bluuebunny/crossref_metadata_2025 huggingface dataset:
Radiosynthesis of a Novel PET Fluoronicotinamide for Melanoma Tumour PET Imaging; [18F]MEL050
Authors: Greguric Ivan , Taylor Stephen , Pham Tien , Wyatt Naomi , Jiang Cathy D. , Bourdier Thomas , Loc'h Christian , Roselt Peter , Neels Oliver C. , Katsifis Andrew
Published: July 2011

[18F]6-Fluoro-N-[2-(diethylamino)ethyl]nicotinamide [18F]MEL050 is a novel nicotinamide-based radiotracer, designed to target random metastatic dissemination of melanoma tumours by targeting melanin. Preclinical studies suggest that [18F]MEL050 has an excellent potential to improve diagnosis and staging of melanoma. Here we report the radiochemical optimization conditions of [18F]MEL050 and its large scale automated synthesis using a GE FXFN automated radiosynthesis module for clinical, phase-1 investigation. [18F]MEL050 was prepared via a one-step synthesis using no-carrier added K[18F]F-Krytpofix® 222 (DMSO, 170°C, 5 min) followed by HPLC purification. Using 6-chloro-N-[2-(diethylamino)ethyl]nicotinamide as precursor, [18F]MEL050 was obtained in 40–46% radiochemical yield (non-decay corrected), in greater than 99.9% radiochemical purity and specific activity ranging from 240 to 325 GBq μmol–1. Total synthesis time including formulation was 40 min and [18F]MEL050 was stable (99.8%) in PBS for 6 h.
Wrapping and Internalization of Nanoparticles by Lipid Bilayers: a Computer Simulation Study
Authors: Yang Kai , Ma Yu-qiang
Published: July 2011

Endocytosis is a basic pathway for nanoparticles to enter or leave cells. However, because of the complexity of the cell membrane, the mechanism of endocytosis is largely elusive. By dissipative particle dynamics (DPD), we investigate the wrapping and internalization processes of different particles (e.g., spheres and ellipsoids) by a lipid vesicle. It is found that rotation is possibly an important mechanism in the particle internalization process under a strong adhesive interaction, which can adjust the configuration of the nanoparticle to the lipid bilayer and facilitate the progress of the wrapping. Furthermore, the fission behaviour of the vesicle and the wrapped particle is also observed when the lipid domain is considered in the system. These simulation results give an insight into the nature of endocytosis.
Simultaneous Determination of 226Ra and 228Ra in Water by Liquid Scintillation Spectrometry
Authors: Cook M. , Kleinschmidt R.
Published: July 2011

Radium is a naturally occurring alkaline earth metal that is present in soils, water, plants, and foods in low concentrations. In the analysis of radium in trace amounts, co-precipitation is the favoured way of separating an element from its matrix. In this case, radium is co-precipitated with barium. The purity and yield of the extraction is controlled by adsorption onto the barium sulfate precipitate and pH manipulation controls the solubility of certain products. This technique enables the removal of interfering lead-210 to yield a purified radium source for analysis, which is done using liquid scintillation spectrometry. The analytical results of spiked water samples are in good agreement with the known activities of radium-226 and radium-228 standard reference materials. Minimum detectable limits for radium-226 and radium-228 are calculated to be 0.01 and 0.06 Bq L–1, respectively. The method provides a fast, reliable, and accurate alternative to traditional radium isotope analysis based on α and gamma spectrometry.
Conjugated Oligomers and Polymers Based on Anthracene, Tetracene, Pentacene, Naphthodithiophene, and Anthradithiophene Building Blocks
Authors: Lehnherr Dan , Tykwinski Rik R.
Published: July 2011

Acene derivatives provide unique materials for organic semiconductor applications. Recent synthetic achievements have provided several oligomers and polymers based on acene building blocks of varied structural motifs, including anthracene, tetracene, pentacene, as well as naphtho- and anthradithiophene. This report highlights recent work in this area, particularly for the higher acenes tetracene, pentacene, and anthradithiophene. When possible, the properties of defined-length oligomers are compared and contrasted to those of mono- and polymeric systems.
The Neutron – The Curie Family's Legacy
Authors: White John W. , White Ailsa B.
Published: July 2011

This article is concerned with the scientific developments that led to the discovery of the neutron by Sir James Chadwick at the Cavendish Laboratory Cambridge in 1932. The Rutherford atom with a heavy nucleus and the problem of the ‘intra-nuclear’ electrons (needed to reconcile nuclear mass and charge) coupled with Marie Curie's discovery of radium as a prime example of natural radioactivity coming from the nucleus were key milestones. Frédéric Joliot and Irène Curie–Joliot almost discovered the neutron in 1931. But the predisposition of the thinking in Chadwick's laboratory allowed conclusive identification of the emission of a heavy neutral particle to be published about a month after the Curie–Joliot experiment. Their Nobel Prize came a few years later with the discovery of artificial radioactivity.
Neutron Diffraction – Recent Applications to Chemical Structure Determination
Authors: Edwards Alison J.
Published: July 2011

A brief introduction to the capabilities of the modern Laue neutron diffraction technique is given, and recent examples of successful solutions of structural problems are highlighted.
Genetic analysis of specific and redundant roles for p38α and p38β MAPKs during mouse development
Authors: del Barco Barrantes Ivan , Coya Juan Manuel , Maina Flavio , Arthur J. Simon C. , Nebreda Angel R.
Published: July 2011

p38α MAPK is an important regulator of cellular responses induced by external cues, but the elucidation of physiological functions for p38α has been complicated by the possible functional redundancy in vivo with the related family member p38β. We found that mice with combined deletion of p38α and p38β display diverse developmental defects at midgestation, including major cardiovascular abnormalities, which are observed neither in single knockout nor in double heterozygous embryos. Expression analysis indicates specific functions of p38α and p38β in the regulation of cardiac gene expression during development. By using knock-in animals that express p38β under control of the endogenous p38α promoter, we also found that p38β cannot perform all of the functions of p38α during embryogenesis. Our results identify essential roles for p38α and p38β during development and suggest that some specific functions may be explained by differences in expression patterns.
Mycolactone impairs T cell homing by suppressing microRNA control of L-selectin expression
Authors: Guenin-Macé Laure , Carrette Florent , Asperti-Boursin François , Le Bon Agnès , Caleechurn Laxmee , Di Bartolo Vincenzo , Fontanet Arnaud , Bismuth Georges , Demangel Caroline
Published: July 2011

Mycolactone is a macrolide produced byMycobacterium ulceranswith immunomodulatory properties. Here, we describe that in mouse, mycolactone injection led to a massive T-cell depletion in peripheral lymph nodes (PLNs) that was associated with defective expression of L-selectin (CD62-L). Importantly, preexposure to mycolactone impaired the capacity of T cells to reach PLNs after adoptive transfer, respond to chemotactic signals, and expand upon antigenic stimulation in vivo. We found that mycolactone-induced suppression of CD62-L expression by human primary T cells was induced rapidly at both the mRNA and protein levels and correlated with the reduced expression of one miRNA: let-7b. Notably, silencing of let-7b was sufficient to inhibit CD62-L gene expression. Conversely, its overexpression tended to up-regulate CD62-L and counteract the effects of mycolactone. Our results identify T-cell homing as a biological process targeted by mycolactone. Moreover, they reveal a mechanism of control of CD62-L expression involving the miRNA let-7b.
Increase developmental plasticity of human keratinocytes with gene suppression
Authors: Li Shengwen Calvin , Jin Yangsun , Loudon William G. , Song Yahui , Ma Zhiwei , Weiner Leslie P. , Zhong Jiang F.
Published: July 2011

Recent evidence indicates that p53 suppression increased the efficiency of induced pluripotent stem cell (iPSC) generation. This occurred even with the enforced expression of as few as two canonical transcription factors, Oct4 and Sox2. In this study, primary human keratinocytes were successfully induced into a stage of plasticity by transient inactivation of p53, without enforced expression of any of the transcription factors previously used in iPSC generation. These cells were later redifferentiated into neural lineages. The gene suppression plastic cells were morphologically indistinguishable from human ES cells. Gene suppression plastic cells were alkaline phosphatase-positive, had normal karyotypes, and expressed p53. Together with the accumulating evidence of similarities and overlapping mechanisms between iPSC generation and cancer formation, this finding sheds light on the emerging picture of p53 sitting at the crossroads between two intricate cellular potentials: stem cell vs. cancer cell generation. This finding further supports the crucial role played by p53 in cellular reprogramming and suggests an alternative method to switch the lineage identity of human cells. This reported method offers the potential for directed lineage switching with the goal of generating autologous cell populations for novel clinical applications for neurodegenerative diseases.
SPR-5 is a histone H3K4 demethylase with a role in meiotic double-strand break repair
Authors: Nottke Amanda C. , Beese-Sims Sara E. , Pantalena Luiz F. , Reinke Valerie , Shi Yang , Colaiácovo Monica P.
Published: July 2011

Regulation of histone methylation levels has long been implicated in multiple cellular processes, many of which involve transcription. Here, however, we report a unique role for the
Caenorhabditis elegans
histone demethylase SPR-5 in meiotic DNA double-strand break repair (DSBR). SPR-5 shows enzymatic activity toward H3K4me2 both in vitro and in the nematode germline, and
spr-5
mutants show several phenotypes indicating a perturbation of DSBR, including increased p53-dependent germ cell apoptosis, increased levels of the DSBR marker RAD-51, and sensitivity toward DSB-inducing treatments.
spr
-5
mutants show no transcriptional misregulation of known DSBR involved genes. Instead, SPR-5 shows a rapid subcellular relocalization upon DSB-inducing treatment, which suggests that SPR-5 may function directly in DSBR.
Self-aggregation of clouds in conditionally unstable moist convection
Authors: Pauluis Olivier , Schumacher Jörg
Published: July 2011

The behavior of moist Rayleigh–Bénard convection is investigated using a Boussinesq model with a simplified thermodynamics for phase transitions. This idealized configuration makes the problem accessible to high-resolution three-dimensional direct numerical simulations without small-scale parameterizations of the turbulence for extended layers with aspect ratios up to 64. Our study is focused on the frequently observed conditionally unstable environment that is stably stratified for unsaturated air, but is unstable for cloudy air. We find that no sharp threshold for the transition to convective turbulence exists, a situation similar to wall-bounded shear flows. Rather, the transition depends on the amplitude of the initial perturbation of the quiescent equilibrium and on the aspect ratio of the convective domain. In contrast to the classical dry Rayleigh–Bénard case, convection is highly asymmetric with respect to the vertical direction. Moist upwelling air inside turbulent cloud aggregates is surrounded by ambient regions of slowly descending unsaturated air. It is also found that conditionally unstable moist convection is inefficient at transporting energy. Our study suggests that there is an upper bound on the Nusselt number in moist convection that is lower than that of the classical dry case.
Mobility in geometrically confined membranes
Authors: Domanov Yegor A. , Aimon Sophie , Toombes Gilman E. S. , Renner Marianne , Quemeneur François , Triller Antoine , Turner Matthew S. , Bassereau Patricia
Published: July 2011

Lipid and protein lateral mobility is essential for biological function. Our theoretical understanding of this mobility can be traced to the seminal work of Saffman and Delbrück, who predicted a logarithmic dependence of the protein diffusion coefficient (
i
) on the inverse of the size of the protein and (
ii
) on the “membrane size” for membranes of finite size [Saffman P, Delbrück M (1975)
Proc Natl Acad Sci USA
72:3111—3113]. Although the experimental proof of the first prediction is a matter of debate, the second has not previously been thought to be experimentally accessible. Here, we construct just such a geometrically confined membrane by forming lipid bilayer nanotubes of controlled radii connected to giant liposomes. We followed the diffusion of individual molecules in the tubular membrane using single particle tracking of quantum dots coupled to lipids or voltage-gated potassium channels KvAP, while changing the membrane tube radius from approximately 250 to 10 nm. We found that both lipid and protein diffusion was slower in tubular membranes with smaller radii. The protein diffusion coefficient decreased as much as 5-fold compared to diffusion on the effectively flat membrane of the giant liposomes. Both lipid and protein diffusion data are consistent with the predictions of a hydrodynamic theory that extends the work of Saffman and Delbrück to cylindrical geometries. This study therefore provides strong experimental support for the ubiquitous Saffman–Delbrück theory and elucidates the role of membrane geometry and size in regulating lateral diffusion.
Linear rate-equilibrium relations arising from ion channel-bilayer energetic coupling
Authors: Greisen Per , Lum Kevin , Ashrafuzzaman Md. , Greathouse Denise V. , Andersen Olaf S. , Lundbæk Jens A.
Published: July 2011

Linear rate-equilibrium (RE) relations, also known as linear free energy relations, are widely observed in chemical reactions, including protein folding, enzymatic catalysis, and channel gating. Despite the widespread occurrence of linear RE relations, the principles underlying the linear relation between changes in activation and equilibrium energy in macromolecular reactions remain enigmatic. When examining amphiphile regulation of gramicidin channel gating in lipid bilayers, we noted that the gating process could be described by a linear RE relation with a simple geometric interpretation. This description is possible because the gating process provides a well-understood reaction, in which structural changes in a bilayer-embedded model protein can be studied at the single-molecule level. It is thus possible to obtain quantitative information about the energetics of the reaction transition state and its position on a spatial coordinate. It turns out that the linear RE relation for the gramicidin monomer-dimer reaction can be understood, and the quantitative relation between changes in activation energy and equilibrium energy can be interpreted, by considering the effects of amphiphiles on the changes in bilayer elastic energy associated with channel gating. We are not aware that a similar simple mechanistic explanation of a linear RE relation has been provided for a chemical reaction in a macromolecule. RE relations generally should be useful for examining how amphiphile-induced changes in bilayer properties modulate membrane protein folding and function, and for distinguishing between direct (e.g., due to binding) and indirect (bilayer-mediated) effects.
Impaired mitochondrial transport and Parkin-independent degeneration of respiratory chain-deficient dopamine neurons in vivo
Authors: Sterky Fredrik H. , Lee Seungmin , Wibom Rolf , Olson Lars , Larsson Nils-Göran
Published: July 2011

Mitochondrial dysfunction is heavily implicated in Parkinson disease (PD) as exemplified by the finding of an increased frequency of respiratory chain-deficient dopamine (DA) neurons in affected patients. An inherited form of PD is caused by impaired function of Parkin, an E3 ubiquitin ligase reported to translocate to defective mitochondria in vitro to facilitate their clearance. We have developed a reporter mouse to assess mitochondrial morphology in DA neurons in vivo and show here that respiratory chain deficiency leads to fragmentation of the mitochondrial network and to the formation of large cytoplasmic bodies derived from mitochondria. Surprisingly, the dysfunctional mitochondria do not recruit Parkin in vivo, and neither the clearance of defective mitochondria nor the neurodegeneration phenotype is affected by the absence of Parkin. We also show that anterograde axonal transport of mitochondria is impaired in respiratory chain-deficient DA neurons, leading to a decreased supply of mitochondria to the axonal terminals.
Cellular correlate of assembly formation in oscillating hippocampal networks in vitro
Authors: Bähner Florian , Weiss Elisa K. , Birke Gunnar , Maier Nikolaus , Schmitz Dietmar , Rudolph Uwe , Frotscher Michael , Traub Roger D. , Both Martin , Draguhn Andreas
Published: July 2011

Neurons form transiently stable assemblies that may underlie cognitive functions, including memory formation. In most brain regions, coherent activity is organized by network oscillations that involve sparse firing within a well-defined minority of cells. Despite extensive work on the underlying cellular mechanisms, a fundamental question remains unsolved: how are participating neurons distinguished from the majority of nonparticipators? We used physiological and modeling techniques to analyze neuronal activity in mouse hippocampal slices during spontaneously occurring high-frequency network oscillations. Network-entrained action potentials were exclusively observed in a defined subset of pyramidal cells, yielding a strict distinction between participating and nonparticipating neurons. These spikes had unique properties, because they were generated in the axon without prior depolarization of the soma. GABA
A
receptors had a dual role in pyramidal cell recruitment. First, the sparse occurrence of entrained spikes was accomplished by intense perisomatic inhibition. Second, antidromic spike generation was facilitated by tonic effects of GABA in remote axonal compartments. Ectopic spike generation together with strong somatodendritic inhibition may provide a cellular mechanism for the definition of oscillating assemblies.
Peptides targeting inflamed synovial vasculature attenuate autoimmune arthritis
Authors: Yang Ying-Hua , Rajaiah Rajesh , Ruoslahti Erkki , Moudgil Kamal D.
Published: July 2011

Autoimmune diseases, such as rheumatoid arthritis, frequently target one major tissue/organ despite the systemic nature of the immune response. This is particularly perplexing in the case of ubiquitously distributed antigens invoked in arthritis induction. We reasoned that selective targeting of the synovial joints in autoimmune arthritis might be due in part to the unique attributes of the joint vasculature. We examined this proposition using the adjuvant-induced arthritis model of human rheumatoid arthritis, and profiled the synovial vasculature using ex vivo and in vivo screening of a defined phage peptide-display library. We identified phage that preferentially homed to the inflamed joints. The corresponding synthetic peptides showed binding to the joint-derived endothelial cells, as well as specificity in inhibiting binding of the respective phage to the synovial vasculature. Intriguingly, the treatment of arthritic rats with one such peptide resulted in efficient inhibition of the progression of arthritis. The suppression of arthritis was attributable in part to the peptide-induced reduction of T-cell trafficking into the joints and the inhibition of angiogenesis. This peptide differed in sequence, in receptor binding specificity, and in angiogenesis/inflammation-related cell signaling from the previously characterized arginine-glycine-aspartic acid–containing peptide. Thus, our study reveals joint-homing peptides that can be further exploited for the selective delivery of antiarthritic agents into the inflamed joints to enhance their efficacy while reducing systemic toxicity, and also for examining intricacies of the pathogenesis of arthritis. This approach can be customized for application to other organ-specific autoimmune diseases as well.
Identification of transmitter systems and learning tag molecules involved in behavioral tagging during memory formation
Authors: Moncada Diego , Ballarini Fabricio , Martinez María Cecilia , Frey Julietta U. , Viola Haydee
Published: July 2011

Long-term memory (LTM) consolidation requires the synthesis of plasticity-related proteins (PRPs). In addition, we have shown recently that LTM formation also requires the setting of a “learning tag” able to capture those PRPs. Weak training, which results only in short-term memory, can set a tag to use PRPs derived from a temporal-spatial closely related event to promote LTM formation. Here, we studied the involvement of glutamatergic, dopaminergic, and noradrenergic inputs on the setting of an inhibitory avoidance (IA) learning tag and the synthesis of PRPs. Rats explored an open field (PRP donor) followed by weak (tag inducer) or strong (tag inducer plus PRP donor) IA training. Throughout pharmacological interventions around open-field and/or IA sessions, we found that hippocampal dopamine D1/D5- and β-adrenergic receptors are specifically required to induce PRP synthesis. Moreover, activation of the glutamatergic NMDA receptors is required for setting the learning tags, and this machinery further required α-Ca
2+
/calmodulin-dependent protein kinase II and PKA but not ERK1/2 activity. Together, the present findings emphasize an essential role of the induction of PRPs and learning tags for LTM formation. The existence of only the PRP or the tag was insufficient for stabilization of the mnemonic trace.
Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)
Authors: Reiland Sonja , Finazzi Giovanni , Endler Anne , Willig Adrian , Baerenfaller Katja , Grossmann Jonas , Gerrits Bertran , Rutishauser Dorothea , Gruissem Wilhelm , Rochaix Jean-David , Baginsky Sacha
Published: July 2011

Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled by protein phosphorylation. Two thylakoid-associated kinases, STN7 and STN8, have distinct roles in short- and long-term photosynthetic acclimation to changes in light quality and quantity. Although some substrates of STN7 and STN8 are known, the complexity of this regulatory kinase system implies that currently unknown substrates connect photosynthetic performance with the regulation of metabolic and regulatory functions. We performed an unbiased phosphoproteome-wide screen with
Arabidopsis
WT and
stn8
mutant plants to identify unique STN8 targets. The phosphorylation status of STN7 was not affected in
stn8
, indicating that kinases other than STN8 phosphorylate STN7 under standard growth conditions. Among several putative STN8 substrates, PGRL1-A is of particular importance because of its possible role in the modulation of cyclic electron transfer. The STN8 phosphorylation site on PGRL1-A is absent in both monocotyledonous plants and algae. In dicots, spectroscopic measurements with
Arabidopsis
WT,
stn7
,
stn8,
and
stn7
/
stn8
double-mutant plants indicate a STN8-mediated slowing down of the transition from cyclic to linear electron flow at the onset of illumination. This finding suggests a possible link between protein phosphorylation by STN8 and fine-tuning of cyclic electron flow during this critical step of photosynthesis, when the carbon assimilation is not commensurate to the electron flow capacity of the chloroplast.
G protein-coupled receptor 56 and collagen III, a receptor-ligand pair, regulates cortical development and lamination
Authors: Luo Rong , Jeong Sung-Jin , Jin Zhaohui , Strokes Natalie , Li Shihong , Piao Xianhua
Published: July 2011

GPR56, an orphan G protein-coupled receptor (GPCR) from the family of adhesion GPCRs, plays an indispensable role in cortical development and lamination. Mutations in the
GPR56
gene cause a malformed cerebral cortex in both humans and mice that resembles cobblestone lissencephaly, which is characterized by overmigration of neurons beyond the pial basement membrane. However, the molecular mechanisms through which GPR56 regulates cortical development remain elusive due to the unknown status of its ligand. Here we identify collagen, type III, alpha-1 (gene symbol
Col3a1
) as the ligand of GPR56 through an in vitro biotinylation/proteomics approach. Further studies demonstrated that
Col3a1
null mutant mice exhibit overmigration of neurons beyond the pial basement membrane and a cobblestone-like cortical malformation similar to the phenotype seen in
Gpr56
null mutant mice. Functional studies suggest that the interaction of collagen III with its receptor GPR56 inhibits neural migration in vitro. As for intracellular signaling, GPR56 couples to the Gα
12/13
family of G proteins and activates RhoA pathway upon ligand binding. Thus, collagen III regulates the proper lamination of the cerebral cortex by acting as the major ligand of GPR56 in the developing brain.
The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere
Authors: Cole Hope A. , Howard Bruce H. , Clark David J.
Published: July 2011

The centromeres of budding yeast are ∼120 bp in size and contain three functional elements: an AT-rich region flanked by binding sites for Cbf1 and CBF3. A specialized nucleosome containing the H3 variant Cse4 (CenH3) is formed at the centromere. Our genome-wide paired-end sequencing of nucleosomal DNA reveals that the centromeric nucleosome contains a micrococcal nuclease-resistant kernel of 123–135 bp, depending on the centromere, and is therefore significantly shorter than the canonical nucleosome. Unlike canonical nucleosomes, the centromeric nucleosome is essentially perfectly positioned. The entire centromere is included, together with at least 1 bp of DNA upstream of the Cbf1 site and at least 4 bp downstream of the CBF3 site. The fact that the binding sites for Cbf1 and CBF3 are included within the centromeric nucleosome has important implications for models of the centromeric nucleosome and for kinetochore function.
Bacteria use type-IV pili to slingshot on surfaces
Authors: Jin Fan , Conrad Jacinta C. , Gibiansky Maxsim L. , Wong Gerard C. L.
Published: July 2011

Bacteria optimize the use of their motility appendages to move efficiently on a wide range of surfaces prior to forming multicellular bacterial biofilms. The “twitching” motility mode employed by many bacterial species for surface exploration uses type-IV pili (TFP) as linear actuators to enable directional crawling. In addition to linear motion, however, motility requires turns and changes of direction. Moreover, the motility mechanism must be adaptable to the continually changing surface conditions encountered during biofilm formation. Here, we develop a novel two-point tracking algorithm to dissect twitching motility in this context. We show that TFP-mediated crawling in
Pseudomonas aeruginosa
consistently alternates between two distinct actions: a translation of constant velocity and a combined translation-rotation that is approximately 20× faster in instantaneous velocity. Orientational distributions of these actions suggest that the former is due to pulling by multiple TFP, whereas the latter is due to release by single TFP. The release action leads to a fast “slingshot” motion that can turn the cell body efficiently by oversteering. Furthermore, the large velocity of the slingshot motion enables bacteria to move efficiently through environments that contain shear-thinning viscoelastic fluids, such as the extracellular polymeric substances (EPS) that bacteria secrete on surfaces during biofilm formation.
Reluctance to membrane binding enables accessibility of the synaptobrevin SNARE motif for SNARE complex formation
Authors: Brewer Kyle D. , Li Wei , Horne Bethany Erin , Rizo Josep
Published: July 2011

SNARE proteins play a critical role in intracellular membrane fusion by forming tight complexes that bring two membranes together and involve sequences called SNARE motifs. These motifs have a high tendency to form amphipathic coiled-coils that assemble into four-helix bundles, and often precede transmembrane regions. NMR studies in dodecylphosphocholine (DPC) micelles suggested that the N-terminal half of the SNARE motif from the neuronal SNARE synaptobrevin binds to membranes, which appeared to contradict previous biophysical studies of synaptobrevin in liposomes. NMR analyses of synaptobrevin reconstituted into nanodiscs and into liposomes now show that most of its SNARE motif, except for the basic C terminus, is highly flexible, exhibiting cross-peak patterns and transverse relaxation rates that are very similar to those observed in solution. Considering the proximity to the bilayer imposed by membrane anchoring, our data show that most of the synaptobrevin SNARE motif has a remarkable reluctance to bind membranes. This conclusion is further supported by NMR experiments showing that the soluble synaptobrevin SNARE motif does not bind to liposomes, even though it does bind to DPC micelles. These results show that nanodiscs provide a much better membrane model than DPC micelles in this system, and that most of the SNARE motif of membrane-anchored synaptobrevin is accessible for SNARE complex formation. We propose that the charge and hydrophobicity of SNARE motifs is optimized to enable formation of highly stable SNARE complexes while at the same time avoiding membrane binding, which could hinder SNARE complex assembly.
Cryptic sexual populations account for genetic diversity and ecological success in a widely distributed, asexual fungus-growing ant
Authors: Rabeling Christian , Gonzales Omar , Schultz Ted R. , Bacci Maurício , Garcia Marcos V. B. , Verhaagh Manfred , Ishak Heather D. , Mueller Ulrich G.
Published: July 2011

Sex and recombination are central processes in life generating genetic diversity. Organisms that rely on asexual propagation risk extinction due to the loss of genetic diversity and the inability to adapt to changing environmental conditions. The fungus-growing ant species
Mycocepurus smithii
was thought to be obligately asexual because only parthenogenetic populations have been collected from widely separated geographic localities. Nonetheless,
M. smithii
is ecologically successful, with the most extensive distribution and the highest population densities of any fungus-growing ant. Here we report that
M. smithii
actually consists of a mosaic of asexual and sexual populations that are nonrandomly distributed geographically. The sexual populations cluster along the Rio Amazonas and the Rio Negro and appear to be the source of independently evolved and widely distributed asexual lineages, or clones. Either apomixis or automixis with central fusion and low recombination rates is inferred to be the cytogenetic mechanism underlying parthenogenesis in
M. smithii
. Males appear to be entirely absent from asexual populations, but their existence in sexual populations is indicated by the presence of sperm in the reproductive tracts of queens. A phylogenetic analysis of the genus suggests that
M. smithii
is monophyletic, rendering a hybrid origin of asexuality unlikely. Instead, a mitochondrial phylogeny of sexual and asexual populations suggests multiple independent origins of asexual reproduction, and a divergence-dating analysis indicates that
M. smithii
evolved 0.5–1.65 million years ago. Understanding the evolutionary origin and maintenance of asexual reproduction in this species contributes to a general understanding of the adaptive significance of sex.
Discrete fracture patterns of virus shells reveal mechanical building blocks
Authors: Ivanovska Irena L. , Miranda Roberto , Carrascosa Jose L. , Wuite Gijs J. L. , Schmidt Christoph F.
Published: July 2011

Viral shells are self-assembled protein nanocontainers with remarkable material properties. They combine simplicity of construction with toughness and complex functionality. These properties make them interesting for bionanotechnology. To date we know little about how virus structure determines assembly pathways and shell mechanics. We have here used atomic force microscopy to study structural failure of the shells of the bacteriophage Φ29. We observed rigidity patterns following the symmetry of the capsid proteins. Under prolonged force exertion, we observed fracture along well-defined lines of the 2D crystal lattice. The mechanically most stable building block of the shells was a trimer. Our approach of “reverse engineering” the virus shells thus made it possible to identify stable structural intermediates. Such stable intermediates point to a hierarchy of interactions among equal building blocks correlated with distinct next-neighbor interactions. The results also demonstrate that concepts from macroscopic materials science, such as fracture, can be usefully employed in molecular engineering.
Individual versus systemic risk and the Regulator's Dilemma
Authors: Beale Nicholas , Rand David G. , Battey Heather , Croxson Karen , May Robert M. , Nowak Martin A.
Published: July 2011

The global financial crisis of 2007–2009 exposed critical weaknesses in the financial system. Many proposals for financial reform address the need for systemic regulation—that is, regulation focused on the soundness of the whole financial system and not just that of individual institutions. In this paper, we study one particular problem faced by a systemic regulator: the tension between the distribution of assets that individual banks would like to hold and the distribution across banks that best supports system stability if greater weight is given to avoiding multiple bank failures. By diversifying its risks, a bank lowers its own probability of failure. However, if many banks diversify their risks in similar ways, then the probability of multiple failures can increase. As more banks fail simultaneously, the economic disruption tends to increase disproportionately. We show that, in model systems, the expected systemic cost of multiple failures can be largely explained by two global parameters of risk exposure and diversity, which can be assessed in terms of the risk exposures of individual actors. This observation hints at the possibility of regulatory intervention to promote systemic stability by incentivizing a more diverse diversification among banks. Such intervention offers the prospect of an additional lever in the armory of regulators, potentially allowing some combination of improved system stability and reduced need for additional capital.
Histone fold modifications control nucleosome unwrapping and disassembly
Authors: Simon Marek , North Justin A. , Shimko John C. , Forties Robert A. , Ferdinand Michelle B. , Manohar Mridula , Zhang Meng , Fishel Richard , Ottesen Jennifer J. , Poirier Michael G.
Published: July 2011

Nucleosomes are stable DNA–histone protein complexes that must be unwrapped and disassembled for genome expression, replication, and repair. Histone posttranslational modifications (PTMs) are major regulatory factors of these nucleosome structural changes, but the molecular mechanisms associated with PTM function remains poorly understood. Here we demonstrate that histone PTMs within distinct structured regions of the nucleosome directly regulate the inherent dynamic properties of the nucleosome. Precise PTMs were introduced into nucleosomes by chemical ligation. Single molecule magnetic tweezers measurements determined that only PTMs near the nucleosome dyad increase the rate of histone release in unwrapped nucleosomes. In contrast, FRET and restriction enzyme analysis reveal that only PTMs throughout the DNA entry–exit region increase unwrapping and enhance transcription factor binding to nucleosomal DNA. These results demonstrate that PTMs in separate structural regions of the nucleosome control distinct dynamic events, where the dyad regulates disassembly while the DNA entry–exit region regulates unwrapping. These studies are consistent with the conclusion that histone PTMs may independently influence nucleosome dynamics and associated chromatin functions.
G protein Gαo is essential for vomeronasal function and aggressive behavior in mice
Authors: Chamero Pablo , Katsoulidou Vicky , Hendrix Philipp , Bufe Bernd , Roberts Richard , Matsunami Hiroaki , Abramowitz Joel , Birnbaumer Lutz , Zufall Frank , Leinders-Zufall Trese
Published: July 2011

The rodent vomeronasal organ (VNO) mediates the regulation of species-specific and interspecies social behaviors. We have used gene targeting to examine the role of the G protein Gαo, encoded by the gene
Gnao1
, in vomeronasal function. We used the Cre-
loxP
system to delete Gαo in those cells that express olfactory marker protein, which includes all vomeronasal sensory neurons of the basal layer of the VNO sensory epithelium. Using electrophysiology and calcium imaging, we show that the conditional null mice exhibit strikingly reduced sensory responses in V2R receptor-expressing vomeronasal sensory neurons to specific molecular cues, including MHC1 antigens, major urinary proteins, and exocrine gland-secreting peptide. Gαo is also vital for vomeronasal sensing of two
N
-formylated mitochondrially encoded peptides derived from NADH dehydrogenase 1. Furthermore, we show that Gαo is an essential requirement for the display of male–male territorial aggression as well as maternal aggression in mice. Finally, we show that Gαo-dependent maternal aggression can be induced by major urinary proteins. These cellular and behavioral phenotypes identify Gαo as the primary G-protein α-subunit mediating the detection of peptide and protein pheromones by sensory neurons of the VNO.
Link between statistical equilibrium fidelity and forecasting skill for complex systems with model error
Authors: Majda Andrew J. , Gershgorin Boris
Published: July 2011

Understanding and improving the predictive skill of imperfect models for complex systems in their response to external forcing is a crucial issue in diverse applications such as for example climate change science. Equilibrium statistical fidelity of the imperfect model on suitable coarse-grained variables is a necessary but not sufficient condition for this predictive skill, and elementary examples are given here demonstrating this. Here, with equilibrium statistical fidelity of the imperfect model, a direct link is developed between the predictive fidelity of specific test problems in the training phase where the perfect natural system is observed and the predictive skill for the forced response of the imperfect model by combining appropriate concepts from information theory with other concepts based on the fluctuation dissipation theorem. Here a suite of mathematically tractable models with nontrivial eddy diffusivity, variance, and intermittent non-Gaussian statistics mimicking crucial features of atmospheric tracers together with stochastically forced standard eddy diffusivity approximation with model error are utilized to illustrate this link.
Caenorhabditis elegans
NPR-1–mediated behaviors are suppressed in the presence of mucoid bacteria
Authors: Reddy Kirthi C. , Hunter Ryan C. , Bhatla Nikhil , Newman Dianne K. , Kim Dennis H.
Published: July 2011

Caenorhabditis elegans
exhibits a diverse range of behaviors in response to bacteria. The presence of bacterial food influences
C. elegans
aerotaxis, aggregation, locomotion, and pathogen avoidance behaviors through the activity of the NPR-1 neuropeptide receptor. Here, we show that mucoid strains of bacteria that produce an exopolysaccharide matrix do not induce NPR-1–dependent behaviors. In the presence of mucoid strains of bacteria, the
C. elegans
laboratory wild-type (WT) strain N2 exhibits behaviors characteristic of wild isolates and mutants with reduced NPR-1 activity. Specifically, N2 exhibits lawn bordering and roaming behavior on mucoid nonpathogenic bacteria and loss of pathogen avoidance on mucoid
Pseudomonas aeruginosa
. Alginate biosynthesis by laboratory and clinical isolates of mucoid
P. aeruginosa
is necessary and sufficient to attenuate NPR-1–mediated behavior and it suppresses
C. elegans
pathogen avoidance behavior. Our data suggest that the specific interaction with nonmucoid bacteria induces NPR-1–dependent behaviors of
C. elegans
. These observations provide an example of how exopolysaccharide matrix biosynthesis by a community of bacteria may inhibit specific host responses to microbes.
Unique carbohydrate–carbohydrate interactions are required for high affinity binding between FcγRIII and antibodies lacking core fucose
Authors: Ferrara Claudia , Grau Sandra , Jäger Christiane , Sondermann Peter , Brünker Peter , Waldhauer Inja , Hennig Michael , Ruf Armin , Rufer Arne Christian , Stihle Martine , Umaña Pablo , Benz Jörg
Published: July 2011

Antibody-mediated cellular cytotoxicity (ADCC), a key immune effector mechanism, relies on the binding of antigen–antibody complexes to Fcγ receptors expressed on immune cells. Antibodies lacking core fucosylation show a large increase in affinity for FcγRIIIa leading to an improved receptor-mediated effector function. Although afucosylated IgGs exist naturally, a next generation of recombinant therapeutic, glycoenginereed antibodies is currently being developed to exploit this finding. In this study, the crystal structures of a glycosylated Fcγ receptor complexed with either afucosylated or fucosylated Fc were determined allowing a detailed, molecular understanding of the regulatory role of Fc-oligosaccharide core fucosylation in improving ADCC. The structures reveal a unique type of interface consisting of carbohydrate–carbohydrate interactions between glycans of the receptor and the afucosylated Fc. In contrast, in the complex structure with fucosylated Fc, these contacts are weakened or nonexistent, explaining the decreased affinity for the receptor. These findings allow us to understand the higher efficacy of therapeutic antibodies lacking the core fucose and also suggest a unique mechanism by which the immune system can regulate antibody-mediated effector functions.
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon
Authors: Gogol Emily B. , Rhodius Virgil A. , Papenfort Kai , Vogel Jörg , Gross Carol A.
Published: July 2011

The
Escherichia coli
σ
E
envelope stress response monitors and repairs the outer membrane, a function central to the life of Gram-negative bacteria. The σ
E
stress response was characterized as a single-tier activation network comprised of ∼100 genes, including the MicA and RybB noncoding sRNAs. These highly expressed sRNAs were thought to carry out the specialized function of halting de novo synthesis of several abundant porins when envelope homeostasis was perturbed. Using a systematic target profiling and validation approach we discovered that MicA and RybB are each global mRNA repressors of both distinct and shared targets, and that the two sRNAs constitute a posttranscriptional repression arm whose regulatory scope rivals that of the protein-based σ
E
activation arm. Intriguingly, porin mRNAs constitute only ∼1/3 of all targets and new nonporin targets predict roles for MicA and RybB in crosstalk with other regulatory responses. This work also provides an example of evolutionarily unrelated sRNAs that are coinduced and bind the same targets, but at different sites. Our finding that expression of either MicA or RybB sRNA protects the cell from the loss of viability experienced when σ
E
activity is inadequate illustrates the importance of the posttranscriptional repression arm of the response. σ
E
is a paradigm of a single-tier stress response with a clear division of labor in which highly expressed noncoding RNAs (MicA, RybB) endow a transcriptional factor intrinsically restricted to gene activation (σ
E
) with the opposite repressor function.
Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress
Authors: Liu Sean T. H. , Sharon-Friling Ronit , Ivanova Pavlina , Milne Stephen B. , Myers David S. , Rabinowitz Joshua D. , Brown H. Alex , Shenk Thomas
Published: July 2011

Human cytomegalovirus induces and requires fatty acid synthesis. This suggests an essential role for lipidome remodeling in viral replication. We used mass spectrometry to quantify glycerophospholipids in mock-infected and virus-infected fibroblasts, as well as in virions. Although the lipid composition of mock-infected and virus-infected fibroblasts was similar, virions were markedly different. The virion envelope contained twofold more phosphatidylethanolamines and threefold less phosphatidylserines than the host cell. This indicates that the virus buds from a membrane with a different lipid composition from the host cell as a whole. Compared with published datasets, the virion envelope showed the greatest similarity to the synaptic vesicle lipidome. Synaptosome-associated protein of 25 kDa (SNAP-25) is a component of the complex that mediates exocytosis of synaptic vesicles in neurons; and its homolog, SNAP-23, functions in exocytosis in many other cell types. Infection induced the relocation of SNAP-23 to the cytoplasmic viral assembly zone, and knockdown of SNAP-23 inhibited the production of virus. We propose that cytomegalovirus capsids acquire their envelope by budding into vesicles with a lipid composition similar to that of synaptic vesicles, which subsequently fuse with the plasma membrane to release virions from the cell.
Accurate measurement of pancreatic islet β-cell mass using a second-generation fluorescent exendin-4 analog
Authors: Reiner Thomas , Thurber Greg , Gaglia Jason , Vinegoni Claudio , Liew Chong Wee , Upadhyay Rabi , Kohler Rainer H. , Li Li , Kulkarni Rohit N. , Benoist Christophe , Mathis Diane , Weissleder Ralph
Published: July 2011

The hallmark of type 1 diabetes is autoimmune destruction of the insulin-producing β-cells of the pancreatic islets. Autoimmune diabetes has been difficult to study or treat because it is not usually diagnosed until substantial β-cell loss has already occurred. Imaging agents that permit noninvasive visualization of changes in β-cell mass remain a high-priority goal. We report on the development and testing of a near-infrared fluorescent β-cell imaging agent. Based on the amino acid sequence of exendin-4, we created a neopeptide via introduction of an unnatural amino acid at the K
12
position, which could subsequently be conjugated to fluorophores via bioorthogonal copper-catalyzed click-chemistry. Cell assays confirmed that the resulting fluorescent probe (E4
×12
-VT750) had a high binding affinity (∼3 nM). Its in vivo properties were evaluated using high-resolution intravital imaging, histology, whole-pancreas visualization, and endoscopic imaging. According to intravital microscopy, the probe rapidly bound to β-cells and, as demonstrated by confocal microscopy, it was internalized. Histology of the whole pancreas showed a close correspondence between fluorescence and insulin staining, and there was an excellent correlation between imaging signals and β-cell mass in mice treated with streptozotocin, a β-cell toxin. Individual islets could also be visualized by endoscopic imaging. In short, E4
×12
-VT750 showed strong and selective binding to glucose-like peptide-1 receptors and permitted accurate measurement of β-cell mass in both diabetic and nondiabetic mice. This near-infrared imaging probe, as well as future radioisotope-labeled versions of it, should prove to be important tools for monitoring diabetes, progression, and treatment in both experimental and clinical contexts.