understand how costimulatory and coinhibitory signals might be integrated, we profiled the changes in gene expression elicited in the hours and days after engagement of Treg and Tconv by anti-CD3 and either anti-CD28, -CTLA4, -ICOS, -PD1, -BLA, or -CD80. In Tconv, a shared “main response” was induced by CD28, ICOS, and, surprisingly, BTLA and CD80, with very limited CD28-specific (primarily
Il2
) or ICOS-specific elements (including Th1 and Th2 but not the follicular T signature). CTLA4 and PD1 had a very subtle impact in this system, similarly inhibiting the response to anti-CD3. Treg responded to the same costimulatory hierarchy and to the same extent as Tconv, but inducing different clusters of genes. In this reductionist system, costimulatory or coinhibitory engagement mainly elicits generic responses, suggesting that the variability of their effects in vivo result from temporal or anatomical differences in their engagement, rather than from inherently different wiring.
Delineating the pathways for the site-directed synthesis of individual nanoparticles on surfaces
Authors: Liu Guoliang , Eichelsdoerfer Daniel J. , Rasin Boris , Zhou Yu , Brown Keith A. , Liao Xing , Mirkin Chad A.
Published: January 2013

Although nanoparticles with exquisite properties have been synthesized for a variety of applications, their incorporation into functional devices is challenging owing to the difficulty in positioning them at specified sites on surfaces. In contrast with the conventional synthesis-then-assembly paradigm, scanning probe block copolymer lithography can pattern precursor materials embedded in a polymer matrix and synthesize desired nanoparticles on site, offering great promise for incorporating nanoparticles into devices. This technique, however, is extremely limited from a materials standpoint. To develop a materials-general method for synthesizing nanoparticles on surfaces for broader applications, a mechanistic understanding of polymer-mediated nanoparticle formation is crucial. Here, we design a four-step synthetic process that enables independent study of the two most critical steps for synthesizing single nanoparticles on surfaces: phase separation of precursors and particle formation. Using this process, we elucidate the importance of the polymer matrix in the diffusion of metal precursors to form a single nanoparticle and the three pathways that the precursors undergo to form nanoparticles. Based on this mechanistic understanding, the synthetic process is generalized to create metal (Au, Ag, Pt, and Pd), metal oxide (Fe
2
O
3
, Co
2
O
3
, NiO, and CuO), and alloy (AuAg) nanoparticles. This mechanistic understanding and resulting process represent a major advance in scanning probe lithography as a tool to generate patterns of tailored nanoparticles for integration with solid-state devices.
Accelerating slow excited state proton transfer
Authors: Stewart David J. , Concepcion Javier J. , Brennaman M. Kyle , Binstead Robert A. , Meyer Thomas J.
Published: January 2013

Visible light excitation of the ligand-bridged assembly [(bpy)
2
Ru
a
II
(L)Ru
b
II
(bpy)(OH
2
)
4+
] (bpy is 2,2′-bipyridine; L is the bridging ligand, 4-phen-tpy) results in emission from the lowest energy, bridge-based metal-to-ligand charge transfer excited state (L
−•
)Ru
b
III
-OH
2
with an excited-state lifetime of 13 ± 1 ns. Near–diffusion-controlled quenching of the emission occurs with added HPO
4
2−
and partial quenching by added acetate anion (OAc
−
) in buffered solutions with pH control. A Stern–Volmer analysis of quenching by OAc
−
gave a quenching rate constant of
k

q

= 4.1 × 10
8
M
−1
⋅s
−1
and an estimated pK
a
* value of ∼5 ± 1 for the [(bpy)
2
Ru
a
II
(L
•−
)Ru
b
III
(bpy)(OH
2
)
4+
]* excited state. Following proton loss and rapid excited-state decay to give [(bpy)
2
Ru
a
II
(L)Ru
b
II
(bpy)(OH)
3+
] in a H
2
PO
4
−
/HPO
4
2−
buffer, back proton transfer occurs from H
2
PO
4
−
to give [(bpy)
2
Ru
a
II
(L)Ru
b
(bpy)(OH
2
)
4+
] with
k
PT,2
= 4.4 × 10
8
M
−1
⋅s
−1
. From the intercept of a plot of
k

obs

vs. [H
2
PO
4
−
],
k
= 2.1 × 10
6
s
−1
for reprotonation by water providing a dramatic illustration of kinetically limiting, slow proton transfer for acids and bases with pK
a
values intermediate between pK
a
(H
3
O
+
) = −1.74 and pK
a
(H
2
O) = 15.7.
Behavioral tagging of extinction learning
Authors: de Carvalho Myskiw Jociane , Benetti Fernando , Izquierdo Iván
Published: January 2013

Extinction of contextual fear in rats is enhanced by exposure to a novel environment at 1–2 h before or 1 h after extinction training. This effect is antagonized by administration of protein synthesis inhibitors anisomycin and rapamycin into the hippocampus, but not into the amygdala, immediately after either novelty or extinction training, as well as by the gene expression blocker 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole administered after novelty training, but not after extinction training. Thus, this effect can be attributed to a mechanism similar to synaptic tagging, through which long-term potentiation can be enhanced by other long-term potentiations or by exposure to a novel environment in a protein synthesis-dependent fashion. Extinction learning produces a tag at the appropriate synapses, whereas novelty learning causes the synthesis of plasticity-related proteins that are captured by the tag, strengthening the synapses that generated this tag.
Entropic pressure between biomembranes in a periodic stack due to thermal fluctuations
Authors: Freund L. B.
Published: January 2013

The phenomenon of thermal fluctuation of a biomembrane within a stack of like membranes was introduced in a pioneering paper [Helfrich W (1978)
Z Naturforsch A
33(3):305–315]. Internal energy arises in a representative membrane through elastic resistance to bending deformation, and membrane motion is further restrained through steric interaction with adjacent membranes. Due to reflective symmetry within the stack, analysis of behavior can be reduced to study of a single membrane fluctuating between parallel rigid planes. The phenomenon is reexamined here from several viewpoints to quantify the dependence of system free energy on the size of the gap between membranes. This analysis is based on essentially the same formulation that was used in the original study, and it is found that analysis based on enforcement of the underlying principles can lead to an exact mathematical solution. On this basis, a self-consistent picture of behavior emerges showing a dependence of free energy on the width of the confining gap that is weaker than has been thought to prevail.
Histone deacetylase inhibitors increase glucocerebrosidase activity in Gaucher disease by modulation of molecular chaperones
Authors: Yang Chunzhang , Rahimpour Shervin , Lu Jie , Pacak Karel , Ikejiri Barbara , Brady Roscoe O. , Zhuang Zhengping
Published: January 2013

Gaucher disease is caused by mutations of the
GBA
gene that encodes the lysosomal enzyme glucocerebrosidase (GCase).
GBA
mutations often result in protein misfolding and premature degradation, but usually exert less effect on catalytic activity. In this study, we identified the molecular mechanism by which histone deacetylase inhibitors increase the quantity and activity of GCase. Specifically, these inhibitors limit the deacetylation of heat shock protein 90, resulting in less recognition of the mutant peptide and GCase degradation. These findings provide insight into a possible therapeutic strategy for Gaucher disease and other genetic disorders by modifying molecular chaperone and protein degradation pathways.
Metformin inhibits the inflammatory response associated with cellular transformation and cancer stem cell growth
Authors: Hirsch Heather A. , Iliopoulos Dimitrios , Struhl Kevin
Published: January 2013

Metformin, the first-line drug for treating diabetes, inhibits cellular transformation and selectively kills cancer stem cells in breast cancer cell lines. In a Src-inducible model of cellular transformation, metformin inhibits the earliest known step in the process, activation of the inflammatory transcription factor NF-κB. Metformin strongly delays cellular transformation in a manner similar to that occurring upon a weaker inflammatory stimulus. Conversely, inhibition of transformation does not occur if metformin is added after the initial inflammatory stimulus. The antitransformation effect of metformin can be bypassed by overexpression of Lin28B or IL1β, downstream targets of NF-κB. Metformin preferentially inhibits nuclear translocation of NF-κB and phosphorylation of STAT3 in cancer stem cells compared with non-stem cancer cells in the same population. The ability of metformin to block tumor growth and prolong remission in xenografts in combination with doxorubicin is associated with decreased function of the inflammatory feedback loop. Lastly, metformin-based combinatorial therapy is effective in xenografts involving inflammatory prostate and melanoma cell lines, whereas it is ineffective in noninflammatory cell lines from these lineages. Taken together, our observations suggest that metformin inhibits a signal transduction pathway that results in an inflammatory response. As metformin alters energy metabolism in diabetics, we speculate that metformin may block a metabolic stress response that stimulates the inflammatory pathway associated with a wide variety of cancers.
S-nitrosylation of AMPA receptor GluA1 regulates phosphorylation, single-channel conductance, and endocytosis
Authors: Selvakumar Balakrishnan , Jenkins Meagan A. , Hussain Natasha K. , Huganir Richard L. , Traynelis Stephen F. , Snyder Solomon H.
Published: January 2013

NMDA receptor activation can elicit synaptic plasticity by augmenting conductance of the AMPA receptor GluA1 subsequent to phosphorylation at S831 by Ca
2+
-dependent kinases. NMDA receptor activation also regulates synaptic plasticity by causing endocytosis of AMPA receptor GluA1. We demonstrate a unique signaling cascade for these processes mediated by NMDA receptor-dependent NO formation and GluA1 S-nitrosylation. Thus, S-nitrosylation of GluA1 at C875 enhances S831 phosphorylation, facilitates the associated AMPA receptor conductance increase, and results in endocytosis by increasing receptor binding to the AP2 protein of the endocytotic machinery.
Verse Epistles on Italian Opera Singers, 1724–1736
Authors: McGeary Thomas
Published: January 2013

Writing from Dublin in February 1724, Jonathan Swift responded to some London gossip and joked about the ‘gallantry’ of the aged military hero the Earl of Peterborough, who had publicly commanded an apology from the castrato Senesino for his impugning the honour of the soprano Anastasia Robinson. This scandal set off a series of obscene, misogynistic, satiric epistles written to or about Mrs Robinson, Senesino, Faustina, Mrs Barbier, and Farinelli that accuse the female singers, British prudes, and others of a variety of deviant, sexually subversive practices. This article introduces and presents annotated texts of this group of epistles written between 1724 and 1736. Several have been discussed by historians of opera and literary scholars, but the whole corpus has not been identified or made readily available to opera scholars.
An Inventory of Mid-Eighteenth-Century Oxford Musical Hands
Authors: Jones Peter Ward , Burrows Donald
Published: January 2013

Between them William Hayes (1708–77) and his eldest son Philip (1738–97) occupied the Oxford music professorship for over half a century. William, who came to Oxford in 1734 as organist of Magdalen College, succeeded Richard Goodson the younger in 1741, and at his death was replaced by Philip, who continued in office for the rest of his own life. In addition, both men continued to hold a variety of other posts, in particular as college organists. The period also saw the opening of the Holywell Music Room in 1748, which gave further impetus to an already flourishing concert scene in the city. Although little remains of the general performing material from the Music Room concerts, the Hayeses' own compositions have in large part survived, and include, besides church music and concertos (many of which were certainly heard at the Music Room), a series of large-scale odes and oratorios, often composed as occasional works for university celebrations. In many cases not only the scores, but also the parts survive, and now form a substantial archive in the Bodleian Library, Oxford. The life and works of the two Hayeses has been thoroughly investigated by Simon Heighes in his Oxford dissertation of 1990, although he did not discuss in detail the problems arising out of the similarity of their musical hands, nor deal with the wider question of copyists active in the city at the time. This inventory attempts to clarify this area, and it forms a companion to a book chapter which originated in a paper that the authors gave at a conference in 1998 celebrating the two hunded and fiftieth anniversary of the opening of the Holywell Music Room.
Liturgical Polyphony in the Pre-Reformation English Parish Church: A Provisional List and Commentary
Authors: Williamson Magnus
Published: January 2013

The great majority of late-medieval lay people encountered the Universal Church most directly, and in some cases exclusively, through their local parish church. The parish has therefore been at the heart of research into lay piety, as witnessed in a range of detailed studies of pre-Reformation beliefs, rituals, rites of passage, clergy, episcopal oversight, parochial administration and social organization. Until recently, however, the ‘soundscape’ of the pre-Reformation parish has received less exhaustive attention, perhaps because the parish has been seen as peripheral or subordinate to the mainstream of musicological research (few first-rank composers are known to have worked within English parish churches), but also because the documentary sources are more disparate and often less complete and informative than the archives of more superficially prestigious institutions. Nevertheless, if the widespread cultivation of polyphonic singing within divine worship was one of the seminal cultural achievements of late-medieval England, what contribution did the parish make towards this revolution? How many parishes maintained polyphonic choirs? What role did the laity play in promoting liturgical polyphony? And what might such initiatives reveal concerning lay attitudes towards liturgical music? Studies of Bristol, London, Louth, Ludlow and York have highlighted the potential of the parish as a focus for musicological research, and have begun to answer some of these questions. The following handlist, an earlier form of which was prepared for the 2002 Harlaxton Medieval Symposium, is intended to serve as a springboard for further research in this field. Although neither complete nor definitive, its aims are to bring together, as comprehensively as possible, the available evidence concerning the singing of liturgical polyphony before 1559, and to provide an overview of the contextual factors which have informed the underlying methodology: to this end, the list itself is preceded by an extended commentary.
‘Eine Liebliche/Von Vielen Violen Bestehende Music’. Ballet Instrumentation at German Protestant Courts, 1650–1700: A Study of Libretti in Wolfenbüttel and Stuttgart Libraries
Authors: Owens Samantha
Published: January 2013

German court ballet of the early modern period is mentioned only rarely in musicological discourse. The present study examines the question of instrumentation in this genre (which incorporated poetry, song and dance), taking as its primary evidence 83 printed libretti from 1650–1700 held by the Herzog August Bibliothek in Wolfenbiittel, the Wiirttembergische Landesbibliothek and the Hauptstaatsarchiv Stuttgart. With their occasional references to specific instruments, these constitute an important source of information on the development of the orchestra, supplying evidence of the continuation of European-wide traditions of instrumental associations with certain theatrical topoi (also confirmed in contemporary German dance manuals), and offering clues regarding the means through which French compositional and performance styles were disseminated throughout the German-speaking lands. The libretti also provide information on the use of costumed musicians, on the widespread employment of a distinctive type of music referred to as ‘lieblich’ (sweet) and of collaboration between dancing masters employed at diverse courts.
The two stages of cell fusion
Authors: Leslie Mitch
Published: January 2013

Cells switch molecular lineups for initial and later phases of fusion.
ATAD5 regulates the lifespan of DNA replication factories by modulating PCNA level on the chromatin
Authors: Lee Kyoo-young , Fu Haiqing , Aladjem Mirit I. , Myung Kyungjae
Published: January 2013

Temporal and spatial regulation of the replication factory is important for efficient DNA replication. However, the underlying molecular mechanisms are not well understood. Here, we report that ATAD5 regulates the lifespan of replication factories. Reduced expression of ATAD5 extended the lifespan of replication factories by retaining proliferating cell nuclear antigen (PCNA) and other replisome proteins on the chromatin during and even after DNA synthesis. This led to an increase of inactive replication factories with an accumulation of replisome proteins. Consequently, the overall replication rate was decreased, which resulted in the delay of S-phase progression. Prevalent detection of PCNA foci in G2 phase cells after ATAD5 depletion suggests that defects in the disassembly of replication factories persist after S phase is complete. ATAD5-mediated regulation of the replication factory and PCNA required an intact ATAD5 ATPase domain. Taken together, our data imply that ATAD5 regulates the cycle of DNA replication factories, probably through its PCNA-unloading activity.
Extracellular annexins and dynamin are important for sequential steps in myoblast fusion
Authors: Leikina Evgenia , Melikov Kamran , Sanyal Sarmistha , Verma Santosh K. , Eun Bokkee , Gebert Claudia , Pfeifer Karl , Lizunov Vladimir A. , Kozlov Michael M. , Chernomordik Leonid V.
Published: January 2013

Myoblast fusion into multinucleated myotubes is a crucial step in skeletal muscle development and regeneration. Here, we accumulated murine myoblasts at the ready-to-fuse stage by blocking formation of early fusion intermediates with lysophosphatidylcholine. Lifting the block allowed us to explore a largely synchronized fusion. We found that initial merger of two cell membranes detected as lipid mixing involved extracellular annexins A1 and A5 acting in a functionally redundant manner. Subsequent stages of myoblast fusion depended on dynamin activity, phosphatidylinositol(4,5)bisphosphate content, and cell metabolism. Uncoupling fusion from preceding stages of myogenesis will help in the analysis of the interplay between protein machines that initiate and complete cell unification and in the identification of additional protein players controlling different fusion stages.
Neurobeachin regulates neurotransmitter receptor trafficking to synapses
Authors: Nair Ramya , Lauks Juliane , Jung SangYong , Cooke Nancy E. , de Wit Heidi , Brose Nils , Kilimann Manfred W. , Verhage Matthijs , Rhee JeongSeop
Published: January 2013

The surface density of neurotransmitter receptors at synapses is a key determinant of synaptic efficacy. Synaptic receptor accumulation is regulated by the transport, postsynaptic anchoring, and turnover of receptors, involving multiple trafficking, sorting, motor, and scaffold proteins. We found that neurons lacking the BEACH (beige-Chediak/Higashi) domain protein Neurobeachin (Nbea) had strongly reduced synaptic responses caused by a reduction in surface levels of glutamate and GABAA receptors. In the absence of Nbea, immature AMPA receptors accumulated early in the biosynthetic pathway, and mature N-methyl-d-aspartate, kainate, and GABAA receptors did not reach the synapse, whereas maturation and surface expression of other membrane proteins, synapse formation, and presynaptic function were unaffected. These data show that Nbea regulates synaptic transmission under basal conditions by targeting neurotransmitter receptors to synapses.
Molecular requirements for the formation of a kinetochore–microtubule interface by Dam1 and Ndc80 complexes
Authors: Lampert Fabienne , Mieck Christine , Alushin Gregory M. , Nogales Eva , Westermann Stefan
Published: January 2013

Kinetochores are large protein complexes that link sister chromatids to the spindle and transduce microtubule dynamics into chromosome movement. In budding yeast, the kinetochore–microtubule interface is formed by the plus end–associated Dam1 complex and the kinetochore-resident Ndc80 complex, but how they work in combination and whether a physical association between them is critical for chromosome segregation is poorly understood. Here, we define structural elements required for the Ndc80–Dam1 interaction and probe their function in vivo. A novel ndc80 allele, selectively impaired in Dam1 binding, displayed growth and chromosome segregation defects. Its combination with an N-terminal truncation resulted in lethality, demonstrating essential but partially redundant roles for the Ndc80 N-tail and Ndc80–Dam1 interface. In contrast, mutations in the calponin homology domain of Ndc80 abrogated kinetochore function and were not compensated by the presence of Dam1. Our experiments shed light on how microtubule couplers cooperate and impose important constraints on structural models for outer kinetochore assembly.
The CCAN recruits CENP-A to the centromere and forms the structural core for kinetochore assembly
Authors: Hori Tetsuya , Shang Wei-Hao , Takeuchi Kozo , Fukagawa Tatsuo
Published: January 2013

CENP-A acts as an important epigenetic marker for kinetochore specification. However, the mechanisms by which CENP-A is incorporated into centromeres and the structural basis for kinetochore formation downstream of CENP-A remain unclear. Here, we used a unique chromosome-engineering system in which kinetochore proteins are targeted to a noncentromeric site after the endogenous centromere is conditionally removed. Using this system, we created two distinct types of engineered kinetochores, both of which were stably maintained in chicken DT40 cells. Ectopic targeting of full-length HJURP, CENP-C, CENP-I, or the CENP-C C terminus generated engineered kinetochores containing major kinetochore components, including CENP-A. In contrast, ectopic targeting of the CENP-T or CENP-C N terminus generated functional kinetochores that recruit the microtubule-binding Ndc80 complex and chromosome passenger complex (CPC), but lack CENP-A and most constitutive centromere-associated network (CCAN) proteins. Based on the analysis of these different engineered kinetochores, we conclude that the CCAN has two distinct roles: recruiting CENP-A to establish the kinetochore and serving as a structural core to directly recruit kinetochore proteins.
Reductionism at the vertebrate kinetochore
Authors: Stankovic Ana , Jansen Lars E.T.
Published: January 2013

The kinetochore forms the site of attachment for mitotic spindle microtubules driving chromosome segregation. The interdependent protein interactions in this large structure have made it difficult to dissect the function of its components. In this issue, Hori et al. (2013. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201210106) present a novel and powerful methodology to address the sufficiency of individual proteins for the creation of a functional de novo centromere.
Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes
Authors: Zhang Qibin , Fillmore Thomas L. , Schepmoes Athena A. , Clauss Therese R.W. , Gritsenko Marina A. , Mueller Patricia W. , Rewers Marian , Atkinson Mark A. , Smith Richard D. , Metz Thomas O.
Published: January 2013

Using global liquid chromatography-mass spectrometry (LC-MS)–based proteomics analyses, we identified 24 serum proteins that were significantly variant between those with type 1 diabetes (T1D) and healthy controls. Functionally, these proteins represent innate immune responses, the activation cascade of complement, inflammatory responses, and blood coagulation. Targeted verification analyses were performed on 52 surrogate peptides representing these proteins, with serum samples from an antibody standardization program cohort of 100 healthy control and 50 type 1 diabetic subjects. 16 peptides were verified as having very good discriminating power, with areas under the receiver operating characteristic curve ≥0.8. Further validation with blinded serum samples from an independent cohort (10 healthy control and 10 type 1 diabetics) demonstrated that peptides from platelet basic protein and C1 inhibitor achieved both 100% sensitivity and 100% specificity for classification of samples. The disease specificity of these proteins was assessed using sera from 50 age-matched type 2 diabetic individuals, and a subset of proteins, C1 inhibitor in particular, were exceptionally good discriminators between these two forms of diabetes. The panel of biomarkers distinguishing those with T1D from healthy controls and those with type 2 diabetes suggests that dysregulated innate immune responses may be associated with the development of this disorder.
The cell fate determinant Llgl1 influences HSC fitness and prognosis in AML
Authors: Heidel Florian H. , Bullinger Lars , Arreba-Tutusaus Patricia , Wang Zhu , Gaebel Julia , Hirt Carsten , Niederwieser Dietger , Lane Steven W. , Döhner Konstanze , Vasioukhin Valera , Fischer Thomas , Armstrong Scott A.
Published: January 2013

A unique characteristic of hematopoietic stem cells (HSCs) is the ability to self-renew. Several genes and signaling pathways control the fine balance between self-renewal and differentiation in HSCs and potentially also in leukemia stem cells. Recently, studies have shed light on developmental molecules and evolutionarily conserved signals as regulators of stem cells in hematopoiesis and leukemia. In this study, we provide evidence that the cell fate determinant Llgl1 (lethal giant larvae homolog 1) plays an important role in regulation of HSCs. Loss of Llgl1 leads to an increase in HSC numbers that show increased repopulation capacity and competitive advantage after transplantation. This advantage increases upon serial transplantation or when stress is applied to HSCs. Llgl1−/− HSCs show increased cycling but neither exhaust nor induce leukemia in recipient mice. Llgl1 inactivation is associated with transcriptional repression of transcription factors such as KLF4 (Krüppel-like factor 4) and EGR1 (early-growth-response 1) that are known inhibitors of HSC self-renewal. Decreased Llgl1 expression in human acute myeloid leukemia (AML) cells is associated with inferior patient survival. Thus, inactivation of Llgl1 enhances HSC self-renewal and fitness and is associated with unfavorable outcome in human AML.