bluuebunny/crossref_metadata_2025 huggingface dataset:
Tetrahydrobiopterin: biochemistry and pathophysiology
Authors: Werner Ernst R. , Blau Nenad , Thöny Beat
Published: April 2013

BH4 (6R-L-erythro-5,6,7,8-tetrahydrobiopterin) is an essential cofactor of a set of enzymes that are of central metabolic importance, including four aromatic amino acid hydroxylases, alkylglycerol mono-oxygenase and three NOS (NO synthase) isoenzymes. Consequently, BH4 is present in probably every cell or tissue of higher organisms and plays a key role in a number of biological processes and pathological states associated with monoamine neurotransmitter formation, cardiovascular and endothelial dysfunction, the immune response and pain sensitivity. BH4 is formed de novo from GTP via a sequence of three enzymatic steps carried out by GTP cyclohydrolase I, 6-pyruvoyltetrahydropterin synthase and sepiapterin reductase. An alternative or salvage pathway involves dihydrofolate reductase and may play an essential role in peripheral tissues. Cofactor regeneration requires pterin-4a-carbinolamine dehydratase and dihydropteridine reductase, except for NOSs, in which the BH4 cofactor undergoes a one-electron redox cycle without the need for additional regeneration enzymes. With regard to the regulation of cofactor biosynthesis, the major controlling point is GTP cyclohydrolase I. BH4 biosynthesis is controlled in mammals by hormones and cytokines. BH4 deficiency due to autosomal recessive mutations in all enzymes, except for sepiapterin reductase, has been described as a cause of hyperphenylalaninaemia. A major contributor to vascular dysfunction associated with hypertension, ischaemic reperfusion injury, diabetes and others, appears to be an effect of oxidized BH4, which leads to an increased formation of oxygen-derived radicals instead of NO by decoupled NOS. Furthermore, several neurological diseases have been suggested to be a consequence of restricted cofactor availability, and oral cofactor replacement therapy to stabilize mutant phenylalanine hydroxylase in the BH4-responsive type of hyperphenylalaninaemia has an advantageous effect on pathological phenylalanine levels in patients.
Elevated SGK1 predicts resistance of breast cancer cells to Akt inhibitors
Authors: Sommer Eeva M. , Dry Hannah , Cross Darren , Guichard Sylvie , Davies Barry R. , Alessi Dario R.
Published: April 2013

The majority of human cancers harbour mutations promoting activation of the Akt protein kinase, and Akt inhibitors are being evaluated in clinical trials. An important question concerns the understanding of the innate mechanisms that confer resistance of tumour cells to Akt inhibitors. SGK (serum- and glucocorticoid-regulated kinase) is closely related to Akt and controlled by identical upstream regulators {PI3K (phosphoinositide 3-kinase), PDK1 (phosphoinositide-dependent kinase 1) and mTORC2 [mTOR (mammalian target of rapamycin) complex 2]}. Mutations that trigger activation of Akt would also stimulate SGK. Moreover, Akt and SGK possess analogous substrate specificities and are likely to phosphorylate overlapping substrates to promote proliferation. To investigate whether cancers possessing high SGK activity could possess innate resistance to Akt-specific inhibitors (that do not target SGK), we analysed SGK levels and sensitivity of a panel of breast cancer cells towards two distinct Akt inhibitors currently in clinical trials (AZD5363 and MK-2206). This revealed a number of Akt-inhibitor-resistant lines displaying markedly elevated SGK1 that also exhibited significant phosphorylation of the SGK1 substrate NDRG1 [N-Myc (neuroblastoma-derived Myc) downstream-regulated gene 1]. In contrast, most Akt-inhibitor-sensitive cell lines displayed low/undetectable levels of SGK1. Intriguingly, despite low SGK1 levels, several Akt-inhibitor-sensitive cells showed marked NDRG1 phosphorylation that was, unlike in the resistant cells, suppressed by Akt inhibitors. SGK1 knockdown markedly reduced proliferation of Akt-inhibitor-resistant, but not -sensitive, cells. Furthermore, treatment of Akt-inhibitor-resistant cells with an mTOR inhibitor suppressed proliferation and led to inhibition of SGK1. The results of the present study suggest that monitoring SGK1 levels as well as responses of NDRG1 phosphorylation to Akt inhibitor administration could have a use in predicting the sensitivity of tumours to compounds that target Akt. Our findings highlight the therapeutic potential that SGK inhibitors or dual Akt/SGK inhibitors might have for treatment of cancers displaying elevated SGK activity.
Magnetic properties of Fe doped, Co doped, and Fe+Co co-doped ZnO
Authors: Beltrán J. J. , Osorio J. A. , Barrero C. A. , Hanna C. B. , Punnoose A.
Published: April 2013

The structural, electronic, and magnetic properties of Zn0.95Co0.05O, Zn0.95Fe0.05O, and Zn0.90Fe0.05Co0.05O nanoparticles prepared by a sol-gel method are presented and discussed. X-ray diffraction and optical analysis indicated that high spin Co2+ ions substitute for the Zn2+ ions in tetrahedral sites. 57Fe Mössbauer spectroscopy showed the presence of isolated paramagnetic Fe3+ ions in both Fe doped and Fe+Co co-doped ZnO, however, no evidence of ferromagnetically ordered Fe3+ ions is observed. In the Zn0.95Fe0.05O sample, weak presence of ZnFe2O4 was detected as an impurity phase, whereas Zn0.90Fe0.05Co0.05O was impurity-free within detection limit in all those measurements. Results of these studies suggest that Fe and Co ions in the Fe+Co co-doped sample has a strong synergistic effect because they eliminated the presence of impurities and gave the strongest ferromagnetic signal. Possible role of charge transfer ferromagnetism involving mixed valence ions is considered as a potential mechanism in these nanoparticles. Presence of both Co2+ and Fe3+ might promote more efficient charge transfer in the co-doped Zn0.90Fe0.05Co0.05O, leading to the enhanced ferromagnetism observed in this sample. However, more evidence is necessary to confirm the role of charge transfer ferromagnetism.
A simple approximation for forces exerted on an AFM tip in liquid
Authors: Watkins Matthew , Reischl Bernhard
Published: April 2013

The critical quantity in understanding imaging using an atomic force microscope is the force the sample exerts on the tip. We put forward a simple one-to-one force to water density relationship, explain exactly how it occurs, and in which circumstances it holds. We argue that two wide classes of atomic force microscope (AFM) tip should lead to at least qualitative agreement with our model and represent a significant fraction of AFM tips as currently prepared. This connection between the short-range force and the unperturbed equilibrium water density removes the need to perform simulations for each tip location, conservatively speeding up simulations by around three orders of magnitude compared to current methods that explicitly calculate the force on a tip model at each point in space.
NMR study of small molecule adsorption in MOF-74-Mg
Authors: Lopez M. G. , Canepa Pieremanuele , Thonhauser T.
Published: April 2013

We calculate the carbon nuclear magnetic resonance (NMR) shielding for CO2 and the hydrogen shieldings for both H2 and H2O inside the metal organic framework MOF-74-Mg. Our ab initio calculations are at the density functional theory level using the van der Waals including density functional vdW-DF. The shieldings are obtained while placing the small molecules throughout the structure, including the calculated adsorption site for various loading scenarios. We then explore relationships between loading, rotational and positional characteristics, and the NMR shieldings for each adsorbate. Our NMR calculations show a change in the shielding depending on adsorbate, position, and loading in a range that is experimentally observable. We further provide a simple model for the energy and the NMR shieldings throughout the cavity of the MOF. By providing this mapping of shielding to position and loading for these adsorbates, we argue that NMR probes could be used to provide additional information about the position at which these small molecules bind within the MOF, as well as the loading of the adsorbed molecule.
Molecular force fields for aqueous electrolytes: SPC/E-compatible charged LJ sphere models and their limitations
Authors: Moučka Filip , Nezbeda Ivo , Smith William R.
Published: April 2013

Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012)10.1021/jp301447z]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.
Scanning noise microscopy
Authors: Schaffert J. , Cottin M. C. , Sonntag A. , Karacuban H. , Utzat D. , Bobisch C. A. , Möller R.
Published: April 2013

The paper describes a simple scheme enabling the real-time characterization of fluctuations, e.g., of the conductance in scanning tunneling microscopy. The technique can be used in parallel to other data acquisition, evaluating the rate, the amplitude, and the duty cycle of telegraphic noise in the tunneling current. This kind of scanning probe microscopy allows to evaluate the noise parameters as a function of the average tunneling current, the electron energy, and the lateral position. Images of the noise with Ångstrom spatial resolution are acquired simultaneously to the topographic information providing a direct correlation between the structural information and the noise. The method can be applied to a large variety of systems to monitor dynamics on the nanoscale, e.g., the localization of tunneling current induced switching within a single molecule. Noise spectroscopy may reveal the involved molecular orbitals, even if they cannot be resolved in standard scanning tunneling spectroscopy. As an example we present experimental data of the organic molecule copper phthalocyanine on a Cu(111) surface [J. Schaffert, M. C. Cottin, A. Sonntag, H. Karacuban, C. A. Bobisch, N. Lorente, J.-P. Gauyacq, and R. Möller, Nature Mater. 12, 223–227 (2013)10.1038/nmat3527].
Exchange bias of perpendicularly magnetized [Co/Pt]3/IrMn multilayer on porous anodized alumina
Authors: Shi Z. , Fan X. X. , He P. , Zhou S. M. , Hu H. N. , Yang M. , Du J.
Published: April 2013

The exchange bias of [Co/Pt]3/IrMn multilayers deposited on porous anodized alumina oxide template has been investigated. The perpendicular exchange bias has been successfully established on the anodized alumina template and Si substrate. For samples on the anodized alumina templates, a larger exchange field was obtained but smaller coercivity was observed, in comparison with those on flat Si substrate. Unlike conventional observations, the asymmetry of angular dependence of coercive fields of two branches for nanostructured samples is less prominent than that of the continuous samples.
Effect of resonant tunneling on exciton dynamics in coupled dot-well nanostructures
Authors: Guzun D. , Mazur Yu. I. , Dorogan V. G. , Ware M. E. , Marega E. , Tarasov G. G. , Lienau C. , Salamo G. J.
Published: April 2013

Excitonic dynamics in a hybrid dot-well system composed of InAs quantum dots (QDs) and an InGaAs quantum well (QW) is studied by means of femtosecond pump-probe reflection and continuous wave (cw) photoluminescence (PL) spectroscopy. The system is engineered to bring the QW ground exciton state into resonance with the third QD excited state. The resonant tunneling rate is varied by changing the effective barrier thickness between the QD and QW layers. This strongly affects the exciton dynamics in these hybrid structures as compared to isolated QW or QD systems. Optically measured decay times of the coupled system demonstrate dramatically different response to temperature change depending on the strength of the resonant tunneling or coupling strength. This reflects a competition between purely quantum mechanical and thermodynamical processes.
Ultra-small excitonic fine structure splitting in highly symmetric quantum dots on GaAs (001) substrate
Authors: Huo Y. H. , Rastelli A. , Schmidt O. G.
Published: April 2013

We prepare symmetry-controlled GaAs/AlGaAs quantum dots (QDs) on (001) GaAs substrates by infilling GaAs into AlGaAs nanoholes. For the most symmetric QDs, we measure an average excitonic fine structure splitting (FSS) of only (3.9 ± 1.8) μeV. The FSS and polarization direction of the two bright excitonic recombination lines directly reflect the degree of the QD symmetry. Since the FSS is comparable to typical homogeneous linewidths of excitonic recombination, these strain-free GaAs/AlGaAs QDs might offer a practical platform to generate entangled photons in future quantum devices.
Reduction of contact resistance by selective contact doping in fullerene n-channel organic field-effect transistors
Authors: Singh Sanjeev , Mohapatra Swagat K. , Sharma Asha , Fuentes-Hernandez Canek , Barlow Stephen , Marder Seth R. , Kippelen Bernard
Published: April 2013

We have investigated the contact-doping effect on high performance n-channel C60 organic field-effect transistors (OFETs) using the air-stable rhodocene dimer as an n-type dopant. The average charge mobility improved from a value of 0.48 cm2/(Vs) in a reference device to 1.65 cm2/(Vs) for contact-doped devices with a channel length of 25 μm. The operational stability of contact-doped OFETs under continuous stress bias was found similar to the reference devices.
Enhanced direct flexoelectricity in paraelectric phase of Ba(Ti0.87Sn0.13)O3 ceramics
Authors: Shu Longlong , Wei Xiaoyong , Jin Li , Li Yong , Wang Hong , Yao Xi
Published: April 2013

Enhanced direct flexoelectricity has been observed in paraelectric phase of Ba(Ti0.87Sn0.13)O3 ceramics by using a quasi-static cantilever beam system. The transverse flexoelectric coefficient was found to be about 53 μC/m near the Curie temperature. Temperature-dependence of the transverse flexoelectric coefficient was studied, exhibiting a nonlinear relationship with dielectric constant.
Role of p63 and the Notch pathway in cochlea development and sensorineural deafness
Authors: Terrinoni Alessandro , Serra Valeria , Bruno Ernesto , Strasser Andreas , Valente Elizabeth , Flores Elsa R. , van Bokhoven Hans , Lu Xin , Knight Richard A. , Melino Gerry
Published: April 2013

The ectodermal dysplasias are a group of inherited autosomal dominant syndromes associated with heterozygous mutations in the Tumor Protein p63 (
TRP63
) gene. Here we show that, in addition to their epidermal pathology, a proportion of these patients have distinct levels of deafness. Accordingly, p63 null mouse embryos show marked cochlea abnormalities, and the transactivating isoform of p63 (TAp63) protein is normally found in the organ of Corti. TAp63 transactivates hairy and enhancer of split 5 (Hes5) and atonal homolog 1 (Atoh1), components of the Notch pathway, known to be involved in cochlear neuroepithelial development. Strikingly, p63 null mice show morphological defects of the organ of Corti, with supernumerary hair cells, as also reported for
Hes5
null mice. This phenotype is related to loss of a differentiation property of TAp63 and not to loss of its proapoptotic function, because cochleas in mice lacking the critical Bcl-2 homology domain (BH-3) inducers of p53- and p63-mediated apoptosis—Puma, Noxa, or both—are normal. Collectively, these data demonstrate that TAp63, acting via the Notch pathway, is crucial for the development of the organ of Corti, providing a molecular explanation for the sensorineural deafness in ectodermal dysplasia patients with TRP63 mutations.
Europe’s other debt crisis caused by the long legacy of future extinctions
Authors: Dullinger Stefan , Essl Franz , Rabitsch Wolfgang , Erb Karl-Heinz , Gingrich Simone , Haberl Helmut , Hülber Karl , Jarošík Vojtech , Krausmann Fridolin , Kühn Ingolf , Pergl Jan , Pyšek Petr , Hulme Philip E.
Published: April 2013

Rapid economic development in the past century has translated into severe pressures on species survival as a result of increasing land-use change, environmental pollution, and the spread of invasive alien species. However, though the impact of these pressures on biodiversity is substantial, it could be seriously underestimated if population declines of plants and animals lag behind contemporary environmental degradation. Here, we test for such a delay in impact by relating numbers of threatened species appearing on national red lists to historical and contemporary levels of socioeconomic pressures. Across 22 European countries, the proportions of vascular plants, bryophytes, mammals, reptiles, dragonflies, and grasshoppers facing medium-to-high extinction risks are more closely matched to indicators of socioeconomic pressures (i.e., human population density, per capita gross domestic product, and a measure of land use intensity) from the early or mid-, rather than the late, 20th century. We conclude that, irrespective of recent conservation actions, large-scale risks to biodiversity lag considerably behind contemporary levels of socioeconomic pressures. The negative impact of human activities on current biodiversity will not become fully realized until several decades into the future. Mitigating extinction risks might be an even greater challenge if temporal delays mean many threatened species might already be destined toward extinction.
NIF-type iron-sulfur cluster assembly system is duplicated and distributed in the mitochondria and cytosol of
Mastigamoeba balamuthi
Authors: Nývltová Eva , Šuták Robert , Harant Karel , Šedinová Miroslava , Hrdý Ivan , Pačes Jan , Vlček Čestmír , Tachezy Jan
Published: April 2013

In most eukaryotes, the mitochondrion is the main organelle for the formation of iron-sulfur (FeS) clusters. This function is mediated through the iron-sulfur cluster assembly machinery, which was inherited from the α-proteobacterial ancestor of mitochondria. In Archamoebae, including pathogenic
Entamoeba histolytica
and free-living
Mastigamoeba balamuthi
, the complex iron-sulfur cluster machinery has been replaced by an ε-proteobacterial nitrogen fixation (NIF) system consisting of two components: NifS (cysteine desulfurase) and NifU (scaffold protein). However, the cellular localization of the NIF system and the involvement of mitochondria in archamoebal FeS assembly are controversial. Here, we show that the genes for both NIF components are duplicated within the
M. balamuthi
genome. One paralog of each protein contains an amino-terminal extension that targets proteins to mitochondria (NifS-M and NifU-M), and the second paralog lacks a targeting signal, thereby reflecting the cytosolic form of the NIF machinery (NifS-C and NifU-C). The dual localization of the NIF system corresponds to the presence of FeS proteins in both cellular compartments, including detectable hydrogenase activity in
Mastigamoeba
cytosol and mitochondria. In contrast,
E. histolytica
possesses only single genes encoding NifS and NifU, respectively, and there is no evidence for the presence of the NIF machinery in its reduced mitochondria. Thus,
M. balamuthi
is unique among eukaryotes in that its FeS cluster formation is mediated through two most likely independent NIF machineries present in two cellular compartments.
Agricultural intensification escalates future conservation costs
Authors: Phelps Jacob , Carrasco Luis Roman , Webb Edward L. , Koh Lian Pin , Pascual Unai
Published: April 2013

The supposition that agricultural intensification results in land sparing for conservation has become central to policy formulations across the tropics. However, underlying assumptions remain uncertain and have been little explored in the context of conservation incentive schemes such as policies for Reducing Emissions from Deforestation and forest Degradation, conservation, sustainable management, and enhancement of carbon stocks (REDD+). Incipient REDD+ forest carbon policies in a number of countries propose agricultural intensification measures to replace extensive “slash-and-burn” farming systems. These may result in conservation in some contexts, but will also increase future agricultural land rents as productivity increases, creating new incentives for agricultural expansion and deforestation. While robust governance can help to ensure land sparing, we propose that conservation incentives will also have to increase over time, tracking future agricultural land rents, which might lead to runaway conservation costs. We present a conceptual framework that depicts these relationships, supported by an illustrative model of the intensification of key crops in the Democratic Republic of Congo, a leading REDD+ country. A von Thünen land rent model is combined with geographic information systems mapping to demonstrate how agricultural intensification could influence future conservation costs. Once postintensification agricultural land rents are considered, the cost of reducing forest sector emissions could significantly exceed current and projected carbon credit prices. Our analysis highlights the importance of considering escalating conservation costs from agricultural intensification when designing conservation initiatives.
Cost-effectiveness of a community-based intervention for reducing the transmission ofSchistosoma haematobiumand HIV in Africa
Authors: Ndeffo Mbah Martial L. , Kjetland Eyrun F. , Atkins Katherine E. , Poolman Eric M. , Orenstein Evan W. , Meyers Lauren Ancel , Townsend Jeffrey P. , Galvani Alison P.
Published: April 2013

Epidemiological studies from sub-Saharan Africa show that genital infection withSchistosoma haematobiummay increase the risk for HIV infection in young women. Therefore, preventing schistosomiasis has the potential to reduce HIV transmission in sub-Saharan Africa. We developed a transmission model of female genital schistosomiasis and HIV infections that we fit to epidemiological data of HIV and female genital schistosomiasis prevalence and coinfection in rural Zimbabwe. We used the model to evaluate the cost-effectiveness of a multifaceted community-based intervention for preventing schistosomiasis and, consequently, HIV infections in rural Zimbabwe, from the perspective of a health payer. The community-based intervention combined provision of clean water, sanitation, and health education (WSH) with administration of praziquantel to school-aged children. Considering variation in efficacy between 10% and 70% of WSH for reducingS. haematobiumtransmission, our model predicted that community-based intervention is likely to be cost-effective in Zimbabwe at an aggregated WSH cost corresponding to US $725–$1,000 per individual over a 20-y intervention period. These costs compare favorably with empirical measures of WSH provision in developing countries, indicating that integrated community-based intervention for reducing the transmission ofS. haematobiumis an economically attractive strategy for reducing schistosomiasis and HIV transmission in sub-Saharan Africa that would have a powerful impact on averting infections and saving lives.
Direct real-time detection of the actin-activated power stroke within the myosin catalytic domain
Authors: Muretta Joseph M. , Petersen Karl J. , Thomas David D.
Published: April 2013

We have used transient kinetics, nanosecond time-resolved fluorescence resonance energy transfer (FRET), and kinetics simulations to resolve a structural transition in the
Dictyostelium
myosin II relay helix during the actin-activated power stroke. The relay helix plays a critical role in force generation in myosin, coupling biochemical changes in the ATPase site with the force-transducing rotation of the myosin light-chain domain. Previous research in the absence of actin showed that ATP binding to myosin induces a dynamic equilibrium between a bent prepower stroke state of the relay helix and a straight postpower stroke state, which dominates in the absence of ATP or when ADP is bound. We now ask whether actin binding reverses this transition and if so, how this reversal is coordinated with actin-activated phosphate release. We labeled a Cys-lite
Dictyostelium
myosin II motor domain with donor and acceptor probes at two engineered Cys residues designed to detect relay helix bending. We then performed transient time-resolved FRET following stopped-flow mixing of actin with labeled myosin, preincubated with ATP. We determined the kinetics of actin-activated phosphate release, using fluorescent phosphate-binding protein. The results show that actin binding to the myosin.ADP.P complex straightens the relay helix before phosphate dissociation. This actin-activated relay helix straightening is reversible, but phosphate irreversibly dissociates from the postpower stroke state, preventing reversal of the power stroke. Thus, relay helix straightening gates phosphate dissociation, whereas phosphate dissociation provides the thermodynamic driving force underlying force production.
Camouflage mismatch in seasonal coat color due to decreased snow duration
Authors: Mills L. Scott , Zimova Marketa , Oyler Jared , Running Steven , Abatzoglou John T. , Lukacs Paul M.
Published: April 2013

Most examples of seasonal mismatches in phenology span multiple trophic levels, with timing of animal reproduction, hibernation, or migration becoming detached from peak food supply. The consequences of such mismatches are difficult to link to specific future climate change scenarios because the responses across trophic levels have complex underlying climate drivers often confounded by other stressors. In contrast, seasonal coat color polyphenism creating camouflage against snow is a direct and potentially severe type of seasonal mismatch if crypsis becomes compromised by the animal being white when snow is absent. It is unknown whether plasticity in the initiation or rate of coat color change will be able to reduce mismatch between the seasonal coat color and an increasingly snow-free background. We find that natural populations of snowshoe hares exposed to 3 y of widely varying snowpack have plasticity in the rate of the spring white-to-brown molt, but not in either the initiation dates of color change or the rate of the fall brown-to-white molt. Using an ensemble of locally downscaled climate projections, we also show that annual average duration of snowpack is forecast to decrease by 29–35 d by midcentury and 40–69 d by the end of the century. Without evolution in coat color phenology, the reduced snow duration will increase the number of days that white hares will be mismatched on a snowless background by four- to eightfold by the end of the century. This novel and visually compelling climate change-induced stressor likely applies to >9 widely distributed mammals with seasonal coat color.
Rational design of thermostable vaccines by engineered peptide-induced virus self-biomineralization under physiological conditions
Authors: Wang Guangchuan , Cao Rui-Yuan , Chen Rong , Mo Lijuan , Han Jian-Feng , Wang Xiaoyu , Xu Xurong , Jiang Tao , Deng Yong-Qiang , Lyu Ke , Zhu Shun-Ya , Qin E-De , Tang Ruikang , Qin Cheng-Feng
Published: April 2013

The development of vaccines against infectious diseases represents one of the most important contributions to medical science. However, vaccine-preventable diseases still cause millions of deaths each year due to the thermal instability and poor efficacy of vaccines. Using the human enterovirus type 71 vaccine strain as a model, we suggest a combined, rational design approach to improve the thermostability and immunogenicity of live vaccines by self-biomineralization. The biomimetic nucleating peptides are rationally integrated onto the capsid of enterovirus type 71 by reverse genetics so that calcium phosphate mineralization can be biologically induced onto vaccine surfaces under physiological conditions, generating a mineral exterior. This engineered self-biomineralized virus was characterized in detail for its unique structural, virological, and chemical properties. Analogous to many exteriors, the mineral coating confers some new properties on enclosed vaccines. The self-biomineralized vaccine can be stored at 26 °C for more than 9 d and at 37 °C for approximately 1 wk. Both in vitro and in vivo experiments demonstrate that this engineered vaccine can be used efficiently after heat treatment or ambient temperature storage, which reduces the dependence on a cold chain. Such a combination of genetic technology and biomineralization provides an economic solution for current vaccination programs, especially in developing countries that lack expensive refrigeration infrastructures.
Atypical lipid composition in the purified relict plastid (apicoplast) of malaria parasites
Authors: Botté Cyrille Y. , Yamaryo-Botté Yoshiki , Rupasinghe Thusitha W. T. , Mullin Kylie A. , MacRae James I. , Spurck Timothy P. , Kalanon Ming , Shears Melanie J. , Coppel Ross L. , Crellin Paul K. , Maréchal Eric , McConville Malcolm J. , McFadden Geoffrey I.
Published: April 2013

The human malaria parasite
Plasmodium falciparum
harbors a relict, nonphotosynthetic plastid of algal origin termed the apicoplast. Although considerable progress has been made in defining the metabolic functions of the apicoplast, information on the composition and biogenesis of the four delimiting membranes of this organelle is limited. Here, we report an efficient method for preparing highly purified apicoplasts from red blood cell parasite stages and the comprehensive lipidomic analysis of this organelle. Apicoplasts were prepared from transgenic parasites expressing an epitope-tagged triosephosphate transporter and immunopurified on magnetic beads. Gas and liquid chromatography MS analyses of isolated apicoplast lipids indicated significant differences compared with total parasite lipids. In particular, apicoplasts were highly enriched in phosphatidylinositol, consistent with a suggested role for phosphoinositides in targeting membrane vesicles to apicoplasts. Apicoplast phosphatidylinositol and other phospholipids were also enriched in saturated fatty acids, which could reflect limited acyl exchange with other membrane phospholipids and/or a requirement for specific physical properties. Lipids atypical for plastids (sphingomyelins, ceramides, and cholesterol) were detected in apicoplasts. The presence of cholesterol in apicoplast membranes was supported by filipin staining of isolated apicoplasts. Galactoglycerolipids, dominant in plant and algal plastids, were not detected in
P. falciparum
apicoplasts, suggesting that these glycolipids are a hallmark of photosynthetic plastids and were lost when these organisms assumed a parasitic lifestyle. Apicoplasts thus contain an atypical melange of lipids scavenged from the human host alongside lipids remodeled by the parasite cytoplasm, and stable isotope labeling shows some apicoplast lipids are generated de novo by the organelle itself.
Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore
Authors: Zhang Fan , Scheerer Patrick , Oberpichler Inga , Lamparter Tilman , Krauß Norbert
Published: April 2013

The (6-4) photolyases use blue light to reverse UV-induced (6-4) photoproducts in DNA. This (6-4) photorepair was thought to be restricted to eukaryotes. Here we report a prokaryotic (6-4) photolyase, PhrB from
Agrobacterium tumefaciens
, and propose that (6-4) photolyases are broadly distributed in prokaryotes. The crystal structure of photolyase related protein B (PhrB) at 1.45 Å resolution suggests a DNA binding mode different from that of the eukaryotic counterparts. A His-His-X-X-Arg motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. The PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore and a [4Fe-4S] cluster bound to the catalytic domain. A significant part of the Fe-S fold strikingly resembles that of the large subunit of eukaryotic and archaeal primases, suggesting that the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. Our study presents a unique prokaryotic (6-4) photolyase and proposes that the prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family.
Allosteric mechanisms can be distinguished using structural mass spectrometry
Authors: Dyachenko Andrey , Gruber Ranit , Shimon Liat , Horovitz Amnon , Sharon Michal
Published: April 2013

The activity of many proteins, including metabolic enzymes, molecular machines, and ion channels, is often regulated by conformational changes that are induced or stabilized by ligand binding. In cases of multimeric proteins, such allosteric regulation has often been described by the concerted Monod–Wyman–Changeux and sequential Koshland–Némethy–Filmer classic models of cooperativity. Despite the important functional implications of the mechanism of cooperativity, it has been impossible in many cases to distinguish between these various allosteric models using ensemble measurements of ligand binding in bulk protein solutions. Here, we demonstrate that structural MS offers a way to break this impasse by providing the full distribution of ligand-bound states of a protein complex. Given this distribution, it is possible to determine all the binding constants of a ligand to a highly multimeric cooperative system, and thereby infer its allosteric mechanism. Our approach to the dissection of allosteric mechanisms relies on advances in MS—which provide the required resolution of ligand-bound states—and in data analysis. We validated our approach using the well-characterized
Escherichia coli
chaperone GroEL, a double-heptameric ring containing 14 ATP binding sites, which has become a paradigm for molecular machines. The values of the 14 binding constants of ATP to GroEL were determined, and the ATP-loading pathway of the chaperone was characterized. The methodology and analyses presented here are directly applicable to numerous other cooperative systems and are therefore expected to promote further research on allosteric systems.
Structural effect of size on interracial friendship
Authors: Cheng Siwei , Xie Yu
Published: April 2013

Social contexts exert structural effects on individuals’ social relationships, including interracial friendships. In this study, we posit that, net of group composition, total context size has a distinct effect on interracial friendship. Under the assumptions of (
i
) maximization of preference in choosing a friend, (
ii
) multidimensionality of preference, and (
iii
) preference for same-race friends, we conducted analyses using microsimulation that yielded three main findings. First, increased context size decreases the likelihood of forming an interracial friendship. Second, the size effect increases with the number of preference dimensions. Third, the size effect is diluted by noise, i.e., the random component affecting friendship formation. Analysis of actual friendship data among 4,745 American high school students yielded results consistent with the main conclusion that increased context size promotes racial segregation and discourages interracial friendship.
Adaptation to steady light by intrinsically photosensitive retinal ganglion cells
Authors: Do Michael Tri Hoang , Yau King-Wai
Published: April 2013

Intrinsically photosensitive retinal ganglion cells (ipRGCs) are recently discovered photoreceptors in the mammalian eye. These photoreceptors mediate primarily nonimage visual functions, such as pupillary light reflex and circadian photoentrainment, which are generally expected to respond to the absolute light intensity. The classical rod and cone photoreceptors, on the other hand, mediate image vision by signaling contrast, accomplished by adaptation to light. Experiments by others have indicated that the ipRGCs do, in fact, light-adapt. We found the same but, in addition, have now quantified this light adaptation for the M1 ipRGC subtype. Interestingly, in incremental-flash-on-background experiments, the ipRGC’s receptor current showed a flash sensitivity that adapted in background light according to the Weber–Fechner relation, well known to describe the adaptation behavior of rods and cones. Part of this light adaptation by ipRGCs appeared to be triggered by a Ca
2+
influx, in that the flash response elicited in the absence of extracellular Ca
2+
showed a normal rising phase but a slower decay phase, resulting in longer time to peak and higher sensitivity. There is, additionally, a prominent Ca
2+
-independent component of light adaptation not typically seen in rods and cones or in invertebrate rhabdomeric photoreceptors.
Hammondia hammondi
, an avirulent relative of
Toxoplasma gondii
, has functional orthologs of known
T. gondii
virulence genes
Authors: Walzer Katelyn A. , Adomako-Ankomah Yaw , Dam Rachel A. , Herrmann Daland C. , Schares Gereon , Dubey Jitender P. , Boyle Jon P.
Published: April 2013

Toxoplasma gondii
is a ubiquitous protozoan parasite capable of infecting all warm-blooded animals, including humans. Its closest extant relative,
Hammondia hammondi,
has never been found to infect humans and, in contrast to
T. gondii
, is highly attenuated in mice. To better understand the genetic bases for these phenotypic differences, we sequenced the genome of a
H. hammondi
isolate (HhCatGer041) and found the genomic synteny between
H. hammondi
and
T. gondii
to be >95%. We used this genome to determine the
H. hammondi
primary sequence of two major
T. gondii
mouse virulence genes,
TgROP5
and
TgROP18
. When we expressed these genes in
T. gondii
, we found that
H. hammondi
orthologs of TgROP5 and TgROP18 were functional. Similar to
T. gondii
, the
HhROP5
locus is expanded, and two distinct HhROP5 paralogs increased the virulence of a
T. gondii TgROP5
knockout strain. We also identified a 107 base pair promoter region, absent only in type III
TgROP18
, which is necessary for TgROP18 expression. This result indicates that the
ROP18
promoter was active in the most recent common ancestor of these two species and that it was subsequently inactivated in progenitors of the type III lineage. Overall, these data suggest that the virulence differences between these species are not solely due to the functionality of these key virulence factors. This study provides evidence that other mechanisms, such as differences in gene expression or the lack of currently uncharacterized virulence factors, may underlie the phenotypic differences between these species.
Prognostic microRNA/mRNA signature from the integrated analysis of patients with invasive breast cancer
Authors: Volinia Stefano , Croce Carlo M.
Published: April 2013

The optimal management of breast cancer (BC) presents challenges due to the heterogeneous molecular classification of the disease. We performed survival analysis on a cohort of 466 patients with primary invasive ductal carcinoma (IDC), the most frequent type of BC, by integrating mRNA, microRNA (miRNA), and DNA methylation next-generation sequencing data from The Cancer Genome Atlas (TCGA). Expression data from eight other BC cohorts were used for validation. The prognostic value of the resulting miRNA/mRNA signature was compared with that of other prognostic BC signatures. Thirty mRNAs and seven miRNAs were associated with overall survival across different clinical and molecular subclasses of a 466-patient IDC cohort from TCGA. The prognostic RNAs included
PIK3CA
, one of the two most frequently mutated genes in IDC, and miRNAs such as hsa-miR-328, hsa-miR-484, and hsa-miR-874. The area under the curve of the receiver-operator characteristic for the IDC risk predictor in the TCGA cohort was 0.74 at 60 mo of overall survival (
P
< 0.001). Most relevant for clinical application, the integrated signature had the highest prognostic value in early stage I and II tumors (receiver-operator characteristic area under the curve = 0.77,
P
value < 0.001). The genes in the RNA risk predictor had an independent prognostic value compared with the clinical covariates, as shown by multivariate analysis. The integrated RNA signature was successfully validated on eight BC cohorts, comprising a total of 2,399 patients, and it had superior performance for risk stratification with respect to other RNA predictors, including the mRNAs used in MammaPrint and Oncotype DX assays.
Relationship of DNA degradation by
Saccharomyces cerevisiae
Exonuclease 1 and its stimulation by RPA and Mre11-Rad50-Xrs2 to DNA end resection
Authors: Cannavo Elda , Cejka Petr , Kowalczykowski Stephen C.
Published: April 2013

Homologous recombination is a major pathway for repair of DNA double-strand breaks. This repair process is initiated by resection of the 5′-terminated strand at the break site. In yeast, resection is carried out by three nucleolytic complexes: Mre11-Rad50-Xrs2, which functions at the initial step and also stimulates the two processive pathways, Sgs1-Dna2 and Exonuclease 1 (Exo1). Here we investigated the relationship between the three resection pathways with a focus on Exo1. Exo1 preferentially degrades the 5′-terminal stand of duplex DNA that is single stranded at the 3′ end, in agreement with its role downstream of the Mre11-Rad50-Xrs2 complex. Replication protein A (RPA) stimulates DNA end resection by Exo1 by both preventing nonspecific binding of Exo1 to and preventing degradation of single-stranded DNA. Nucleolytic degradation of DNA by Exo1 is inhibited by the helicase-deficient Sgs1 K706A mutant protein and, reciprocally, the nuclease-deficient Exo1 D173A mutant protein inhibits DNA unwinding by Sgs1. Thus, the activities of Sgs1 and Exo1 at DNA ends are mutually exclusive, establishing biochemically that both machineries function independently in DNA end processing. We also reconstituted Sgs1-Top3-Rmi1-RPA-Dna2 and Exo1 resection reactions both individually and combined, either with or without the Mre11-Rad50-Xrs2 complex. We show that the yeast Sgs1-Dna2 and Exo1 pathways do not stimulate one another and function as independent and separate DNA end-processing machineries, even in the presence of the stimulatory Mre11-Rad50-Xrs2 complex.
Phosphoinositides and membrane curvature switch the mode of actin polymerization via selective recruitment of toca-1 and Snx9
Authors: Gallop Jennifer L. , Walrant Astrid , Cantley Lewis C. , Kirschner Marc W.
Published: April 2013

The membrane–cytosol interface is the major locus of control of actin polymerization. At this interface, phosphoinositides act as second messengers to recruit membrane-binding proteins. We show that curved membranes, but not flat ones, can use phosphatidylinositol 3-phosphate [PI(3)P] along with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P
2
] to stimulate actin polymerization. In this case, actin polymerization requires the small GTPase cell cycle division 42 (Cdc42), the nucleation-promoting factor neural Wiskott–Aldrich syndrome protein (N-WASP) and the actin nucleator the actin-related protein (Arp) 2/3 complex. In liposomes containing PI(4,5)P2 as the sole phosphoinositide, actin polymerization requires transducer of Cdc42 activation-1 (toca-1). In the presence of phosphatidylinositol 3-phosphate, polymerization is both more efficient and independent of toca-1. Under these conditions, sorting nexin 9 (Snx9) can be implicated as a specific adaptor that replaces toca-1 to mobilize neural Wiskott–Aldrich syndrome protein and the Arp2/3 complex. This switch in phosphoinositide and adaptor specificity for actin polymerization from membranes has implications for how different types of actin structures are generated at precise times and locations in the cell.
Structural evidence for a bifurcated mode of action in the antibody-mediated neutralization of hepatitis C virus
Authors: Deng Lu , Zhong Lilin , Struble Evi , Duan Hongying , Ma Li , Harman Christine , Yan Hailing , Virata Maria Luisa , Zhao Zhong , Feinstone Stephen , Alter Harvey , Zhang Pei
Published: April 2013

Hepatitis C virus (HCV) envelope glycoprotein E2 has been considered as a major target for vaccine design. Epitope II, mapped between residues 427–446 within the E2 protein, elicits antibodies that are either neutralizing or nonneutralizing. The fundamental mechanism of antibody-mediated neutralization at epitope II remains to be defined at the atomic level. Here we report the crystal structure of the epitope II peptide in complex with a monoclonal antibody (mAb#8) capable of neutralizing HCV. The complex structure revealed that this neutralizing antibody engages epitope II via interactions with both the C-terminal α-helix and the N-terminal loop using a bifurcated mode of action. Our structural insights into the key determinants for the antibody-mediated neutralization may contribute to the immune prophylaxis of HCV infection and the development of an effective HCV vaccine.
Selective degradation of mRNAs by the HSV host shutoff RNase is regulated by the U
L
47 tegument protein
Authors: Shu Minfeng , Taddeo Brunella , Zhang Weiran , Roizman Bernard
Published: April 2013

Significance

Herpes simplex virus encodes an RNase linked to the shutoff of host gene expression early in infection (virion host shutoff-RNase), and recent studies showed that its activity is highly selective: it targets stable host mRNAs and α (immediate early) mRNAs but spares other viral mRNAs. Here we report that RNase’s function early in infections is regulated by a viral protein designated U
L
47. U
L
47 is packed in virions; it binds the RNase and attenuates the degradation of all viral mRNAs but has no effect on the processing of the stress response mRNAs targeted by the viral RNase.
Upper Thermal Tolerance of Mountain Whitefish Eggs and Fry
Authors: Brinkman Stephen F. , Crockett Harry J. , Rogers Kevin B.
Published: April 2013

Some populations of Mountain Whitefish Prosopium williamsoni, a widely distributed native Rocky Mountain salmonid, have experienced catastrophic declines while other populations remain robust. To assess the possibility that the declines have arisen from climate‐related factors, several experiments were conducted to determine the upper thermal tolerances of embryos and fry and the effects of temperature on growth. Hatching of eggs was measured at 5.7, 6.4, 8.4, and 10.4°C (three replicates each). Survival and growth of fry were measured for 33 d at 5.7, 8.2, 11.8, 16.5, 19.1, 22.2, and 25.2°C (three replicates each). Mean hatching success was 96.7% (SD, 2.9) at 5.7°C, 98.3% (2.9) at 6.4°C, 90.0% (8.7) at 8.4°C and 38.3% (10.4) at 10.4°C. The ultimate upper incipient lethal temperature for fry was 23.6°C (95% CI, 23.5–23.7°C) after 7 d, which decreased with time to 22.6°C (22.1–23.0°C) after 33 d. The critical thermal maximum was 26.7°C (SD, 0.8) for fry acclimated to 13.4°C. The temperature for maximum growth was 13.8°C (95% CI, 10.8–16.8°C). Growth rates above and below the temperature for maximum growth decreased sharply to about 40% of the maximum at 5.7°C and 22.2°C. Based on these experimental data, the criteria for the protection of Mountain Whitefish fry are 21.6°C for acute water temperature and 16.8°C for chronic water temperature. The acute criterion for reproduction—based on the maximum temperature for successful incubation—is 8.4°C. The low upper thermal tolerance of Mountain Whitefish relative to those of other salmonids suggests that they will be very vulnerable to the increasing stream temperatures resulting from climate change.