bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of S-nitrosated mitochondrial proteins by S-nitrosothiol difference in gel electrophoresis (SNO-DIGE): implications for the regulation of mitochondrial function by reversible S-nitrosation
Authors: Chouchani Edward T. , Hurd Thomas R. , Nadtochiy Sergiy M. , Brookes Paul S. , Fearnley Ian M. , Lilley Kathryn S. , Smith Robin A. J. , Murphy Michael P.
Published: June 2010

The S-nitrosation of mitochondrial proteins as a consequence of NO metabolism is of physiological and pathological significance. We previously developed a MitoSNO (mitochondria-targeted S-nitrosothiol) that selectively S-nitrosates mitochondrial proteins. To identify these S-nitrosated proteins, here we have developed a selective proteomic methodology, SNO-DIGE (S-nitrosothiol difference in gel electrophoresis). Protein thiols in control and MitoSNO-treated samples were blocked, then incubated with copper(II) and ascorbate to selectively reduce S-nitrosothiols. The samples were then treated with thiol-reactive Cy3 (indocarbocyanine) or Cy5 (indodicarbocyanine) fluorescent tags, mixed together and individual protein spots were resolved by 2D (two-dimensional) gel electrophoresis. Fluorescent scanning of these gels revealed S-nitrosated proteins by an increase in Cy5 red fluorescence, allowing for their identification by MS. Parallel analysis by Redox-DIGE enabled us to distinguish S-nitrosated thiol proteins from those which became oxidized due to NO metabolism. We identified 13 S-nitrosated mitochondrial proteins, and a further four that were oxidized, probably due to evanescent S-nitrosation relaxing to a reversible thiol modification. We investigated the consequences of S-nitrosation for three of the enzymes identified using SNO-DIGE (aconitase, mitochondrial aldehyde dehydrogenase and α-ketoglutarate dehydrogenase) and found that their activity was selectively and reversibly inhibited by S-nitrosation. We conclude that the reversible regulation of enzyme activity by S-nitrosation modifies enzymes central to mitochondrial metabolism, whereas identification and functional characterization of these novel targets provides mechanistic insight into the potential physiological and pathological roles played by this modification. More generally, the development of SNO-DIGE facilitates robust investigation of protein S-nitrosation across the proteome.
Inhibition of the renin–angiotensin system prevents seizures in a rat model of epilepsy
Authors: Pereira Marilia G.A.G. , Becari Christiane , Oliveira José A.C. , Salgado Maria Cristina O. , Garcia-Cairasco Norberto , Costa-Neto Claudio M.
Published: June 2010

The RAS (renin–angiotensin system) is classically involved in BP (blood pressure) regulation and water–electrolyte balance, and in the central nervous system it has been mostly associated with homoeostatic processes, such as thirst, hormone secretion and thermoregulation. Epilepsies are chronic neurological disorders characterized by recurrent epileptic seizures that affect 1–3% of the world's population, and the most commonly used anticonvulsants are described to be effective in approx. 70% of the population with this neurological alteration. Using a rat model of epilepsy, we found that components of the RAS, namely ACE (angiotensin-converting enzyme) and the AT1 receptor (angiotensin II type 1 receptor) are up-regulated in the brain (2.6- and 8.2-fold respectively) following repetitive seizures. Subsequently, epileptic animals were treated with clinically used doses of enalapril, an ACE inhibitor, and losartan, an AT1 receptor blocker, leading to a significant decrease in seizure severities. These results suggest that centrally acting drugs that target the RAS deserve further investigation as possible anticonvulsant agents and may represent an additional strategy in the management of epileptic patients.
Impaired muscle protein anabolic response to insulin and amino acids in heart failure patients: relationship with markers of immune activation
Authors: Toth Michael J. , LeWinter Martin M. , Ades Philip A. , Matthews Dwight E.
Published: June 2010

Patients with chronic HF (heart failure) experience muscle atrophy during the course of the disease. The mechanisms underlying muscle atrophy in HF, however, are not understood. Thus we evaluated leg phenylalanine balance and kinetics in HF patients and controls following a brief fast (24 h) and under euglycaemic–hyperinsulinaemic–hyperaminoacidaemic conditions to determine whether HF increases muscle protein catabolism in response to nutritional deprivation and/or diminishes the anabolic response to meal-related stimuli (insulin and amino acids) and whether alterations in protein metabolism correlate to circulating cytokine levels. No differences in phenylalanine balance, rate of appearance or rate of disappearance were found between patients and controls under fasting conditions. However, the anabolic response to hyperinsulinaemia–hyperaminoacidaemia was reduced by more than 50% in patients compared with controls. The diminished anabolic response was due to reduced suppression of the leg phenylalanine appearance rate, an index of protein breakdown, in HF patients; whereas no group difference was found in the increase in the leg phenylalanine disappearance rate, an index of protein synthesis. The diminished responses of both phenylalanine balance and appearance rate to hyperinsulinaemia–hyperaminoacidaemia were related to greater circulating IL-6 (interleukin-6) levels. Our results suggest that, following a brief period of nutritional deprivation, HF patients demonstrate an impaired muscle protein anabolic response to meal-related stimuli, due to an inability to suppress muscle proteolysis, and that this diminished protein anabolic response correlates with markers of immune activation. The inability to stimulate muscle protein anabolism following periods of nutritional deficiency may contribute to muscle wasting in HF patients.
Quantum-dynamical consequences of the permutation symmetry of methyl groups
Authors: Grohmann Thomas , Leibscher Monika
Published: June 2010

We identify the nuclear spin isomers of nitromethane (CH3NO2) and discuss how symmetry arguments may be used to determine the spectrum and eigenfunctions of the spatial and spin-dependent Hamiltonians in an elegant way. Furthermore, we explore the effect of nuclear spin on the dynamics of the methyl group induced by a time-dependent magnetic field. We demonstrate that dipolar interactions between the protons can give rise to rotation of the methyl group and show within a one-dimensional model and first order time-dependent perturbation theory that the induced motion is unidirectional and nuclear-spin selective.
A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations
Authors: Patargias Georgios N. , Harris Sarah A. , Harding John H.
Published: June 2010

The dielectric properties of proteins are important in determining responses to changes in pH, responses to external electric fields, and the energy associated with charge injection or charge transfer. Although the importance of electrostatic interactions in proteins is well established and they are routinely included in simulations, the dielectric properties of proteins are less frequently discussed. We use a combination of atomistic molecular dynamics simulation and continuum electrostatics models to calculate the local dielectric constant within regions of the model protein hen egg white lysozyme. The local dielectric response of the protein was found to be highly inhomogeneous and strongly dependent on the local chemical environment. In light of these findings, we discuss the use of models using a single effective dielectric constant for the whole protein and the relationship between variations in local protein dielectric response and the activity of protein sites.
Temporal effects on spectroscopic line shapes, resolution, and sensitivity of the broad-band sum frequency generation
Authors: Stiopkin Igor V. , Jayathilake Himali D. , Weeraman Champika , Benderskii Alexander V.
Published: June 2010

Sum frequency generation (SFG) is a surface-selective spectroscopy that provides a wealth of molecular-level information on the structure and dynamics at surfaces and interfaces. This paper addresses the general issue of spectral resolution and sensitivity of the broad-band (BB) SFG that involves a spectrally narrow nonresonant (usually visible) and a BB resonant (usually infrared) laser pulses. We examine how the spectral width and temporal shape of the two pulses, and the time delay between them, relate to the spectroscopic line shape and signal level in the BB-SFG measurement. By combining experimental and model calculations, we show that the best spectral resolution and highest signal level are simultaneously achieved when the nonresonant narrow-band upconversion pulse arrives with a nonzero time delay after the resonant BB pulse. The nonzero time delay partially avoids the linear trade-off of improving spectral resolution at the expense of decreasing signal intensity, which is common in BB-SFG schemes utilizing spectral filtering to produce narrow-band visible pulses.
Equilibrium self-assembly of colloids with distinct interaction sites: Thermodynamics, percolation, and cluster distribution functions
Authors: Tavares J. M. , Teixeira P. I. C. , Telo da Gama M. M. , Sciortino F.
Published: June 2010

We calculate the equilibrium thermodynamic properties, percolation threshold, and cluster distribution functions for a model of associating colloids, which consists of hard spherical particles having on their surfaces three short-ranged attractive sites (sticky spots) of two different types, A and B. The thermodynamic properties are calculated using Wertheim’s perturbation theory of associating fluids. This also allows us to find the onset of self-assembly, which can be quantified by the maxima of the specific heat at constant volume. The percolation threshold is derived, under the no-loop assumption, for the correlated bond model: In all cases it is two percolated phases that become identical at a critical point, when one exists. Finally, the cluster size distributions are calculated by mapping the model onto an effective model, characterized by a—state-dependent—functionality f¯ and unique bonding probability p¯. The mapping is based on the asymptotic limit of the cluster distributions functions of the generic model and the effective parameters are defined through the requirement that the equilibrium cluster distributions of the true and effective models have the same number-averaged and weight-averaged sizes at all densities and temperatures. We also study the model numerically in the case where BB interactions are missing. In this limit, AB bonds either provide branching between A-chains (Y-junctions) if ϵAB/ϵAA is small, or drive the formation of a hyperbranched polymer if ϵAB/ϵAA is large. We find that the theoretical predictions describe quite accurately the numerical data, especially in the region where Y-junctions are present. There is fairly good agreement between theoretical and numerical results both for the thermodynamic (number of bonds and phase coexistence) and the connectivity properties of the model (cluster size distributions and percolation locus).
Toward elucidating the mechanism of femtosecond pulse shaping control in photodynamics of molecules by velocity map photoelectron and ion imaging
Authors: Irimia Daniel , Janssen Maurice H. M.
Published: June 2010

The control of photofragmentation and ionization in a polyatomic molecule has been studied by femtosecond chirped laser pulse excitation and velocity map photoelectron and ion imaging. The experiments aimed at controlling and investigating the photodynamics in CH2BrCl using tunable chirped femtosecond pulses in the visible wavelength region 509–540 nm at maximum intensities of about 4×1013 W/cm2. We observe that the time-of-flight mass spectra as well as the photoelectron images can be strongly modified by manipulating the chirp parameter of ultrashort laser pulses. Specifically, a strong enhancement of the CH2Cl+/CH2BrCl+ ion ratio by a factor of five and changes in the photoelectron spectra are observed for positively chirped pulses centered near 520 nm. These changes are only observed within a narrow window of wavelengths around 520 nm and only for positively chirped pulses. From the combination of the photoelectron spectra and the ion recoil energy of the CH2Cl+ fragment we can deduce that the parent ionization and fragmentation is induced by a multiphoton excitation with five photons. The photoelectron images and the fragment ion images also provide the anisotropy (β-parameter) of the various electron bands and fragment ions. We conclude that multiphoton excitation of the highest occupied 22a′ and 8a″ CH2BrCl molecular orbitals of Br-character are both involved in the five-photon ionization, however, only excitation of the 22a′ orbital appears to be (mostly) involved in the chirped control dynamics leading to enhanced fragmentation to CH2Cl+(X̃A′)+Br(P23/2). We propose that a wavepacket following or a time-delay resonance mechanism between the two-photon excited nx(Br,22a′)→(2A′) repulsive surface and the three-photon near-resonant nx(Br,22a′)→Rydberg(A′) state of the neutral CH2BrCl molecule is responsible for the enhanced excitation of the nx(Br,22a′) molecular orbital with up-chirped pulses. This leads to enhanced ionization to a configuration in the CH2BrCl+(X̃A′) continuum just above the dissociation limit of the CH2Cl++Br(P23/2) channel, resulting in enhanced fragmentation.
X-ray absorption and luminescence studies of Ba2Ca(BO3)2: Ce3+/Na+ phosphors
Authors: Ko J. Y. Peter , Yiu Yun-Mui , Liang Hongbin , Sham Tsun-Kong
Published: June 2010

X-ray excited optical luminescence (XEOL) spectroscopy has been used to investigate the optical emission properties of Ce3+ activated Ba2Ca(BO3)2 with a charge-compensating Na+ and the results are compared with the optical emission properties from UV excitation. Further, x-ray absorption near-edge structure (XANES) has been employed to study the chemical environment and energy transfer efficiency to optical emission upon x-ray excitation. XEOL results agree well with optical emission with UV excitation. XANES results across various absorption edges show that while the chemical environment of host materials does not change significantly with doping, luminescence yield decreases significantly at absorption edges due to an abrupt change in the de-excitation mechanism.
CdTe Schottky diodes from colloidal nanocrystals
Authors: Olson J. D. , Rodriguez Y. W. , Yang L. D. , Alers G. B. , Carter S. A.
Published: June 2010

We have fabricated ultrathin photovoltaic cadmium telluride (CdTe) film solar cells from colloidal nanorod solutions with a power conversion efficiency of 5.0% and internal quantum efficiency approaching unity near the band edge. Sintering of the CdTe nanorod films was necessary to facilitate grain growth and enhanced optical absorption. By analyzing electrode dependence, capacitance-voltage, temperature dependence, and current-voltage characteristics, the device performance is shown to be dominated by the formation of a p-CdTe/Al Schottky junction. The reduced need for material and cheaper processing make this an attractive technology for solar power generation.
Coexistence of inverse and normal magnetocaloric effect in A-site ordered NdBaMn2O6
Authors: Zhang Q. , Guillou F. , Wahl A. , Bréard Y. , Hardy V.
Published: June 2010

NdBaMn 2 O 6 exhibits a sequence of two following magnetic transitions: a second-order paramagnetic-ferromagnetic transition at TC=290 K, followed by a first-order ferromagnetic-antiferromagnetic transition around TN=210 K, leading to normal and inverse magnetocaloric effects (MCE), respectively. For ΔB=5 T, the combined |−ΔSMmax| around TC and TN is found to be 2.5 J/kg K and 1.4 J/kgK, respectively. Moreover, the presence of these two −ΔSM peaks spanning over a broad range of temperature leads to a remarkably wide working temperature region, yielding a significant performance in terms of refrigerant efficiency. The present study demonstrates that adjusting the degree of A-site cation ordering in perovskite oxides is an efficient strategy to induce room-temperature MCE.
Phase control of magnetic state of graphite thin films by electric field
Authors: Otani Minoru , Takagi Yoshiteru , Koshino Mikito , Okada Susumu
Published: June 2010

Based on first-principle total-energy calculations, we have found that by applying an external electric field it is possible to control the magnetic state of graphite thin film with the rhombohedral stacking arrangement. When exposed to a moderate electric field normal to the film, the surface of a thin film of rhombohedral graphite undergoes a magnetic phase transition from the antiferromagnetic state to the ferromagnetic state. The polarized electron spin is primarily distributed in the bottommost layer of the film, which forms the interface with the negative electrode. The amount of polarized electron spin is calculated to be 0.067 μB/nm2. The ferromagnetic ordering with the characteristic distribution of the polarized electron spin opens the possibility of using graphite thin films in electronic devices with spin degree of freedom.
Current-controlled negative differential resistance effect induced by Gunn-type instability in n-type GaN epilayers
Authors: Ma N. , Shen B. , Xu F. J. , Lu L. W. , Feng Z. H. , Zhang Z. G. , Dun S. B. , Wen C. P. , Wang J. Y. , Lin F. , Zhang D. T. , Sun M.
Published: June 2010

High-field carrier transport properties probed by pulsed current-voltage characteristics in n-type GaN epilayers have been investigated at room temperature. The threshold electric field of the Gunn effect is experimentally determined to be about 400 kV/cm with an electron peak velocity of about 1.9×107 cm/s. The current-controlled negative differential resistance effect induced by the Gunn-type instability in n-type GaN is observed, which takes the early electric breakdown of the GaN epilayers in charge.
A tropical horde of counterfeit predator eyes
Authors: Janzen Daniel H. , Hallwachs Winnie , Burns John M.
Published: June 2010

We propose that the many different, but essentially similar, eye-like and face-like color patterns displayed by hundreds of species of tropical caterpillars and pupae—26 examples of which are displayed here from the dry, cloud, and rain forests of Area de Conservacion Guanacaste (ACG) in northwestern Costa Rica—constitute a huge and pervasive mimicry complex that is evolutionarily generated and sustained by the survival behavior of a large and multispecific array of potential predators: the insect-eating birds. We propose that these predators are variously and innately programmed to flee when abruptly confronted, at close range, with what appears to be an eye of one oftheirpredators. Such a mimetic complex differs from various classical Batesian and Müllerian mimicry complexes of adult butterflies in that (i) the predators sustain it for the most part by innate traits rather than by avoidance behavior learned through disagreeable experiences, (ii) the more or less harmless, sessile, and largely edible mimics vastly outnumber the models, and (iii) there is no particular selection for the eye-like color pattern to closely mimic the eye or face of any particular predator of the insect-eating birds or that of any other member of this mimicry complex. Indeed, selection may not favor exact resemblance among these mimics at all. Such convergence through selection could create a superabundance of one particular false eyespot or face pattern, thereby increasing the likelihood of a bird species or guild learning to associate that pattern with harmless prey.
Transience in polarization of cytolytic effectors is required for efficient killing and controlled by Cdc42
Authors: Sinai Parisa , Nguyen Chau , Schatzle John D. , Wülfing Christoph
Published: June 2010

Cytolytic effectors polarize toward target cells for effective killing and IFN-γ secretion. The spatiotemporal features of this polarization and their importance for cytolysis have not been resolved. In cytotoxic T cells and natural killer (NK) cells, transient polarization was consistently associated with effective killing. Polarization was regulated by Cdc42, a small Rho family GTPase universally critical for cytoskeletal dynamics. Transient accumulation of active Cdc42 at the cytolytic effector/target cell interface and focus of such accumulation on the interface center were closely related to cytolysis. Surprisingly, however, the intensity of Cdc42 activation was not. We interfered with Cdc42 activation in NK cells such that sustained polarization in long lasting nonkilling cell couples was selectively blocked. Thus the proportion of the NK cell population displaying transient polarization was increased. As a consequence, cytolytic responder frequency and IFN-γ production were enhanced upon such interference with Cdc42 activation. These data support the notion that transience in polarization is critical for cytolytic effector function, likely by preventing cytolytic effectors from becoming trapped in nonproductive target cell interactions.
Human polynucleotide phosphorylase selectively and preferentially degrades microRNA-221 in human melanoma cells
Authors: Das Swadesh K. , Sokhi Upneet K. , Bhutia Sujit K. , Azab Belal , Su Zhao-zhong , Sarkar Devanand , Fisher Paul B.
Published: June 2010

MicroRNAs (miRNA), small noncoding RNAs, affect a broad range of biological processes, including tumorigenesis, by targeting gene products that directly regulate cell growth. Human polynucleotide phosphorylase (

hPNPase
old-35

), a type I IFN-inducible 3′-5′ exoribonuclease, degrades specific mRNAs and small noncoding RNAs. The present study examined the effect of this enzyme on miRNA expression in human melanoma cells. miRNA microarray analysis of human melanoma cells infected with empty adenovirus or with an adenovirus expressing

hPNPase
old-35

identified miRNAs differentially and specifically regulated by

hPNPase
old-35

. One of these, miR-221, a regulator of the cyclin-dependent kinase inhibitor p27
kip1
, displayed robust down-regulation with ensuing up-regulation of p27
kip1
by expression of

hPNPase
old-35

, which also occurred in multiple human melanoma cells upon IFN-β treatment. Using both in vivo immunoprecipitation followed by Northern blotting and RNA degradation assays, we confirm that mature miR-221 is the target of hPNPase
old-35
. Inhibition of

hPNPase
old-35

by shRNA or stable overexpression of miR-221 protected melanoma cells from IFN-β–mediated growth inhibition, accentuating the importance of

hPNPase
old-35

induction and miR-221 down-regulation in mediating IFN-β action. Moreover, we now uncover a mechanism of miRNA regulation involving selective enzymatic degradation. Targeted overexpression of

hPNPase
old-35

might provide an effective therapeutic strategy for miR-221–overexpressing and IFN-resistant tumors, such as melanoma.
Repeated loss of coloniality and symbiosis in scleractinian corals
Authors: Barbeitos Marcos S. , Romano Sandra L. , Lasker Howard R.
Published: June 2010

The combination of coloniality and symbiosis in Scleractinia is thought to confer competitive advantage over other benthic invertebrates, and it is likely the key factor for the dominance of corals in tropical reefs. However, the extant Scleractinia are evenly split between zooxanthellate and azooxanthellate species. Most azooxanthellate species are solitary and nearly absent from reefs, but have much wider geographic and bathymetric distributions than reef corals. Molecular phylogenetic analyses have repeatedly recovered clades formed by colonial/zooxanthellate and solitary/azooxanthellate taxa, suggesting that coloniality and symbiosis were repeatedly acquired and/or lost throughout the history of the Scleractinia. Using Bayesian ancestral state reconstruction, we found that symbiosis was lost at least three times and coloniality lost at least six times, and at least two instances in which both characters were lost. All of the azooxanthellate lineages originated from ancestors that were reconstructed as symbiotic, corroborating the onshore–offshore diversification trend recorded in marine taxa. Symbiotic sister taxa of two of these descendant lineages are extant in Caribbean reefs but disappeared from the Mediterranean before the end of the Miocene, whereas extant azooxanthellate lineages have trans-Atlantic distributions. Thus, the phyletic link between reef and nonreef communities may have played an important role in the dynamics of extinction and recovery that marks the evolutionary history of scleractinians, and some reef lineages may have escaped local extinction by diversifying into offshore environments. However, this macroevolutionary mechanism offers no hope of mitigating the effects of climate change on coral reefs in the next century.
Surface residues dynamically organize water bridges to enhance electron transfer between proteins
Authors: de la Lande Aurélien , Babcock Nathan S. , Řezáč Jan , Sanders Barry C. , Salahub Dennis R.
Published: June 2010

Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins methylamine dehydrogenase and amicyanin from
Paracoccus denitrificans
. We used molecular dynamics simulations to generate configurations over a duration of 40 ns (sampled at 100-fs intervals) in conjunction with an ET pathway analysis to estimate the ET coupling strength of each configuration. In the wild-type complex, we find that the most frequently occurring molecular configurations afford superior electronic coupling due to the consistent presence of a water molecule hydrogen-bonded between the donor and acceptor sites. We attribute the persistence of this water bridge to a “molecular breakwater” composed of several hydrophobic residues surrounding the acceptor site. The breakwater supports the function of nearby solvent-organizing residues by limiting the exchange of water molecules between the sterically constrained ET region and the more turbulent surrounding bulk. When the breakwater is affected by a mutation, bulk solvent molecules disrupt the water bridge, resulting in reduced electronic coupling that is consistent with recent experimental findings. Our analysis suggests that, in addition to enabling the association and docking of the proteins, surface residues stabilize and control interprotein solvent dynamics in a concerted way.
Parkin overexpression selects against a deleterious mtDNA mutation in heteroplasmic cybrid cells
Authors: Suen Der-Fen , Narendra Derek P. , Tanaka Atsushi , Manfredi Giovanni , Youle Richard J.
Published: June 2010

Mitochondrial genomes with deleterious mutations can replicate in cells along with wild-type genomes in a state of heteroplasmy, and are a cause of severe inherited syndromes, such as mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke (MELAS), neuropathy, ataxia, retinitis pigmentosa-maternally inherited Leigh syndrome (NARP-MILS), and Leber's hereditary optic neuropathy (LHON). The cytosolic E3 ligase, Parkin, commonly mutated in recessive familial parkinsonism, translocates to depolarized mitochondria and induces their autophagic elimination, suggesting that Parkin may signal the selective removal of defective mitochondria within the cell. We report that long-term overexpression of Parkin can eliminate mitochondria with deleterious COXI mutations in heteroplasmic cybrid cells, thereby enriching cells for wild-type mtDNA and restoring cytochrome
c
oxidase activity. After relieving cybrid cells of Parkin overexpression, a more favorable wild-type to mutant mitochondrial genome ratio is stably maintained. These data support the model that Parkin functions in a mitochondrial quality control pathway. Additionally, they suggest that transiently increasing levels of Parkin expression might ameliorate certain mitochondrial diseases.
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity
Authors: Willner Dana , Furlan Mike , Schmieder Robert , Grasis Juris A. , Pride David T. , Relman David A. , Angly Florent E. , McDole Tracey , Mariella Ray P. , Rohwer Forest , Haynes Matthew
Published: June 2010

The human oropharynx is a reservoir for many potential pathogens, including streptococcal species that cause endocarditis. Although oropharyngeal microbes have been well described, viral communities are essentially uncharacterized. We conducted a metagenomic study to determine the composition of oropharyngeal DNA viral communities (both phage and eukaryotic viruses) in healthy individuals and to evaluate oropharyngeal swabs as a rapid method for viral detection. Viral DNA was extracted from 19 pooled oropharyngeal swabs and sequenced. Viral communities consisted almost exclusively of phage, and complete genomes of several phage were recovered, including
Escherichia coli
phage T3,
Propionibacterium acnes
phage PA6, and
Streptococcus mitis
phage SM1. Phage relative abundances changed dramatically depending on whether samples were chloroform treated or filtered to remove microbial contamination. pblA and pblB genes of phage SM1 were detected in the metagenomes. pblA and pblB mediate the attachment of
S. mitis
to platelets and play a significant role in
S. mitis
virulence in the endocardium, but have never previously been detected in the oral cavity. These genes were also identified in salivary metagenomes from three individuals at three time points and in individual saliva samples by PCR. Additionally, we demonstrate that phage SM1 can be induced by commonly ingested substances. Our results indicate that the oral cavity is a reservoir for pblA and pblB genes and for phage SM1 itself. Further studies will determine the association between pblA and pblB genes in the oral cavity and the risk of endocarditis.
Early Miocene hippopotamids (Cetartiodactyla) constrain the phylogenetic and spatiotemporal settings of hippopotamid origin
Authors: Orliac Maeva , Boisserie Jean-Renaud , MacLatchy Laura , Lihoreau Fabrice
Published: June 2010

The affinities of the Hippopotamidae are at the core of the phylogeny of Cetartiodactyla (even-toed mammals: cetaceans, ruminants, camels, suoids, and hippos). Molecular phylogenies support Cetacea as sister group of the Hippopotamidae, implying a long ghost lineage between the earliest cetaceans (∼53 Ma) and the earliest hippopotamids (∼16 Ma). Morphological studies have proposed two different sister taxa for hippopotamids: suoids (notably palaeochoerids) or anthracotheriids. Evaluating these phylogenetic hypotheses requires substantiating the poorly known early history of the Hippopotamidae. Here, we undertake an original morphological phylogenetic analysis including several “suiform” families and previously unexamined early Miocene taxa to test previous conflicting hypotheses. According to our results,Morotochoerus ugandensisandKulutherium rusingensis, until now regarded as the sole African palaeochoerid and the sole African bunodont anthracotheriid, respectively, are unambiguously included within the Hippopotamidae. They are the earliest known hippopotamids and set the family fossil record back to the early Miocene (∼21 Ma). The analysis reveals that hippopotamids displayed an unsuspected taxonomic and body size diversity and remained restricted to Africa during most of their history, until the latest Miocene. Our results also confirm the deep nesting of Hippopotamidae within the paraphyletic Anthracotheriidae; this finding allows us to reconstruct the sequence of dental innovations that links advanced selenodont anthracotheriids to hippopotamids, previously a source of major disagreements on hippopotamid origins. The analysis demonstrates a close relationship between Eocene choeropotamids and anthracotheriids, a relationship that potentially fills the evolutionary gap between earliest hippopotamids and cetaceans implied by molecular analyses.
Single-molecule spectroscopy of protein folding in a chaperonin cage
Authors: Hofmann Hagen , Hillger Frank , Pfeil Shawn H. , Hoffmann Armin , Streich Daniel , Haenni Dominik , Nettels Daniel , Lipman Everett A. , Schuler Benjamin
Published: June 2010

Molecular chaperones are known to be essential for avoiding protein aggregation in vivo, but it is still unclear how they affect protein folding mechanisms. We use single-molecule Förster resonance energy transfer to follow the folding of a protein inside the GroEL/GroES chaperonin cavity over a time range from milliseconds to hours. Our results show that confinement in the chaperonin decelerates the folding of the C-terminal domain in the substrate protein rhodanese, but leaves the folding rate of the N-terminal domain unaffected. Microfluidic mixing experiments indicate that strong interactions of the substrate with the cavity walls impede the folding process, but the folding hierarchy is preserved. Our results imply that no universal chaperonin mechanism exists. Rather, a competition between intra- and intermolecular interactions determines the folding rates and mechanisms of a substrate inside the GroEL/GroES cage.
Double dissociation of two cognitive control networks in patients with focal brain lesions
Authors: Nomura Emi M. , Gratton Caterina , Visser Renee M. , Kayser Andrew , Perez Fernando , D'Esposito Mark
Published: June 2010

Neuroimaging studies of cognitive control have identified two distinct networks with dissociable resting state connectivity patterns. This study, in patients with heterogeneous damage to these networks, demonstrates network independence through a double dissociation of lesion location on two different measures of network integrity: functional correlations among network nodes and within-node graph theory network properties. The degree of network damage correlates with a decrease in functional connectivity within that network while sparing the nonlesioned network. Graph theory properties of intact nodes within the damaged network show evidence of dysfunction compared with the undamaged network. The effect of anatomical damage thus extends beyond the lesioned area, but remains within the bounds of the existing network connections. Together this evidence suggests that networks defined by their role in cognitive control processes exhibit independence in resting data.
Improved IL-2 immunotherapy by selective stimulation of IL-2 receptors on lymphocytes and endothelial cells
Authors: Krieg Carsten , Létourneau Sven , Pantaleo Giuseppe , Boyman Onur
Published: June 2010

IL-2 immunotherapy is an attractive treatment option for certain metastatic cancers. However, administration of IL-2 to patients can lead, by ill-defined mechanisms, to toxic adverse effects including severe pulmonary edema. Here, we show that IL-2–induced pulmonary edema is caused by direct interaction of IL-2 with functional IL-2 receptors (IL-2R) on lung endothelial cells in vivo. Treatment of mice with high-dose IL-2 led to efficient expansion of effector immune cells expressing high levels of IL-2Rβγ, including CD8+T cells and natural killer cells, which resulted in a considerable antitumor response against s.c. and pulmonary B16 melanoma nodules. However, high-dose IL-2 treatment also affected immune cell lineage marker-negative CD31+pulmonary endothelial cells via binding to functional αβγ IL-2Rs, expressed at low to intermediate levels on these cells, thus causing pulmonary edema. Notably, IL-2–mediated pulmonary edema was abrogated by a blocking antibody to IL-2Rα (CD25), genetic disruption of CD25, or the use of IL-2Rβγ–directed IL-2/anti-IL-2 antibody complexes, thereby interfering with IL-2 binding to IL-2Rαβγ+pulmonary endothelial cells. Moreover, IL-2/anti-IL-2 antibody complexes led to vigorous activation of IL-2Rβγ+effector immune cells, which generated a dramatic antitumor response. Thus, IL-2/anti-IL-2 antibody complexes might improve current strategies of IL-2–based tumor immunotherapy.
An implicit body representation underlying human position sense
Authors: Longo Matthew R. , Haggard Patrick
Published: June 2010

Knowing the body's location in external space is a fundamental perceptual task. Perceiving the location of body parts through proprioception requires that information about the angles of each joint (i.e., body posture) be combined with information about the size and shape of the body segments between joints. Although information about body posture is specified by on-line afferent signals, no sensory signals are directly informative about body size and shape. Thus, human position sense must refer to a stored body model of the body's metric properties, such as body part size and shape. The need for such a model has long been recognized; however, the properties of this model have never been systematically investigated. We developed a technique to isolate and measure this body model. Participants judged the location in external space of 10 landmarks on the hand. By analyzing the internal configuration of the locations of these points, we produced implicit maps of the mental representation of hand size and shape. We show that this part of the body model is massively distorted, in a reliable and characteristic fashion, featuring shortened fingers and broadened hands. Intriguingly, these distortions appear to retain several characteristics of primary somatosensory representations, such as the Penfield homunculus.
Defining sporadic Creutzfeldt-Jakob disease strains and their transmission properties
Authors: Bishop Matthew T. , Will Robert G. , Manson Jean C.
Published: June 2010

The biological determinants of the phenotypic variation in sporadic Creutzfeldt-Jakob disease (sCJD) are unknown. To categorize sCJD cases, the prion protein (PrP) codon 129 genotype and the biochemical characteristics of the disease-associated form of PrP (PrPSc) can be combined to form six subgroups (MM1, MM2, MV1, MV2, VV1, and VV2). This classification largely correlates with the known variation in the clinical and pathological features of sCJD, with the MM1 and MV1 cases representing the “classic” phenotype of sCJD. To address how this classification relates to different strains of sCJD we have inoculated each subgroup of sCJD to a panel of mice expressing different forms of the humanPRNPgene (129MM, 129VV, and 129MV). We have established that all subtypes are transmissible to at least one genotype of mouse, and both agent and host factors determine transmission efficiency and the form of PrPScdeposited in the brain. Moreover, we have identified four distinct strains of sCJD using our in vivo strain typing panel.
Programmable transdermal drug delivery of nicotine using carbon nanotube membranes
Authors: Wu Ji , Paudel Kalpana S. , Strasinger Caroline , Hammell Dana , Stinchcomb Audra L. , Hinds Bruce J.
Published: June 2010

Carbon nanotube (CNT) membranes were employed as the active element of a switchable transdermal drug delivery device that can facilitate more effective treatments of drug abuse and addiction. Due to the dramatically fast flow through CNT cores, high charge density, and small pore dimensions, highly efficient electrophoretic pumping through functionalized CNT membrane was achieved. These membranes were integrated with a nicotine formulation to obtain switchable transdermal nicotine delivery rates on human skin (in vitro) and are consistent with a Fickian diffusion in series model. The transdermal nicotine delivery device was able to successfully switch between high (1.3 ± 0.65 
μ
mol/hr-cm
2
) and low (0.33 ± 0.22 
μ
mol/hr-cm
2
) fluxes that coincide with therapeutic demand levels for nicotine cessation treatment. These highly energy efficient programmable devices with minimal skin irritation and no skin barrier disruption would open an avenue for single application long-wear patches for therapies that require variable or programmable delivery rates.
A pro-resolution mediator, prostaglandin D
2
, is specifically up-regulated in individuals in long-term remission from ulcerative colitis
Authors: Vong Linda , Ferraz Jose G. P. , Panaccione Remo , Beck Paul L. , Wallace John L.
Published: June 2010

Patients with ulcerative colitis (UC) experience unpredictable bouts of active inflammation and ulceration. Relatively little attention has been paid to the role of antiinflammatory mediators in the pathogenesis of UC, although rodent studies suggest an important role of prostaglandin (PG) D
2
in the resolution of tissue injury and inflammation. The present study was performed to determine if colonic PGD
2
synthesis was altered in patients in remission from UC and if expression of the key enzymes and receptors related to PGD
2
was altered. During routine colon-cancer screening, colonic biopsies were obtained from healthy individuals, some of whom had been in remission from UC, without treatment, for >4 y. UC patients with active disease or in medically induced remission were also biopsied. Only patients with active UC exhibited elevated expression of several proinflammatory cytokines (TNFα and IFNγ) and colonic PGE
2
synthesis. In contrast, colonic PGD
2
synthesis was only elevated (∼3-fold) in the healthy individuals with a prior history of UC. This group also exhibited significantly elevated expression of DP1, the key receptor mediating the antiinflammatory actions of PGD
2
. Expression of the synthetic enzymes cyclooxygenase-1, cyclooxygenase-2, and hematopoietic PGD synthase was not altered in the healthy individuals with a prior history of UC. These results show a marked up-regulation of synthesis of an antiinflammatory prostanoid and expression of its receptor, specifically in individuals in long-term remission from UC. This is consistent with animal studies showing the importance of PGD
2
in the induction and maintenance of remission from colitis.
Scale-free correlations in starling flocks
Authors: Cavagna Andrea , Cimarelli Alessio , Giardina Irene , Parisi Giorgio , Santagati Raffaele , Stefanini Fabio , Viale Massimiliano
Published: June 2010

From bird flocks to fish schools, animal groups often seem to react to environmental perturbations as if of one mind. Most studies in collective animal behavior have aimed to understand how a globally ordered state may emerge from simple behavioral rules. Less effort has been devoted to understanding the origin of collective response, namely the way the group as a whole reacts to its environment. Yet, in the presence of strong predatory pressure on the group, collective response may yield a significant adaptive advantage. Here we suggest that collective response in animal groups may be achieved through scale-free behavioral correlations. By reconstructing the 3D position and velocity of individual birds in large flocks of starlings, we measured to what extent the velocity fluctuations of different birds are correlated to each other. We found that the range of such spatial correlation does not have a constant value, but it scales with the linear size of the flock. This result indicates that behavioral correlations are scale free: The change in the behavioral state of one animal affects and is affected by that of all other animals in the group, no matter how large the group is. Scale-free correlations provide each animal with an effective perception range much larger than the direct interindividual interaction range, thus enhancing global response to perturbations. Our results suggest that flocks behave as critical systems, poised to respond maximally to environmental perturbations.
Pheromone-induced anisotropy in yeast plasma membrane phosphatidylinositol-4,5-
bis
phosphate distribution is required for MAPK signaling
Authors: Garrenton Lindsay S. , Stefan Christopher J. , McMurray Michael A. , Emr Scott D. , Thorner Jeremy
Published: June 2010

During response of budding yeast to peptide mating pheromone, the cell becomes markedly polarized and MAPK scaffold protein Ste5 localizes to the resulting projection (shmoo tip). We demonstrated before that this recruitment is essential for sustained MAPK signaling and requires interaction of a pleckstrin homology (PH) domain in Ste5 with phosphatidylinositol 4,5-
bis
phosphate [PtdIns(4,5)P
2
] in the plasma membrane. Using fluorescently tagged high-affinity probes specific for PtdIns(4,5)P
2
, we have now found that this phosphoinositide is highly concentrated at the shmoo tip in cells responding to pheromone. Maintenance of this strikingly anisotropic distribution of PtdIns(4,5)P
2
, stable tethering of Ste5 at the shmoo tip, downstream MAPK activation, and expression of a mating pathway-specific reporter gene all require continuous function of the plasma membrane-associated PtdIns 4-kinase Stt4 and the plasma membrane-associated PtdIns4P 5-kinase Mss4 (but not the Golgi-associated PtdIns 4-kinase Pik1). Our observations demonstrate that PtdIns(4,5)P
2
is the primary determinant for restricting localization of Ste5 within the plasma membrane and provide direct evidence that an extracellular stimulus-evoked self-reinforcing mechanism generates a spatially enriched pool of PtdIns(4,5)P
2
necessary for the membrane anchoring and function of a signaling complex.
Pathogen-specific regulatory T cells delay the arrival of effector T cells in the lung during early tuberculosis
Authors: Shafiani Shahin , Tucker-Heard Glady’s , Kariyone Ai , Takatsu Kiyoshi , Urdahl Kevin B.
Published: June 2010

The ability of the adaptive immune system to restrict Mycobacterium tuberculosis (Mtb) is impeded by activated Foxp3+ regulatory T (T reg) cells. The importance of pathogen-specific T reg cells in this process has not been addressed. We show that T reg cell expansion after aerosol Mtb infection does not occur until Mtb is transported to the pulmonary lymph node (pLN), and Mtb-specific T reg cells have an increased propensity to proliferate. Even small numbers of Mtb-specific T reg cells are capable of delaying the priming of effector CD4+ and CD8+ T cells in the pLN and their subsequent accumulation in the lung, the primary site of infection. This delay likely prolongs the initial phase of bacterial expansion and explains the higher bacterial burden observed in these mice. Thus, T reg cells recognizing Mtb-derived antigens specifically and potently restrict protective immune responses during tuberculosis.