bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of magnetic field on the thermal conductivity of Bi2Sr2CaCu2Ox in the superconducting phase transition region
Authors: Ragimov S. S. , Aliev S. A. , Aliev V. M.
Published: December 2009

A study of the influence of magnetic field on the thermal conductivity of Bi2Sr2CaCu2Ox is made. It is found that the thermal conductivity increases under the influence of magnetic field because the electronic part of the thermal conductivity increases on account of breaking of the Cooper pairs and a decrease of the phonon-vortex scattering.
Influence of microwave irradiation on the dc resistive state of a wide superconducting film
Authors: Dmitriev V. M. , Zolochevskii I. V. , Salenkova T. V.
Published: December 2009

The influence of a microwave field on the resistive state brought on in a wide film by the passage of a dc current is investigated experimentally. In this situation the resistivity arises as a consequence of two processes: the motion of Pearl–Abrikosov vortices of the self-magnetic field of the current, and phase slip of the superconducting order parameter. It is shown that under microwave irradiation the resistivity of the film due to the vortex mechanism decreases, and at high power levels (P>0.4Pc) it vanishes, and then the resistivity of the film is due solely to phase slip processes, as in narrow vortex-free channels. It is found experimentally that, starting at some power level P*<Pc, the electromagnetic field plays a governing role in the processes giving rise to phase-slip lines. A similar conclusion is reached from a study of the influence of a microwave field on the differential resistance of a phase-slip center in narrow vortex-free channels; this suggests that phase-slip processes in wide and narrow films share a common nature.
Excitation of electromagnons in the ferroelectromagnet TbMnO3 by an alternating electric field
Authors: Chupis I. E.
Published: December 2009

The excitation of electromagnons in the ferroelectromagnetic phase of TbMnO3 by an electromagnetic wave is considered for different polarizations of the wave. In the case when the electric field of the wave is oriented perpendicular to the spontaneous polarization of the crystal, the results of calculations show that the frequency of the resonance absorption is independent of temperature, in agreement with experiment. When the electric field is directed along the spontaneous polarization it is predicted that the temperature and frequency dependence of the dielectric loss will have anomalies near the temperature of the ferroelectric transition.
Resistivity of bulk amorphous Zr41.2Be22.5Ti13.8Cu12.5Ni10 and its polycrystalline analogue
Authors: Vasil’ev A. A. , Kovtun K. V. , Malykhin S. V. , Merisov B. A. , Pugachev A. T. , Trembach O. V. , Khadzhaĭ G. Ya.
Published: December 2009

The resistivity of the bulk amorphous alloy Zr41.2Be22.5Ti13.8Cu12.5Ni10 and a polycrystal with the same composition has been measured in the temperature interval 1.5–300K. The Faber-Ziman model (bulk amorphous alloy) and the Bloch-Grüneisen model (polycrystal) are used as a basis to make a fit to the temperature dependences obtained.
Experimental evidence of the role of quasilocalized phonons in the thermal conductivity of simple alcohols in orientationally ordered crystalline phases
Authors: Krivchikov A. I. , Sharapova I. V. , Korolyuk O. A. , Romantsova O. O. , Bermejo F. J.
Published: December 2009

The thermal conductivity κ(T) of crystalline alcohols (methyl, ethyl and 1-propyl) within their thermodynamic equilibrium phases for T⩾2K and under the equilibrium vapor pressures has been measured and analyzed. While such compounds usually exhibit a rich polymorphism including amorphous and partially ordered crystals, the phases here explored correspond to crystals showing complete orientational order. The results show that the temperature dependence of κ(T) above its maximum deviates from the expected 1∕T-law decrease with increasing temperature, arising from anharmonic interactions involving acoustic excitations. Such a deviation is here attributed to the presence of a component κII(T) corresponding to the shortest-lifetime phonons (Cahill-Pohl model), in addition to the component κI(T) related to propagating phonons and thus: κ(T)=κI(T)+κII(T). Above T=40K, κI(T) does follow the 1∕T law and κII(T) is basically temperature independent. The component κI(T) is well described by the Debye-Peierls model taking into account the phonon-phonon umklapp processes and phonon scattering by dislocations. In turn, the contribution κII(T) is attributed to the effects of higher-lying excitations which get thermally populated above some 40K. Finally, a systematic trend is found concerning the strength of phonon-phonon scattering, which is seen to diminish as the number of carbon atoms in the alcohol molecule increases.
A mathematical theory of stochastic microlensing. II. Random images, shear, and the Kac–Rice formula
Authors: Petters A. O. , Rider B. , Teguia A. M.
Published: December 2009

Continuing our development of a mathematical theory of stochastic microlensing, we study the random shear and expected number of random lensed images of different types. In particular, we characterize the first three leading terms in the asymptotic expression of the joint probability density function (pdf) of the random shear tensor due to point masses in the limit of an infinite number of stars. Up to this order, the pdf depends on the magnitude of the shear tensor, the optical depth, and the mean number of stars through a combination of radial position and the star’s mass. As a consequence, the pdf’s of the shear components are seen to converge, in the limit of an infinite number of stars, to shifted Cauchy distributions, which shows that the shear components have heavy tails in that limit. The asymptotic pdf of the shear magnitude in the limit of an infinite number of stars is also presented. All the results on the random microlensing shear are given for a general point in the lens plane. Extending to the general random distributions (not necessarily uniform) of the lenses, we employ the Kac–Rice formula and Morse theory to deduce general formulas for the expected total number of images and the expected number of saddle images. We further generalize these results by considering random sources defined on a countable compact covering of the light source plane. This is done to introduce the notion of global expected number of positive parity images due to a general lensing map. Applying the result to microlensing, we calculate the asymptotic global expected number of minimum images in the limit of an infinite number of stars, where the stars are uniformly distributed. This global expectation is bounded, while the global expected number of images and the global expected number of saddle images diverge as the order of the number of stars.
The magnetization of epitaxial nanometric CoFe2O4(001) layers
Authors: Rigato F. , Geshev J. , Skumryev V. , Fontcuberta J.
Published: December 2009

We have studied the magnetic anisotropy of nanometric CoFe2O4 (CFO) thin films grown on (100)SrTiO3 (STO) substrates. It has been found that epitaxial substrate-induced compressive strain makes the normal-to-film axis harder than the in-plane directions. In agreement with some previous reports, the magnetization loops are found to display a characteristic shrinking at low fields. Detailed structural and microstructural analyses, together with a modeling of the magnetization loops, revealed that the microstructure of the films, namely, the coexistence of a continuous CFO and a distribution of pyramidal CFO huts emerging from the surface, are responsible for this peculiar feature. We argue that this behavior, which significantly impacts the magnetic properties, could be a general trend of spinel films grow on (001)STO substrates.
An integrated approach to NMR spin relaxation in flexible biomolecules: Application to β-D-glucopyranosyl-(1→6)-α-D-mannopyranosyl-OMe
Authors: Zerbetto Mirco , Polimeno Antonino , Kotsyubynskyy Dmytro , Ghalebani Leila , Kowalewski Jozef , Meirovitch Eva , Olsson Ulrika , Widmalm Göran
Published: December 2009

The description of the reorientational dynamics of flexible molecules is a challenging task, in particular when the rates of internal and global motions are comparable. The commonly used simple mode-decoupling models are based on the assumption of statistical independence between these motions. This assumption is not valid when the time scale separation between their rates is small, a situation that was found to arise in oligosaccharides in the context of certain internal motions. To make possible the interpretation of NMR spin relaxation data from such molecules, we developed a comprehensive approach generally applicable to flexible rotators with one internal degree of freedom. This approach integrates a stochastic description of coupled global tumbling and internal torsional motion, quantum chemical calculations of the local potential and the local geometry at the site of the restricted torsion, and hydrodynamics-based calculations of the diffusive properties. The method is applied to the disaccharide β-D-Glcp-(1→6)-α-D-[6-C13]-Manp-OMe dissolved in a DMSO-d6/D2O cryosolvent. The experimental NMR relaxation parameters, associated with the C13H2 probe residing at the glycosidic linkage, include C13 T1 and T2 and C13-{H1} nuclear Overhauser enhancement (NOE) as well as longitudinal and transverse dipole-dipole cross-correlated relaxation rates, acquired in the temperature range of 253–293 K. These data are predicted successfully by the new theory with only the H–C–H angle allowed to vary. Previous attempts to fit these data using mode-decoupling models failed.
State-selective spectroscopy of water up to its first dissociation limit
Authors: Grechko Maxim , Boyarkin Oleg V. , Rizzo Thomas R. , Maksyutenko Pavlo , Zobov Nikolay F. , Shirin Sergei V. , Lodi Lorenzo , Tennyson Jonathan , Császár Attila G. , Polyansky Oleg L.
Published: December 2009

A joint experimental and first-principles quantum chemical study of the vibration-rotation states of the water molecule up to its first dissociation limit is presented. Triple-resonance, quantum state-selective spectroscopy is used to probe the entire ladder of water’s stretching vibrations up to 19 quanta of OH stretch, the last stretching state below dissociation. A new ground state potential energy surface of water is calculated using a large basis set and an all-electron, multireference configuration interaction procedure, which is augmented by relativistic corrections and fitted to a flexible functional form appropriate for a dissociating system. Variational nuclear motion calculations on this surface are used to give vibrational assignments. A total of 44 new vibrational states and 366 rotation-vibration energy levels are characterized; these span the region from 35 508 to 41 126 cm−1 above the vibrational ground state.
Carbon nanofiber supercapacitors with large areal capacitances
Authors: McDonough James R. , Choi Jang Wook , Yang Yuan , La Mantia Fabio , Zhang Yuegang , Cui Yi
Published: December 2009

We develop supercapacitor (SC) devices with large per-area capacitances by utilizing three-dimensional (3D) porous substrates. Carbon nanofibers (CNFs) functioning as active SC electrodes are grown on 3D nickel foam. The 3D porous substrates facilitate a mass loading of active electrodes and per-area capacitance as large as 60 mg/cm2 and 1.2 F/cm2, respectively. We optimize SC performance by developing an annealing-free CNF growth process that minimizes undesirable nickel carbide formation. Superior per-area capacitances described here suggest that 3D porous substrates are useful in various energy storage devices in which per-area performance is critical.
Time-delay compensated monochromator for the spectral selection of extreme-ultraviolet high-order laser harmonics
Authors: Poletto Luca , Villoresi Paolo , Frassetto Fabio , Calegari Francesca , Ferrari Federico , Lucchini Matteo , Sansone Giuseppe , Nisoli Mauro
Published: December 2009

The design and the characterization of a monochromator for the spectral selection of ultrashort high-order laser harmonics in the extreme ultraviolet are presented. The instrument adopts the double-grating configuration to preserve the length of the optical paths of different diffracted rays, without altering the extremely short duration of the pulse. The gratings are used in the off-plane mount to have high efficiency. The performances of the monochromator have been characterized in terms of spectral response, efficiency, photon flux, imaging properties, and temporal response. In particular, the temporal characterization of the harmonic pulses has been obtained using a cross-correlation method: Pulses as short as 8 fs have been measured at the output of the monochromators, confirming the effectiveness of the time-delay compensated configuration.
Zero field spin splitting in AlSb/InAs/AlSb quantum wells induced by surface proximity effects
Authors: Nishioka Masaya , Gurney Bruce A. , Marinero Ernesto E. , Mireles Francisco
Published: December 2009

InAs quantum well heterostructures are of considerable interest for mesoscopic device applications such as scanning probe and magnetic recording sensors, which require the channel to be close to the surface. Here we report on magnetotransport measurements of AlSb/InAs/AlSb Hall bars at a shallow depth of 20 nm. Analysis of the observed Shubnikov-de Haas oscillations and modeling show that spin splitting energies in excess of 2.3 meV occur at zero magnetic field. We conclude that the spin-splitting results from the Rashba effect due to the band bending in the quantum well. This is caused by substantial electron transfer from the surface to the quantum well and becomes significant when the quantum well is located near the surface.
Si Esaki diodes with high peak to valley current ratios
Authors: Oehme M. , Hähnel D. , Werner J. , Kaschel M. , Kirfel O. , Kasper E. , Schulze J.
Published: December 2009

We report room temperature current voltage characteristics of Si p+-i-n+ Esaki diodes integrated on silicon substrates. The diodes were fabricated by low-temperature molecular beam epitaxy. Very high and abrupt p- and n-type dopant transitions into the 1020 cm−3 ranges are achieved by boron and antimony, respectively. The integrated devices are realized without a postgrowth annealing step. The silicon Esaki diodes show negative differential resistance at room temperature with excellent peak to valley current ratios up to 3.94. A variation in the thickness of the silicon tunneling barrier changes the peak current density over three orders of magnitude.
Integrating Urban Form and Demographics in Water-Demand Management: An Empirical Case Study of Portland, Oregon
Authors: Shandas Vivek , Parandvash G Hossein
Published: December 2009

Theories of water-resource management suggest that water demand is mediated by three interacting factors: technological innovations, pricing structures, and individual behaviors and demographics. While these factors provide useful insights for ongoing water conservation strategies, such as outreach and education campaigns, pricing schemes, and incentives aimed at residential developments, few studies examine the relationship between land-use planning and water demand. This paper reports the results of a study on land-use zoning and development-induced water consumption in Portland, Oregon. We used a geographic information system to integrate land-use records, water-consumption data, sociodemographics, and property tax information for over 122 550 parcels of varying land uses, and employed multiregression analyses to measure the effect of urban form—as measured by both the type and the structure of land uses—on regional water demand. While our results corroborate previous studies that link demographic characteristics to water demand, we go further by identifying zoning and structural attributes of the households as explaining over 93% of water use in all parcels. The paper concludes with a discussion of the opportunities and challenges for coordinating water-resource management with land-use planning.
Improving taro (Colocasia esculenta var. esculenta) production using biotechnological approaches
Authors: Deo Pradeep C. , Tyagi Anand P. , Taylor Mary , Becker Douglas K. , Harding Robert M.
Published: December 2009

Taro (Colocasia esculenta L. Schott) is an important crop worldwide but is of particular significance in many Pacific Island countries where it forms part of the staple diet and serves as an export commodity. Escalating pest and disease problems are jeopardizing taro production with serious implications to food security and trade. Biotechnological approaches to addressing pest and disease problems, such as somatic embryogenesis and transgenesis, are potentially viable options. However, despite biotechnological advancements in higher profile agronomic crops, such progress in relation to Colocasia esculenta var. esculenta has been slow. This paper reviews taro biology, highlights the cultural and economic significance of taro in Pacific Island countries and discusses the progress made towards the molecular breeding of this important crop to date.
Effects of nickel salt concentrations on germination and development of Grevillea exul var. rubiginosa
Authors: Chandra R. , Tyagi A. P. , Bouraima-Saliou M. , Leon V. , Pineau R.
Published: December 2009

Endemic plant species have been considered as one of the best means of ecological restoration of exploited mine sites in New Caledonia. These plants have the adaptability characteristics that allow them to thrive on serpentine soils. This study has investigated
the physiological effects of nickel concentrations at different developmental stages on Grevillea exul var. rubiginosa an endemic New Caledonian species. The first two stages of a plant life cycle germination and post germination under controlled conditions were studied. The experiment involved Petri dish germination and growth of seeds and seedlings respectively particularly root development and length in different salts of nickel (acetate, chloride and sulphate) with 0�500 ppm concentrations. Decrease in both studied parameters: germination rates and root lengths were observed with increasing concentrations of nickel solutions supplied to seeds. A minimum concentration of 5 ppm of nickel in the medium had a positive effect on germination rate as well as root length. Results suggest that it is the concentration of nickel used in the present investigation to test the germination rate and root elongation in Grevillea exul var. rubiginosa which are essential for experimental work in the field rather than the form (salt) of nickel. These results will be help-full in re-vegetation efforts of nickel mining sites in New Caledonia.
Gene effects for different metric traits under normal and high temperature stress environments in wheat (T. aestivum L. Em Thell)
Authors: Sheikh Sameena , Behl R. K. , Dhanda S. S. , Kumar Ashwani
Published: December 2009

The present investigation was conducted to analyze gene effects for grain yield and its components under two different environments.
Nine wheat genotypes were selected to generate the experimental material comprised six parental and segregating generations (P1, P2, F1, F2, BC1 and BS1 of BC1 of each of the following six crosses – PBW 343 x WH 283, PBW 343 x WH 542, PBW 343 x PBW 435, UP 2565 x UP 2425, EIGN 1 x Raj 3765 and EIGN 8 x UP 2425. Joint scaling tests revealed the presence of epitasis. Six parameter model revealed the significance of additive gene effects (d) for biological and grain yield and their components in most of the crosses. The relative magnitude of (h) was higher than (d) in all the crosses for most of the characters while additive x additive (i) effects appeared to be significant for grain yield per plant (E1) and number of grain per spike (E2) in PBW 343 x WH 283. Significant (i) type of interaction was recorded in PBW 343 x WH 542 for number of grain per spike (E1), number of tillers per plant (E2) in PBW 343 x PBW 435 and for 1000-grain weight in UP 2565 x UP 2425. Pedigree method and simple selection in crosses like PBW 343 x PBW 435, UP 2565 x UP 2425, PBW 343 x WH 283 and PBW 343 x WH 542 should be used for improvement of traits governed by additive and additive x additive gene effect.
RAPD analysis for genetic polymorphism in bread wheat (Triticum aestivum L. Em Thell) genotypes varying for grain protein content
Authors: Nimbal Somvir , Behl R. K. , Chhabra A. K.
Published: December 2009

Genetic polymorphism was investigated among nine spring wheat genotypes, differing in grain protein content, including C-306M10 (mutant of drought tolerant variety C306), DI 8, DI 9, DI 16, DI 20, DI 716, DI 717, DI 728 (near isogenic lines) and HGPC (from Wheat x Rye crosses) using 55 RAPD primers. Out of 55 primers used, only 36 amplified and generated 2(OPG08, OPD05) and 12 (OPD02) bands. A total of 342 amplified products were observed, of which 168 were polymorphic (49.12%) while 174 were monomorphic. The primer OPC-05 and OPC-07 revealed 92.86% and 80.00% polymorphism, respectively and these primers were most useful in characterization of nine wheat genotypes included in this study. The primer OPG-08 showed no polymorphism. It is concluded that the primers OPC-05 and OPC-07 were very
effective in distinguishing wheat genotypes in the present study. Twenty six RAPD primers produced a total of 48 unique bands for high protein content that were either present or absent in HGPC a-high grain protein genotype and thus can be used in wheat improvement through marker-assisted selection (for the bands which are unique by their presence). Data (RAPD analysis) were used to generate the similarity coefficients using `siMqual' subprogram of software NTSYS-PC. The similarity coefficient values ranged from 0.97(DI8 and DI9) to 0.68 (DI9 and HGPC), indicating high genetic variability among the selected wheat genotypes. The cluster analysis and principle component analysis broadly divided the wheat genotypes into two groups and showed that DI 9 and HGPC were most divergent genotypes.
Studies on biodegradation of crude oil by Aspergillus niger
Authors: Mittal Anupama , Singh Padma
Published: December 2009

Hydrocarbon degrading microorganisms play a major role in the environment. In the present study crude oil degrading fungal strain Aspergillus niger was isolated from oil contaminated soil near crude oil production well (Lingala) Andhra Pradesh. The rate of reduction in some petroleum hydrocarbon fractions, such as n-alkanes, aromatics, nitrogen, sulfur and oxygen (NSO)-containing compounds and polycyclic aromatic hydrocarbons (PAHs), were monitored by means of gas chromatography. The nC17/Pristine and nC18/Phytane ratios, extrapolated from the GC profiles decreased from the initial value of 2.510 and 7.289 to 0.132 and 0.474 respectively at day 60.
Microbial degradation of polyethylene (PE)
Authors: Kumari Kiran , Aanad R. C. , Narula Neeru
Published: December 2009

Thirty two bacterial isolates were obtained from soil by soil burial method followed by enrichment culture technique in film culturing (FC) media. Bacterial isolates differing in morphology were selected, purified and maintained at 4°C. Thirty % of these isolates were found to be Gram negative and 50% showed positive starch hydrolysis test and were screened for their ability to degrade Low Density Polyethylene (untreated, UV and heat strips) in film culturing media and percent weight loss of polyethylene after 4th week was determined. Among various isolates, highest degradation was by Is 3, Is 22 and Is 31 to the range of 25–27%, of UV treated
polyethylene strips. High temperature (40°C), was found to enhance degradation rate of polyethylene more effectively by 24–28% compared to low temperature at 30°C (18–21%). Degradation of treated polyethylene strips (UV, heat steam) was up to 4% by compost treatment as studied by using CO2 evolution, an estimation tool to analyze % degradation. Bacterial activity was also affected by various environmental factors like sunlight, temperature, oxygen etc.
A FOXA1-binding enhancer regulates
Hoxb13
expression in the prostate gland
Authors: McMullin Ryan P. , Dobi Albert , Mutton Laura N. , Orosz András , Maheshwari Shilpi , Shashikant Cooduvalli S. , Bieberich Charles J.
Published: December 2009

Hoxb13
is robustly transcribed in derivatives of posterior endoderm including the colon, rectum, and the prostate gland. Transcriptional activity in the prostate persists unabated under conditions of androgen deprivation and throughout the course of disease progression in a mouse prostate cancer model. To elucidate the molecular basis of prostate-restricted transcriptional activation of
Hoxb13
, a bacterial artificial chromosome (BAC)-based reporter gene deletion analysis was performed in transgenic mice. Two regions downstream of the
Hoxb13
coding region were found to be required to support transcriptional activity in the prostate but were completely dispensable for expression in the colon and rectum. Bioinformatic analyses of one region identified a 37-bp element conserved in mammals. This element, which bears two potential binding sites for Forkhead class transcription factors, is occupied by FOXA1 in a human prostate cancer cell line. Precise replacement of this enhancer with an extended LoxP site in the context of a 218,555-bp BAC reporter nearly extinguished
Hoxb13
-mediated transcriptional activity in the mouse prostate. These data demonstrate that FOXA1 directly regulates
HOXB13
in human prostate epithelial cells, and show that this prostate-specific regulatory mechanism is conserved in mice.
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD
Authors: Thorsen Thor S. , Madsen Kenneth L. , Rebola Nelson , Rathje Mette , Anggono Victor , Bach Anders , Moreira Irina S. , Stuhr-Hansen Nicolai , Dyhring Tino , Peters Dan , Beuming Thijs , Huganir Richard , Weinstein Harel , Mulle Christophe , Strømgaard Kristian , Rønn Lars Christian B. , Gether Ulrik
Published: December 2009

Proteins containing PSD-95/Discs-large/ZO-1 homology (PDZ) domains play key roles in the assembly and regulation of cellular signaling pathways and represent putative targets for new pharmacotherapeutics. Here we describe the first small-molecule inhibitor (FSC231) of the PDZ domain in protein interacting with C kinase 1 (PICK1) identified by a screening of ~44,000 compounds in a fluorescent polarization assay. The inhibitor bound the PICK1 PDZ domain with an affinity similar to that observed for endogenous peptide ligands (
K
i
~10.1 μM). Mutational analysis, together with computational docking of the compound in simulations starting from the PDZ domain structure, identified the binding mode of FSC231. The specificity of FSC231 for the PICK1 PDZ domain was supported by the lack of binding to PDZ domains of postsynaptic density protein 95 (PSD-95) and glutamate receptor interacting protein 1 (GRIP1). Pretreatment of cultured hippocampal neurons with FSC231 inhibited coimmunopreciptation of the AMPA receptor GluR2 subunit with PICK1. In agreement with inhibiting the role of PICK1 in GluR2 trafficking, FSC231 accelerated recycling of pHluorin-tagged GluR2 in hippocampal neurons after internalization in response to NMDA receptor activation. FSC231 blocked the expression of both long-term depression and long-term potentiation in hippocampal CA1 neurons from acute slices, consistent with inhibition of the bidirectional function of PICK1 in synaptic plasticity. Given the proposed role of the PICK1/AMPA receptor interaction in neuropathic pain, excitotoxicity, and cocaine addiction, FSC231 might serve as a lead in the future development of new therapeutics against these conditions.
Homeostatic imbalance of regulatory and effector T cells due to IL-2 deprivation amplifies murine lupus
Authors: Humrich Jens Y. , Morbach Henner , Undeutsch Reinmar , Enghard Philipp , Rosenberger Stefan , Weigert Olivia , Kloke Lutz , Heimann Juliane , Gaber Timo , Brandenburg Susan , Scheffold Alexander , Huehn Jochen , Radbruch Andreas , Burmester Gerd-Rüdiger , Riemekasten Gabriela
Published: December 2009

The origins and consequences of a regulatory T cell (Treg) disorder in systemic lupus erythematosus (SLE) are poorly understood. In the (NZBxNZW) F1mouse model of lupus, we found that CD4+Foxp3+Treg failed to maintain a competitive pool size in the peripheral lymphoid organs resulting in a progressive homeostatic imbalance of CD4+Foxp3+Treg and CD4+Foxp3−conventional T cells (Tcon). In addition, Treg acquired phenotypic changes that are reminiscent of IL-2 deficiency concomitantly to a progressive decline in IL-2-producing Tcon and an increase in activated, IFN-γ-producing effector Tcon. Nonetheless, Treg from lupus-prone mice were functionally intact and capable to influence the course of disease. Systemic reduction of IL-2 levels early in disease promoted Tcon hyperactivity, induced the imbalance of Treg and effector Tcon, and strongly accelerated disease progression. In contrast, administration of IL-2 partially restored the balance of Treg and effector Tcon by promoting the homeostatic proliferation of endogenous Treg and impeded the progression of established disease. Thus, an acquired and self-amplifying disruption of the Treg-IL-2 axis contributed essentially to Tcon hyperactivity and the development of murine lupus. The reversibility of this homeostatic Treg disorder provides promising approaches for the treatment of SLE.
Evidence disputing deforestation as the cause for the collapse of the ancient Maya polity of Copan, Honduras
Authors: McNeil Cameron L. , Burney David A. , Burney Lida Pigott
Published: December 2009

Archaeologists have proposed diverse hypotheses to explain the collapse of the southern Maya lowland cities between the 8th and 10th centuries A.D. Although it generally is believed that no single factor was responsible, a commonly accepted cause is environmental degradation as a product of large-scale deforestation. To date, the most compelling scientific evidence used to support this hypothesis comes from the archaeological site of Copan, Honduras, where the analysis of a sediment core suggested a dramatic increase in forest clearance in the Late Classic period (A.D. 600–900). By contrast, in the work presented here, the authors’ analysis of a longer sediment core demonstrates that forest cover increased from A.D. 400 to A.D. 900, with arboreal pollen accounting for 59.8–71.0% of the pollen assemblage by approximately A.D. 780–980. The highest levels of deforestation are found about 900 B.C. when, at its peak, herb pollen made up 89.8% of the assemblage. A second, although less pronounced, period of elevated deforestation peaked at approximately A.D. 400 when herb pollen reached 65.3% of the assemblage. The first deforestation event likely coincided with the widespread adoption of agriculture, a pattern found elsewhere in Mesoamerica. The second period of forest clearance probably was associated with the incursion of Maya speakers into the Copan Valley and their subsequent construction of the earliest levels of the Copan Acropolis. These results refute the former hypothesis that the ancient Maya responded to their increasingly large urban population by exhausting, rather than conserving, natural resources.
The N-terminus of histone H3 is required for de novo DNA methylation in chromatin
Authors: Hu Jia-Lei , Zhou Bo O. , Zhang Run-Rui , Zhang Kang-Ling , Zhou Jin-Qiu , Xu Guo-Liang
Published: December 2009

DNA methylation and histone modification are two major epigenetic pathways that interplay to regulate transcriptional activity and other genome functions. Dnmt3L is a regulatory factor for the de novo DNA methyltransferases Dnmt3a and Dnmt3b. Although recent biochemical studies have revealed that Dnmt3L binds to the tail of histone H3 with unmethylated lysine 4 in vitro, the requirement of chromatin components for DNA methylation has not been examined, and functional evidence for the connection of histone tails to DNA methylation is still lacking. Here, we used the budding yeast
Saccharomyces cerevisiae
as a model system to investigate the chromatin determinants of DNA methylation through ectopic expression of murine Dnmt3a and Dnmt3L. We found that the N terminus of histone H3 tail is required for de novo methylation, while the central part encompassing lysines 9 and 27, as well as the H4 tail are dispensable. DNA methylation occurs predominantly in heterochromatin regions lacking H3K4 methylation. In mutant strains depleted of H3K4 methylation, the DNA methylation level increased 5-fold. The methylation activity of Dnmt3a largely depends on the Dnmt3L's PHD domain recognizing the histone H3 tail with unmethylated lysine 4. Functional analysis of Dnmt3L in mouse ES cells confirmed that the chromatin-recognition ability of Dnmt3L's PHD domain is indeed required for efficient methylation at the promoter of the endogenous
Dnmt3L
gene. These findings establish the N terminus of histone H3 tail with an unmethylated lysine 4 as a chromatin determinant for DNA methylation.
Somatic tetraploidy in specific chick retinal ganglion cells induced by nerve growth factor
Authors: Morillo Sandra M. , Escoll Pedro , de la Hera Antonio , Frade José M.
Published: December 2009

A subset of neurons in the normal vertebrate nervous system contains double the normal amount of DNA in their nuclei. These neurons are all thought to derive from aberrant mitoses in neuronal precursor cells. Here we show that endogenous NGF induces DNA replication in a subpopulation of differentiating chick retinal ganglion cells that express both the neurotrophin receptor p75 and the E2F1 transcription factor, but that lack the retinoblastoma protein. Many of these neurons avoid G2/M transition and remain alive in the retina as tetraploid cells with large cell somas and extensive dendritic trees, and most of them express β2 nicotinic acetylcholine receptor subunits, a specific marker of retinal ganglion cells innervating lamina F in the stratum-griseum-et-fibrosum-superficiale of the tectal cortex. Tetraploid neurons were also observed in the adult mouse retina. Thus, a developmental program leading to somatic tetraploidy in specific retinal neurons exists in vertebrates. This program might occur in other vertebrate neurons during normal or pathological situations.
Gene amplification confers glyphosate resistance in
Amaranthus palmeri
Authors: Gaines Todd A. , Zhang Wenli , Wang Dafu , Bukun Bekir , Chisholm Stephen T. , Shaner Dale L. , Nissen Scott J. , Patzoldt William L. , Tranel Patrick J. , Culpepper A. Stanley , Grey Timothy L. , Webster Theodore M. , Vencill William K. , Sammons R. Douglas , Jiang Jiming , Preston Christopher , Leach Jan E. , Westra Philip
Published: December 2009

The herbicide glyphosate became widely used in the United States and other parts of the world after the commercialization of glyphosate-resistant crops. These crops have constitutive overexpression of a glyphosate-insensitive form of the herbicide target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (
EPSPS
). Increased use of glyphosate over multiple years imposes selective genetic pressure on weed populations. We investigated recently discovered glyphosate-resistant
Amaranthus palmeri
populations from Georgia, in comparison with normally sensitive populations. EPSPS enzyme activity from resistant and susceptible plants was equally inhibited by glyphosate, which led us to use quantitative PCR to measure relative copy numbers of the
EPSPS
gene. Genomes of resistant plants contained from 5-fold to more than 160-fold more copies of the
EPSPS
gene than did genomes of susceptible plants. Quantitative RT-PCR on cDNA revealed that
EPSPS
expression was positively correlated with genomic
EPSPS
relative copy number. Immunoblot analyses showed that increased EPSPS protein level also correlated with
EPSPS
genomic copy number.
EPSPS
gene amplification was heritable, correlated with resistance in pseudo-F
2
populations, and is proposed to be the molecular basis of glyphosate resistance. FISH revealed that
EPSPS
genes were present on every chromosome and, therefore, gene amplification was likely not caused by unequal chromosome crossing over. This occurrence of gene amplification as an herbicide resistance mechanism in a naturally occurring weed population is particularly significant because it could threaten the sustainable use of glyphosate-resistant crop technology.
Epigenetic inactivation of the Sotos overgrowth syndrome gene histone methyltransferase NSD1 in human neuroblastoma and glioma
Authors: Berdasco María , Ropero Santiago , Setien Fernando , Fraga Mario F. , Lapunzina Pablo , Losson Régine , Alaminos Miguel , Cheung Nai-Kong , Rahman Nazneen , Esteller Manel
Published: December 2009

Sotos syndrome is an autosomal dominant condition characterized by overgrowth resulting in tall stature and macrocephaly, together with an increased risk of tumorigenesis. The disease is caused by loss-of-function mutations and deletions of the nuclear receptor SET domain containing protein-1 (NSD1) gene, which encodes a histone methyltransferase involved in chromatin regulation. However, despite its causal role in Sotos syndrome and the typical accelerated growth of these patients, little is known about the putative contribution of NSD1 to human sporadic malignancies. Here, we report that NSD1 function is abrogated in human neuroblastoma and glioma cells by transcriptional silencing associated with CpG island-promoter hypermethylation. We also demonstrate that the epigenetic inactivation of NSD1 in transformed cells leads to the specifically diminished methylation of the histone lysine residues H4-K20 and H3-K36. The described phenotype is also observed in Sotos syndrome patients with NSD1 genetic disruption. Expression microarray data from NSD1-depleted cells, followed by ChIP analysis, revealed that the oncogene MEIS1 is one of the main NSD1 targets in neuroblastoma. Furthermore, we show that the restoration of NSD1 expression induces tumor suppressor-like features, such as reduced colony formation density and inhibition of cellular growth. Screening a large collection of different tumor types revealed that NSD1 CpG island hypermethylation was a common event in neuroblastomas and gliomas. Most importantly, NSD1 hypermethylation was a predictor of poor outcome in high-risk neuroblastoma. These findings highlight the importance of NSD1 epigenetic inactivation in neuroblastoma and glioma that leads to a disrupted histone methylation landscape and might have a translational value as a prognostic marker.
Multiscale mobility networks and the spatial spreading of infectious diseases
Authors: Balcan Duygu , Colizza Vittoria , Gonçalves Bruno , Hu Hao , Ramasco José J. , Vespignani Alessandro
Published: December 2009

Among the realistic ingredients to be considered in the computational modeling of infectious diseases, human mobility represents a crucial challenge both on the theoretical side and in view of the limited availability of empirical data. To study the interplay between short-scale commuting flows and long-range airline traffic in shaping the spatiotemporal pattern of a global epidemic we (
i
) analyze mobility data from 29 countries around the world and find a gravity model able to provide a global description of commuting patterns up to 300 kms and (
ii
) integrate in a worldwide-structured metapopulation epidemic model a timescale-separation technique for evaluating the force of infection due to multiscale mobility processes in the disease dynamics. Commuting flows are found, on average, to be one order of magnitude larger than airline flows. However, their introduction into the worldwide model shows that the large-scale pattern of the simulated epidemic exhibits only small variations with respect to the baseline case where only airline traffic is considered. The presence of short-range mobility increases, however, the synchronization of subpopulations in close proximity and affects the epidemic behavior at the periphery of the airline transportation infrastructure. The present approach outlines the possibility for the definition of layered computational approaches where different modeling assumptions and granularities can be used consistently in a unifying multiscale framework.
Electrokinesis is a microbial behavior that requires extracellular electron transport
Authors: Harris H. W. , El-Naggar M. Y. , Bretschger O. , Ward M. J. , Romine M. F. , Obraztsova A. Y. , Nealson K. H.
Published: December 2009

We report a previously undescribed bacterial behavior termed
electrokinesis
. This behavior was initially observed as a dramatic increase in cell swimming speed during reduction of solid MnO
2
particles by the dissimilatory metal-reducing bacterium
Shewanella oneidensis
MR-1. The same behavioral response was observed when cells were exposed to small positive applied potentials at the working electrode of a microelectrochemical cell and could be tuned by adjusting the potential on the working electrode. Electrokinesis was found to be different from both chemotaxis and galvanotaxis but was absent in mutants defective in electron transport to solid metal oxides. Using in situ video microscopy and cell tracking algorithms, we have quantified the response for different strains of
Shewanella
and shown that the response correlates with current-generating capacity in microbial fuel cells. The electrokinetic response was only exhibited by a subpopulation of cells closest to the MnO
2
particles or electrodes. In contrast, the addition of 1 mM 9,10-anthraquinone-2,6-disulfonic acid, a soluble electron shuttle, led to increases in motility in the entire population. Electrokinesis is defined as a behavioral response that requires functional extracellular electron transport and that is observed as an increase in cell swimming speeds and lengthened paths of motion that occur in the proximity of a redox active mineral surface or the working electrode of an electrochemical cell.
A feeling for the numbers in biology
Authors: Phillips Rob , Milo Ron
Published: December 2009

Although the quantitative description of biological systems has been going on for centuries, recent advances in the measurement of phenomena ranging from metabolism to gene expression to signal transduction have resulted in a new emphasis on biological numeracy. This article describes the confluence of two different approaches to biological numbers. First, an impressive array of quantitative measurements make it possible to develop intuition about biological numbers ranging from how many gigatons of atmospheric carbon are fixed every year in the process of photosynthesis to the number of membrane transporters needed to provide sugars to rapidly dividingEscherichia colicells. As a result of the vast array of such quantitative data, the BioNumbers web site has recently been developed as a repository for biology by the numbers. Second, a complementary and powerful tradition of numerical estimates familiar from the physical sciences and canonized in the so-called “Fermi problems” calls for efforts to estimate key biological quantities on the basis of a few foundational facts and simple ideas from physics and chemistry. In this article, we describe these two approaches and illustrate their synergism in several particularly appealing case studies. These case studies reveal the impact that an emphasis on numbers can have on important biological questions.
Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI)
Authors: Dertinger T. , Colyer R. , Iyer G. , Weiss S. , Enderlein J.
Published: December 2009

Super-resolution optical microscopy is a rapidly evolving area of fluorescence microscopy with a tremendous potential for impacting many fields of science. Several super-resolution methods have been developed over the last decade, all capable of overcoming the fundamental diffraction limit of light. We present here an approach for obtaining subdiffraction limit optical resolution in all three dimensions. This method relies on higher-order statistical analysis of temporal fluctuations (caused by fluorescence blinking/intermittency) recorded in a sequence of images (movie). We demonstrate a 5-fold improvement in spatial resolution by using a conventional wide-field microscope. This resolution enhancement is achieved in iterative discrete steps, which in turn allows the evaluation of images at different resolution levels. Even at the lowest level of resolution enhancement, our method features significant background reduction and thus contrast enhancement and is demonstrated on quantum dot-labeled microtubules of fibroblast cells.
Context-dependent interaction leads to emergent search behavior in social aggregates
Authors: Torney Colin , Neufeld Zoltan , Couzin Iain D.
Published: December 2009

Locating the source of an advected chemical signal is a common challenge facing many living organisms. When the advecting medium is characterized by either high Reynolds number or high Peclet number, the task becomes highly nontrivial due to the generation of heterogeneous, dynamically changing filamental concentrations that do not decrease monotonically with distance to the source. Defining search strategies that are effective in these environments has important implications for the understanding of animal behavior and for the design of biologically inspired technology. Here we present a strategy that is able to solve this task without the higher intelligence required to assess spatial gradient direction, measure the diffusive properties of the flow field, or perform complex calculations. Instead, our method is based on the collective behavior of autonomous individuals following simple social interaction rules which are modified according to the local conditions they are experiencing. Through these context-dependent interactions, the group is able to locate the source of a chemical signal and in doing so displays an awareness of the environment not present at the individual level. This behavior illustrates an alternative pathway to the evolution of higher cognitive capacity via the emergent, group-level intelligence that can result from local interactions.
Subnanometer atomic force microscopy of peptide–mineral interactions links clustering and competition to acceleration and catastrophe
Authors: Friddle R. W. , Weaver M. L. , Qiu S. R. , Wierzbicki A. , Casey W. H. , De Yoreo J. J.
Published: December 2009

In vitro observations have revealed major effects on the structure, growth, and composition of biomineral phases, including stabilization of amorphous precursors, acceleration and inhibition of kinetics, and alteration of impurity signatures. However, deciphering the mechanistic sources of these effects has been problematic due to a lack of tools to resolve molecular structures on mineral surfaces during growth. Here we report atomic force microscopy investigations using a system designed to maximize resolution while minimizing contact force. By imaging the growth of calcium-oxalate monohydrate under the influence of aspartic-rich peptides at single-molecule resolution, we reveal how the unique interactions of polypeptides with mineral surfaces lead to acceleration, inhibition, and switching of growth between two distinct states. Interaction with the positively charged face of calcium-oxalate monohydrate leads to formation of a peptide film, but the slow adsorption kinetics and gradual relaxation to a well-bound state result in time-dependent effects. These include a positive feedback between peptide adsorption and step inhibition described by a mathematical catastrophe that results in growth hysteresis, characterized by rapid switching from fast to near-zero growth rates for very small reductions in supersaturation. Interactions with the negatively charged face result in formation of peptide clusters that impede step advancement. The result is a competition between accelerated solute attachment and inhibition due to blocking of the steps by the clusters. The findings have implications for control of pathological mineralization and suggest artificial strategies for directing crystallization.