bluuebunny/crossref_metadata_2025 huggingface dataset:
Negative ion photoelectron spectroscopy of the copper-aspartic acid anion and its hydrated complexes
Authors: Li Xiang , Wang Haopeng , Bowen Kit H. , Martínez Ana , Salpin Jean-Yves , Schermann Jean-Pierre
Published: August 2010

Negative ions of copper-aspartic acid Cu(Asp)− and its hydrated complexes have been produced in the gas phase and studied by anion photoelectron spectroscopy. The vertical detachment energies (VDE) of Cu(Asp)− and Cu(Asp)−(H2O)1,2 were determined to be 1.6, 1.95, and 2.20 eV, respectively. The spectral profiles of Cu(Asp)−(H2O)1 and Cu(Asp)−(H2O)2 closely resembled that of Cu(Asp)−, indicating that hydration had not changed the structure of Cu(Asp)− significantly. The successive shifts to higher electron binding energies by the spectra of the hydrated species provided measures of their stepwise solvation energies. Density functional calculations were performed on anionic Cu(Asp)− and on its corresponding neutral. The agreement between the calculated and measured VDE values implied that the structure of the Cu(Asp)− complex originated with a zwitterionic form of aspartic acid in which a copper atom had inserted into the N–H bond.
Microbial population dynamics by digital in-line holographic microscopy
Authors: Frentz Zak , Kuehn Seppe , Hekstra Doeke , Leibler Stanislas
Published: August 2010

Measurements of population dynamics are ubiquitous in experiments with microorganisms. Studies with microbes elucidating adaptation, selection, and competition rely on measurements of changing populations in time. Despite this importance, quantitative methods for measuring population dynamics microscopically, with high time resolution, across many replicates remain limited. Here we present a new noninvasive method to precisely measure microbial spatiotemporal population dynamics based on digital in-line holographic (DIH) microscopy. Our inexpensive, replicate DIH microscopes imaged hundreds of swimming algae in three dimensions within a volume of several microliters on a time scale of minutes over periods of weeks.
Temperature-dependent photoconductivity in β-In2S3 single crystals
Authors: Ho C. H. , Wang Y. P. , Chan C. H. , Huang Y. S. , Li C. H.
Published: August 2010

The solar-energy absorption material β-In2S3 was characterized using temperature-dependent photoconductivity (PC) measurements in the temperature range between 30 and 340 K in this study, and thermoreflectance (TR) and photoluminescence (PL) measurements were carried out to identify near-band-edge transitions in the β-In2S3 tetragonal crystal. The experimental analyses of PL, PC, and TR confirmed that β-In2S3 is a direct semiconductor with a band gap of 2.073 eV at 30 K and 1.935 eV at 300 K. The PL and PC spectra manifest some defect-related features in the β-In2S3 single crystal. Two defect emissions and two band-edge luminescences were simultaneously detected in the PL spectrum at 30 K, and the temperature-dependent PC spectra of β-In2S3 from 160 to 300 K reveal an additional defectlike or band-to-band feature with an energy located above the conduction band edge (EC). The temperature dependences of the PC transition features in the β-In2S3 defect crystal were analyzed. The origin and mechanism of all defect states and band-edge transitions in the β-In2S3 single crystal are evaluated and discussed.
The effect of graphite surface condition on the composition of Al2O3 by atomic layer deposition
Authors: Pirkle A. , McDonnell S. , Lee B. , Kim J. , Colombo L. , Wallace R. M.
Published: August 2010

We present a study of the nucleation of atomic layer deposition of Al2O3 on highly oriented pyrolytic graphite (HOPG) using trimethlyaluminum (TMA) with ozone as the oxidant (TMA/O3). In situ x-ray photoelectron spectroscopy (XPS) is used to study TMA/O3 depositions on HOPG. We examine the dependence of TMA/O3 nucleation on deposition temperature and characterize the morphology and uniformity of deposited films by ex situ atomic force microscopy. The impact of several predeposition surface treatments of the graphite surface condition is discussed, particularly with regard to the presence of adsorbed atmospheric contamination.
Enhancement of the short circuit current in organic photovoltaic devices with microcavity structures
Authors: Lee Jane , Kim Sei-Yong , Kim Changsoon , Kim Jang-Joo
Published: August 2010

We demonstrate that the use of a microcavity structure can overcome the trade-off between exciton diffusion and optical absorption in planar heterojunction organic photovoltaic cells. Optical simulation based on the copper phthalocyanine (CuPc)-fullerene donor-acceptor system showed that the microcavity device with the spacer layer confines a large electric field inside the cavity so that high external quantum efficiency can be achieved even with a 10-nm-thick CuPc layer, which is comparable to the exciton diffusion length of the layer. The optimized microcavity device leads to an enhancement of the short circuit current of up to 51.6% compared with the conventional device.
Benefits of homoepitaxy on the properties of nonpolar (Zn,Mg)O/ZnO quantum wells on a-plane ZnO substrates
Authors: Chauveau J.-M. , Teisseire M. , Kim-Chauveau H. , Deparis C. , Morhain C. , Vinter B.
Published: August 2010

We report on the properties of nonpolar (Zn,Mg)O/ZnO quantum wells (QW) homoepitaxially grown by molecular beam epitaxy on a-plane ZnO substrates. We demonstrate a drastic improvement of the structural properties. We compare the photoluminescence properties of nonpolar homoepitaxial QWs and nonpolar heteroepitaxial QWs grown on sapphire and show that the reduction in structural defects and the improvement of surface morphology are correlated with a strong enhancement of the photoluminescence properties: reduction in full width at half maximum, strong increase in the luminescence intensities and their thermal stability. The comparison convincingly demonstrates the interest of homoepitaxial nonpolar QWs for bright UV emission applications.
Passive self-tuning energy harvester for extracting energy from rotational motion
Authors: Gu Lei , Livermore Carol
Published: August 2010

This paper presents experiments and models of a passive self-tuning energy harvester for rotational vibration applications. Tensile stress due to centrifugal force in a radially oriented piezoelectric cantilever beam passively tunes the resonant frequency so that the harvester remains at or near its resonant frequency. Because centrifugal force is proportional to the square of driving frequency, the resonant frequency of an optimized harvester can track and match the driving frequency over a wide frequency range. An analytical model is presented to explain the harvester’s operation, advantages, and design parameter selection. A prototype demonstrated significantly improved performance compared with an untuned harvester.
Enhanced efficiency and reduced roll-off in nondoped phosphorescent organic light-emitting devices with triplet multiple quantum well structures
Authors: Liu Shumei , Li Bin , Zhang Liming , Song Hang , Jiang Hong
Published: August 2010

Highly efficient nondoped phosphorescent organic light-emitting devices (NPOLEDs) with triplet multiple quantum well structures are fabricated by using 4,4′-N,N′-dicarbazole-biphenyl and an iridium(III) complex as the potential barrier layer and the potential well layer/light-emitting layer, respectively. Remarkably, such NPOLED with an optimized device configuration achieves reduced current efficiency roll-off, which slightly decreases from its peak value of 31.5 cd/A at 19.8 mA/cm2 to 29.2 cd/A at 100 mA/cm2. We attribute this improvement to the efficient triplet exciton confinement effect and the suppression of triplet-triplet annihilation which occurs via single-step long range (Förster-type) energy transfer between excited molecules.
Woody species of a semi-arid community are only moderately resistant to cavitation
Authors: Miranda Juan de Dios , Padilla Francisco M. , Martínez-Vilalta Jordi , Pugnaire Francisco I.
Published: August 2010

Vulnerability to drought-induced cavitation and seasonal water relations of six shrub species with different functional traits (deep v. superficial roots; evergreen v. summer deciduous; leaves v. cladodes) were measured in a semi-arid plant community strongly limited by water availability. The underlying hypotheses were that species would differ in their hydraulic properties and resistance to drought, reflecting different adaptations to a common environment and that individual adaptations may involve tradeoffs that would cause hydraulic properties to co-vary. Species experiencing the lowest minimum leaf water potentials generally had lower stomatal conductance, but they were not more resistant to xylem embolism than species with higher leaf water potentials and stomatal conductance. Overall, the studied species were more vulnerable to xylem embolism than expected and experienced high rates of native embolism and percent of leafless branches during summer drought. However, recovery rates from leafless branches were also high. Xylem resistance to embolism varied between species but had no relationship with minimum leaf water potential, suggesting that (i) adaptation to arid environments does not necessarily imply high resistance to embolism; and (ii) the costs associated with embolism resistance can be compensated by other components of the hydraulic strategy of a given species.
Carbon and nitrogen balance in beech roots under competitive pressure of soil-borne microorganisms induced by girdling, drought and glucose application
Authors: Winkler Jana B. , Dannenmann Michael , Simon Judy , Pena Rodica , Offermann Christine , Sternad Wolfgang , Clemenz Christian , Naumann Pascale S. , Gasche Rainer , Kögel-Knabner Ingrid , Gessler Arthur , Rennenberg Heinz , Polle Andrea
Published: August 2010

The goal of this work was to increase the understanding of factors regulating nitrogen (N) competition between roots and soil microbes. For this purpose, root assimilate supply was diminished or abolished in beech (Fagus sylvatica L.) seedlings by girdling, drought stress or a combination of both factors. This was revealed by 13C tracer abundance in root tips after 13CO2 pulse labelling of the shoots. Analysis of different root tip fractions revealed that only 6% were ectomycorrhizal. Carbon (C) allocation to ectomycorrhizal and vital non-mycorrhizal root tips was ~26% higher than to distorted root tips. Drought resulted in ~30% increased ammonium (NH4+) and amino acid concentrations in roots and ~65% increased soil NH4+ concentrations, probably because of lower consumption of NH4+ by free-living microorganisms. Root uptake of glutamine of 13 nmol g–1 fresh mass h–1 decreased 2-fold with drought, although the number of vital root tips did not decrease. Carbon content in biomass of free-living microbes increased with glucose application regardless of drought, resulting in significant depletion in soil nitrate (NO3–), root NH4+ and amino acid concentrations. Our results suggest that the root–soil system of young beech trees was C-limited, and this prevented amino acid metabolism in roots and microbial NO3– consumption in the soil, thereby exerting feedback inhibition on uptake of inorganic N by roots. We suggest that rhizodeposition is a key link in regulating the plant–microbial N balance.
High-temperature tolerance of a tropical tree, Ficus insipida: methodological reassessment and climate change considerations
Authors: Krause G. Heinrich , Winter Klaus , Krause Barbara , Jahns Peter , García Milton , Aranda Jorge , Virgo Aurelio
Published: August 2010

In view of anthropogenic global warming, heat tolerance of a neotropical pioneer tree, Ficus insipida Willd., was determined. Sections of sun leaves from a mature tree and from seedlings cultivated at ambient and elevated temperatures were heated to 42–53°C. Leaves from a late-successional tree species, Virola sebifera Aubl., were also studied. Widely used chlorophyll a fluorescence methods based on heat-induced rise of initial fluorescence emission, Fo, and decrease in the ratio of variable to maximum fluorescence, Fv/Fm, were reassessed. Fv/Fm determined 24 h after heat treatment was the fluorescence parameter most suitable to assess the lethal temperature causing permanent tissue damage. Thermo-tolerance was underestimated when Fo and Fv/Fm were recorded immediately after the heat treatment. The limit of thermo-tolerance was between 50 and 53°C, only a few °C above peak leaf temperatures measured in situ. The absence of seasonal changes in thermo-tolerance and only marginal increases in thermo-tolerance of plants grown under elevated temperatures suggest little capacity for further heat acclimation. Heat-stress experiments with intact potted seedlings also revealed irreversible leaf damage at 51–53°C, but plants survived and developed new leaves during post-culture.
Transient and permanent changes of xylem sap exudation by root systems of Zea mays after application of hydrostatic and osmotic forces
Authors: Fritz Michael , Lorenzen Stephan , Popova Maria , Ehwald Rudolf
Published: August 2010

Effects of relatively small changes of hydrostatic and osmotic pressure on root exudation were studied with maize (Zea mays L.) plants grown in hydroculture to estimate the root reflection coefficient for the applied osmolyte (PEG 600). During the first seconds after a change in hydrostatic pressure, the exudation rate measured with a microflow sensor was instantaneously and strongly changed due to elastic deformation of the metaxylem vessels in the branched part of the main root axis. In osmotic experiments, a time of 10–20 s was required before the maximum change of the exudation rate was recorded. This retardation can be explained by diffusive saturation of the non-agitated root surface film and radial turgor propagation. A new standing osmotic gradient was reached within 4 min after a change of the water potential difference (osmotic, hydrostatic). The steady-state exudation rate J was altered by osmotic and hydrostatic forces with nearly equal efficiencies when branch roots were not injured. Hence, the reflection coefficient of the intact root for PEG 600 was close to unity. The results are in accord with nearly ideal reverse osmosis at high rates of water uptake by roots and confirm the absence of a significant hydraulic bypath circumventing the protoplasts.
The evolution of abscisic acid (ABA) and ABA function in lower plants, fungi and lichen
Authors: Hartung Wolfram
Published: August 2010

Abscisic acid (ABA) – the universal stress hormone of cormophytes – was detected in very low concentrations in almost all organisms tested from a range of cyanobacteria, algae, bryophytes, fungi and lichens and higher plants (Fig. 1). There are a few reports only on stress-induced ABA biosynthesis in cyanobacteria and algae. This extra ABA is released to the external medium. Application of external ABA has been shown to produce weak and contradicting effects on development and metabolism of algae. In most studies, extremely high concentrations of external ABA have been applied, those being far beyond any physiological concentration range. It is, therefore, extremely difficult to discuss those data satisfactorily. When organisms start to colonise terrestrial habitats (e.g. aquatic liverworts, mosses), endogenous ABA is increased even under mild drought stress, then desiccation protecting mechanisms are stimulated and the formation of terrestrial organs is induced. The same can be observed in water ferns (Marsilea) and in a range of heterophyllous angiosperms. Sporophytes of hornwort and mosses that bear true stomata, have particularly high ABA levels and their stomata respond to ABA as is the case in cormophytes, although a significant regulatory function of these stomata does not exist. Fungi produce large amounts of ABA that are released into the external medium and do not seem to have a function for the fungus. Fungal ABA, however, may be significant in associations of fungi with cyanophytes and algae (lichens), in mycorrhizal associations and in the rhizosphere of higher plants.
Primary nerve (vein) density influences spatial heterogeneity of photosynthetic response to drought in two Acacia species
Authors: Sommerville Katy E. , Gimeno Teresa E. , Ball Marilyn C.
Published: August 2010

We examined the relationship between variation in phyllode nerve density and the spatio-temporal response of the photosynthetic apparatus to water-stress in two Acacia s.str. species with contrasting nerve patterns: Acacia floribunda (Vent.) Willd and Acacia pycnantha Benth. A. floribunda had greater primary nerve density than A. pycnantha and also showed greater spatial homogeneity in photosynthetic function with drought than phyllodes of A. pycnantha. A. pycnantha had lower maximum quantum efficiency of PSII in phyllode tissue further from primary nerves consistent with its lower primary nerve density. Further, A. floribunda phyllodes maintained function of the photosynthetic apparatus with drought for longer and recovered more swiftly from drought than A. pycnantha. These findings suggest that greater primary nerve density may enhance drought tolerance and are consistent with the observed predominance of acacias with high primary nerve density in areas with lower precipitation.
FGF receptor-4 (FGFR4) polymorphism acts as an activity switch of a membrane type 1 matrix metalloproteinase–FGFR4 complex
Authors: Sugiyama Nami , Varjosalo Markku , Meller Pipsa , Lohi Jouko , Chan Kui Ming , Zhou Zhongjun , Alitalo Kari , Taipale Jussi , Keski-Oja Jorma , Lehti Kaisa
Published: August 2010

Tumor cells use membrane type 1 matrix metalloproteinase (MT1-MMP) for invasion and metastasis. However, the signaling mechanisms that underlie MT1-MMP regulation in cancer have remained unclear. Using a systematic gain-of-function kinome screen for MT1-MMP activity, we have here identified kinases that significantly enhance MT1-MMP activity in tumor cells. In particular, we discovered an MT1-MMP/FGF receptor-4 (FGFR4) membrane complex that either stimulates or suppresses MT1-MMP and FGFR4 activities, depending on a tumor progression-associated polymorphism in FGFR4. The FGFR4-R388 allele, linked to poor cancer prognosis, increased collagen invasion by decreasing lysosomal MT1-MMP degradation. FGFR4-R388 induced MT1-MMP phosphorylation and endosomal stabilization, and surprisingly, the increased MT1-MMP in return enhanced FGFR4-R388 autophosphorylation. A phosphorylation-defective MT1-MMP was stabilized on the cell surface, where it induced simultaneous FGFR4-R388 internalization and dissociation of cell–cell junctions. In contrast, the alternative FGFR4-G388 variant down-regulated MT1-MMP, and the overexpression of MT1-MMP and particularly its phosphorylation-defective mutant vice versa induced FGFR4-G388 degradation. These results provide a mechanistic basis for FGFR4-R388 function in cancer invasion.
Angiotensin-converting enzyme 2 attenuates atherosclerotic lesions by targeting vascular cells
Authors: Zhang Cheng , Zhao Yu Xia , Zhang Yue Hui , Zhu Li , Deng Bi Ping , Zhou Zhao Li , Li Shu Ying , Lu Xiao Ting , Song Li Li , Lei Xue Ming , Tang Wen Bo , Wang Nan , Pan Chun Ming , Song Huai Dong , Liu Chun Xi , Dong Bo , Zhang Yun , Cao Yihai
Published: August 2010

Angiotensin-converting enzyme 2 (ACE2) is a newly discovered homolog of ACE whose actions oppose those of angiotensin II (AngII). However, the underlying mechanisms by which ACE2 effectively suppresses early atherosclerotic lesions remain poorly understood. Here, we show, both in vitro and in vivo, that ACE2 inhibited the development of early atherosclerotic lesions by suppressing the growth of vascular smooth muscle cells (VSMCs) and improving endothelial function. In a relatively large cohort animal study (66 rabbits), aortic segments transfected by Ad-ACE2 showed significantly attenuated fatty streak formation, neointimal macrophage infiltration, and alleviation of impaired endothelial function. Segments also showed decreased expression of monocyte chemoattractant protein 1, lectin-like oxidized low-density lipoprotein receptor 1, and proliferating cell nuclear antigen, which led to the delayed onset of atherosclerotic lesions. At the cellular level, ACE2 significantly modulated AngII-induced growth and migration in human umbilical vein endothelial cells and VSMCs. The antiatherosclerotic effect of ACE2 involved down-regulation of the ERK-p38, JAK-STAT, and AngII-ROS-NF-κB signaling pathways and up-regulation of the PI3K-Akt pathway. These findings revealed the molecular mechanisms of the antiatherosclerotic activity of ACE2 and suggested that modulation of ACE2 could offer a therapeutic option for treating atherosclerosis.
Sex-specific association of X-linked Toll-like receptor 7 (TLR7) with male systemic lupus erythematosus
Authors: Shen Nan , Fu Qiong , Deng Yun , Qian Xiaoxia , Zhao Jian , Kaufman Kenneth M. , Wu Yee Ling , Yu C. Yung , Tang Yuanjia , Chen Ji-Yih , Yang Wanling , Wong Maida , Kawasaki Aya , Tsuchiya Naoyuki , Sumida Takayuki , Kawaguchi Yasushi , Howe Hwee Siew , Mok Mo Yin , Bang So-Young , Liu Fei-Lan , Chang Deh-Ming , Takasaki Yoshinari , Hashimoto Hiroshi , Harley John B. , Guthridge Joel M. , Grossman Jennifer M. , Cantor Rita M. , Song Yeong Wook , Bae Sang-Cheol , Chen Shunle , Hahn Bevra H. , Lau Yu Lung , Tsao Betty P.
Published: August 2010

Systemic lupus erythematosus (SLE) is a multisystem, autoimmune disease that predominantly affects women. Previous findings that duplicated Toll-like receptor 7 (
Tlr7
) promotes lupus-like disease in male BXSB mice prompted us to evaluate
TLR7
in human SLE. By using a candidate gene approach, we identified and replicated association of a
TLR7
3′UTR SNP, rs3853839 (G/C), with SLE in 9,274 Eastern Asians (
P
combined
= 6.5 × 10
−10
), with a stronger effect in male than female subjects [odds ratio, male vs. female = 2.33 (95% CI = 1.64–3.30) vs. 1.24 (95% CI = 1.14–1.34);
P
= 4.1 × 10
−4
]. G-allele carriers had increased
TLR7
transcripts and more pronounced IFN signature than C-allele carriers; heterozygotes had 2.7-fold higher transcripts of G-allele than C-allele. These data established a functional polymorphism in type I IFN pathway gene
TLR7
predisposing to SLE, especially in Chinese and Japanese male subjects.
Discriminating early stage Aβ42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study
Authors: Zhuang Wei , Sgourakis Nikolaos G. , Li Zhenyu , Garcia Angel E. , Mukamel Shaul
Published: August 2010

Elucidating the structural features of the Aβ monomer, the peptide constituent of amyloid fibrils found in Alzheimer’s disease, can enable a direct characterization of aggregation pathways. Recent studies support the view that the ensemble of Aβ42 monomers is a mixture of diverse ordered and disordered conformational species, which can be classified according to the formation of a characteristic β-hairpin conformation in a certain region. Despite the disparity in the structural features of these species, commonly used spectroscopic techniques such as NMR may not directly trace the conformational dynamics in the ensemble due to the limited time resolution and the lack of well-resolved spectral features for different comformers. Here we use molecular dynamics simulations combined with simulations of two-dimensional IR (2DIR) spectra to investigate the structure of these species, their interchange kinetics, and their spectral features. We show that while the discrimination efficiency of the ordinary, nonchiral 2DIR signal is limited due to its intrinsic dependence on common order parameters that are dominated by the generally unstructured part of the sequence, signals with carefully designed chirality-sensitive pulse configurations have the high resolution required for differentiating the various monomer structures. Our combined simulation studies indicate the power of the chirality-induced (CI) 2DIR technique in investigating early events in Aβ42 aggregation and open the possibility for their use as a novel experimental tool.
Distinct 3′UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF)
Authors: Lau Anthony G. , Irier Hasan A. , Gu Jiaping , Tian Donghua , Ku Li , Liu Guanglu , Xia Mingjing , Fritsch Brita , Zheng James Q. , Dingledine Raymond , Xu Baoji , Lu Bai , Feng Yue
Published: August 2010

Expression of the brain-derived neurotrophic factor (BDNF) is under tight regulation to accommodate its intricate roles in controlling brain function. Transcription of BDNF initiates from multiple promoters in response to distinct stimulation cues. However, regardless which promoter is used, all BDNF transcripts are processed at two alternative polyadenylation sites, generating two pools of mRNAs that carry either a long or a short 3′UTR, both encoding the same BDNF protein. Whether and how the two distinct 3′UTRs may differentially regulate BDNF translation in response to neuronal activity changes is an intriguing and challenging question. We report here that the long BDNF 3′UTR is a bona fidecis-acting translation suppressor at rest whereas the short 3′UTR mediates active translation to maintain basal levels of BDNF protein production. Upon neuronal activation, the long BDNF 3′UTR, but not the short 3′UTR, imparts rapid and robust activation of translation from a reporter. Importantly, the endogenous long 3′UTR BDNF mRNA specifically undergoes markedly enhanced polyribosome association in the hippocampus in response to pilocarpine induced-seizure before transcriptional up-regulation of BDNF. Furthermore, BDNF protein level is quickly increased in the hippocampus upon seizure-induced neuronal activation, accompanied by a robust activation of the tropomyosin-related receptor tyrosine kinase B. These observations reveal a mechanism for activity-dependent control of BDNF translation and tropomyosin-related receptor tyrosine kinase B signaling in brain neurons.
Noninvasive method for assessing the human circadian clock using hair follicle cells
Authors: Akashi Makoto , Soma Haruhiko , Yamamoto Takuro , Tsugitomi Asuka , Yamashita Shiko , Yamamoto Takuya , Nishida Eisuke , Yasuda Akio , Liao James K. , Node Koichi
Published: August 2010

A thorough understanding of the circadian clock requires qualitative evaluation of circadian clock gene expression. Thus far, no simple and effective method for detecting human clock gene expression has become available. This limitation has greatly hampered our understanding of human circadian rhythm. Here we report a convenient, reliable, and less invasive method for detecting human clock gene expression using biopsy samples of hair follicle cells from the head or chin. We show that the circadian phase of clock gene expression in hair follicle cells accurately reflects that of individual behavioral rhythms, demonstrating that this strategy is appropriate for evaluating the human peripheral circadian clock. Furthermore, using this method, we indicate that rotating shift workers suffer from a serious time lag between circadian gene expression rhythms and lifestyle. Qualitative evaluation of clock gene expression in hair follicle cells, therefore, may be an effective approach for studying the human circadian clock in the clinical setting.
Highly sensitive and selective odorant sensor using living cells expressing insect olfactory receptors
Authors: Misawa Nobuo , Mitsuno Hidefumi , Kanzaki Ryohei , Takeuchi Shoji
Published: August 2010

This paper describes a highly sensitive and selective chemical sensor using living cells (
Xenopus laevis
oocytes) within a portable fluidic device. We constructed an odorant sensor whose sensitivity is a few parts per billion in solution and can simultaneously distinguish different types of chemicals that have only a slight difference in double bond isomerism or functional group such as ─OH, ─CHO and ─C(═O)─. We developed a semiautomatic method to install cells to the fluidic device and achieved stable and reproducible odorant sensing. In addition, we found that the sensor worked for multiple-target chemicals and can be integrated with a robotic system without any noise reduction systems. Our developed sensor is compact and easy to replace in the system. We believe that the sensor can potentially be incorporated into a portable system for monitoring environmental and physical conditions.
Fine-tuning of neuronal architecture requires two profilin isoforms
Authors: Michaelsen Kristin , Murk Kai , Zagrebelsky Marta , Dreznjak Anita , Jockusch Brigitte M. , Rothkegel Martin , Korte Martin
Published: August 2010

Two profilin isoforms (PFN1 and PFN2a) are expressed in the mammalian brain. Although profilins are essential for regulating actin dynamics in general, the specific role of these isoforms in neurons has remained elusive. We show that knockdown of the neuron-specific PFN2a results in a significant reduction in dendrite complexity and spine numbers of hippocampal neurons. Overexpression of PFN1 in PFN2a-deficient neurons prevents the loss of spines but does not restore dendritic complexity. Furthermore, we show that profilins are involved in differentially regulating actin dynamics downstream of the pan-neurotrophin receptor (p75
NTR
), a receptor engaged in modulating neuronal morphology. Overexpression of PFN2a restores the morphological changes in dendrites caused by p75
NTR
overexpression, whereas PFN1 restores the normal spine density. Our data assign specific functions to the two PFN isoforms, possibly attributable to different affinities for potent effectors also involved in actin dynamics, and suggest that they are important for the signal-dependent fine-tuning of neuronal architecture.
Multidomain assembled states of Hck tyrosine kinase in solution
Authors: Yang Sichun , Blachowicz Lydia , Makowski Lee , Roux Benoît
Published: August 2010

An approach combining small-angle X-ray solution scattering (SAXS) data with coarse-grained (CG) simulations is developed to characterize the assembly states of Hck, a member of the Src-family kinases, under various conditions in solution. First, a basis set comprising a small number of assembly states is generated from extensive CG simulations. Second, a theoretical SAXS profile for each state in the basis set is computed by using the Fast-SAXS method. Finally, the relative population of the different assembly states is determined via a Bayesian-based Monte Carlo procedure seeking to optimize the theoretical scattering profiles against experimental SAXS data. The study establishes the concept of basis-set supported SAXS (BSS-SAXS) reconstruction combining computational and experimental techniques. Here, BSS-SAXS reconstruction is used to reveal the structural organization of Hck in solution and the different shifts in the equilibrium population of assembly states upon the binding of different signaling peptides.
Economic contract theory tests models of mutualism
Authors: Weyl E. Glen , Frederickson Megan E. , Yu Douglas W. , Pierce Naomi E.
Published: August 2010

Although mutualisms are common in all ecological communities and have played key roles in the diversification of life, our current understanding of the evolution of cooperation applies mostly to social behavior within a species. A central question is whether mutualisms persist because hosts have evolved costly punishment of cheaters. Here, we use the economic theory of employment contracts to formulate and distinguish between two mechanisms that have been proposed to prevent cheating in host–symbiont mutualisms, partner fidelity feedback (PFF) and host sanctions (HS). Under PFF, positive feedback between host fitness and symbiont fitness is sufficient to prevent cheating; in contrast, HS posits the necessity of costly punishment to maintain mutualism. A coevolutionary model of mutualism finds that HS are unlikely to evolve de novo,and published data on legume–rhizobia and yucca–moth mutualisms are consistent with PFF and not with HS. Thus, in systems considered to be textbook cases of HS, we find poor support for the theory that hosts have evolved to punish cheating symbionts; instead, we show that even horizontally transmitted mutualisms can be stabilized via PFF. PFF theory may place previously underappreciated constraints on the evolution of mutualism and explain why punishment is far from ubiquitous in nature.
Functional interactions between membrane-bound transporters and membranes
Authors: Öjemyr Linda Näsvik , Lee Hyun Ju , Gennis Robert B. , Brzezinski Peter
Published: August 2010

One key role of many cellular membranes is to hold a transmembrane electrochemical ion gradient that stores free energy, which is used, for example, to generate ATP or to drive transmembrane transport processes. In mitochondria and many bacteria, the gradient is maintained by proton-transport proteins that are part of the respiratory (electron-transport) chain. Even though our understanding of the structure and function of these proteins has increased significantly, very little is known about the specific role of functional protein-membrane and membrane-mediated protein-protein interactions. Here, we have investigated the effect of membrane incorporation on proton-transfer reactions within the membrane-bound proton pump cytochrome
c
oxidase. The results show that the membrane acts to accelerate proton transfer into the enzyme’s catalytic site and indicate that the intramolecular proton pathway is wired via specific amino acid residues to the two-dimensional space defined by the membrane surface. We conclude that the membrane not only acts as a passive barrier insulating the interior of the cell from the exterior solution, but also as a component of the energy-conversion machinery.
Hyper telomere recombination accelerates replicative senescence and may promote premature aging
Authors: Hagelstrom R. Tanner , Blagoev Krastan B. , Niedernhofer Laura J. , Goodwin Edwin H. , Bailey Susan M.
Published: August 2010

Werner syndrome and Bloom syndrome result from defects in the RecQ helicases Werner (WRN) and Bloom (BLM), respectively, and display premature aging phenotypes. Similarly, XFE progeroid syndrome results from defects in the ERCC1-XPF DNA repair endonuclease. To gain insight into the origin of cellular senescence and human aging, we analyzed the dependence of sister chromatid exchange (SCE) frequencies on location [i.e., genomic (G-SCE) vs. telomeric (T-SCE) DNA] in primary human fibroblasts deficient in WRN, BLM, or ERCC1-XPF. Consistent with our other studies, we found evidence of elevated T-SCE in telomerase-negative but not telomerase-positive backgrounds. In telomerase-negative WRN-deficient cells, T-SCE—but not G-SCE—frequencies were significantly increased compared with controls. In contrast, SCE frequencies were significantly elevated in BLM-deficient cells irrespective of genome location. In ERCC1-XPF-deficient cells, neither T- nor G-SCE frequencies differed from controls. A theoretical model was developed that allowed an in silico investigation into the cellular consequences of increased T-SCE frequency. The model predicts that in cells with increased T-SCE, the onset of replicative senescence is dramatically accelerated even though the average rate of telomere loss has not changed. Premature cellular senescence may act as a powerful tumor-suppressor mechanism in telomerase-deficient cells with mutations that cause T-SCE levels to rise. Furthermore, T-SCE-driven premature cellular senescence may be a factor contributing to accelerated aging in Werner and Bloom syndromes, but not XFE progeroid syndrome.
Assembly of Qβ viral RNA polymerase with host translational elongation factors EF-Tu and -Ts
Authors: Takeshita Daijiro , Tomita Kozo
Published: August 2010

Replication and transcription of viral RNA genomes rely on host-donated proteins. Qβ virus infects
Escherichia coli
and replicates and transcribes its own genomic RNA by Qβ replicase. Qβ replicase requires the virus-encoded RNA-dependent RNA polymerase (β-subunit), and the host-donated translational elongation factors EF-Tu and -Ts, as active core subunits for its RNA polymerization activity. Here, we present the crystal structure of the core Qβ replicase, comprising the β-subunit, EF-Tu and -Ts. The β-subunit has a right-handed structure, and the EF-Tu:Ts binary complex maintains the structure of the catalytic core crevasse of the β-subunit through hydrophobic interactions, between the finger and thumb domains of the β-subunit and domain-2 of EF-Tu and the coiled-coil motif of EF-Ts, respectively. These hydrophobic interactions are required for the expression and assembly of the Qβ replicase complex. Thus, EF-Tu and -Ts have chaperone-like functions in the maintenance of the structure of the active Qβ replicase. Modeling of the template RNA and the growing RNA in the catalytic site of the Qβ replicase structure also suggests that structural changes of the RNAs and EF-Tu:Ts should accompany processive RNA polymerization and that EF-Tu:Ts in the Qβ replicase could function to modulate the RNA folding and structure.
Imprinting self-assembled patterns of lines at a semiconductor surface, using heat, light, or electrons
Authors: Harikumar K. R. , McNab Iain R. , Polanyi John C. , Zabet-Khosousi Amir , Hofer Werner A.
Published: August 2010

The fabrication of nano devices at surfaces makes conflicting demands of mobility for self-assembly (SA) and immobility for permanence. The solution proposed in earlier work from this laboratory involved pattern formation in physisorbed molecules by SA, followed by localized reaction to chemically imprint the pattern substantially unchanged, a procedure we termed molecular-scale imprinting (MSI). Here, as proof of generality we extended this procedure, previously applied to imprinting circles on Si(111)-7 × 7, to SA lines of 1-chloropentane (CP) on Si(100)-2 × 1. The physisorbed lines consisted of pairs of CP that grew perpendicular to the Si dimer rows, as shown by scanning tunneling microscopy and ab initio theory. Chemical reaction of these lines with the surface was triggered in separate experiments by three different modes of energization: heat, electrons, or light. In all cases the CP molecules underwent MSI with a Si atom beneath so that the physisorbed lines of CP pairs were imprinted as chemisorbed lines of Cl pairs.
RETRACTED: Detection of MLV-related virus gene sequences in blood of patients with chronic fatigue syndrome and healthy blood donors
Authors: Lo Shyh-Ching , Pripuzova Natalia , Li Bingjie , Komaroff Anthony L. , Hung Guo-Chiuan , Wang Richard , Alter Harvey J.
Published: August 2010

Chronic fatigue syndrome (CFS) is a serious systemic illness of unknown cause. A recent study identified DNA from a xenotropic murine leukemia virus-related virus (XMRV) in peripheral blood mononuclear cells (PBMCs) from 68 of 101 patients (67%) by nested PCR, as compared with 8 of 218 (3.7%) healthy controls. However, four subsequent reports failed to detect any murine leukemia virus (MLV)-related virus gene sequences in blood of CFS patients. We examined 41 PBMC-derived DNA samples from 37 patients meeting accepted diagnostic criteria for CFS and found MLV-like virus
gag
gene sequences in 32 of 37 (86.5%) compared with only 3 of 44 (6.8%) healthy volunteer blood donors. No evidence of mouse DNA contamination was detected in the PCR assay system or the clinical samples. Seven of 8
gag
-positive patients tested again positive in a sample obtained nearly 15 y later. In contrast to the reported findings of near-genetic identity of all XMRVs, we identified a genetically diverse group of MLV-related viruses. The
gag
and
env
sequences from CFS patients were more closely related to those of polytropic mouse endogenous retroviruses than to those of XMRVs and were even less closely related to those of ecotropic MLVs. Further studies are needed to determine whether the same strong association with MLV-related viruses is found in other groups of patients with CFS, whether these viruses play a causative role in the development of CFS, and whether they represent a threat to the blood supply.
H-NS forms a superhelical protein scaffold for DNA condensation
Authors: Arold Stefan T. , Leonard Paul G. , Parkinson Gary N. , Ladbury John E.
Published: August 2010

The histone-like nucleoid structuring (H-NS) protein plays a fundamental role in DNA condensation and is a key regulator of enterobacterial gene expression in response to changes in osmolarity, pH, and temperature. The protein is capable of high-order self-association via interactions of its oligomerization domain. Using crystallography, we have solved the structure of this complete domain in an oligomerized state. The observed superhelical structure establishes a mechanism for the self-association of H-NS via both an N-terminal antiparallel coiled-coil and a second, hitherto unidentified, helix-turn-helix dimerization interface at the C-terminal end of the oligomerization domain. The helical scaffold suggests the formation of a H-NS:plectonemic DNA nucleoprotein complex that is capable of explaining published biophysical and functional data, and establishes a unifying structural basis for coordinating the DNA packaging and transcription repression functions of H-NS.
Superconductivity at ∼100 K in dense SiH
4
(H
2
)
2
predicted by first principles
Authors: Li Yinwei , Gao Guoying , Xie Yu , Ma Yanming , Cui Tian , Zou Guangtian
Published: August 2010

Motivated by the potential high-temperature superconductivity in hydrogen-rich materials, the high-pressure structures of SiH
4
(H
2
)
2
in the pressure range 50–300 GPa were extensively explored by using a genetic algorithm. An intriguing layered orthorhombic (
Ccca
) structure was revealed to be energetically stable above 248 GPa with the inclusion of zero-point energy. The
Ccca
structure is metallic and composed of hydrogen shared SiH
8
dodecahedra layers intercalated by orientationally ordered molecular H
2
. Application of the Allen-Dynes modified McMillan equation yields remarkably high superconducting temperatures of 98–107 K at 250 GPa, among the highest values reported so far for phonon-mediated superconductors. Analysis reveals a unique superconducting mechanism that the direct interactions between H
2
and SiH
4
molecules at high pressure play the major role in the high superconductivity, while the contribution from H
2
vibrons is minor.
12/15-lipoxygenase–derived lipid peroxides control receptor tyrosine kinase signaling through oxidation of protein tyrosine phosphatases
Authors: Conrad Marcus , Sandin Åsa , Förster Heidi , Seiler Alexander , Frijhoff Jeroen , Dagnell Markus , Bornkamm Georg W. , Rådmark Olof , van Huijsduijnen Rob Hooft , Aspenström Pontus , Böhmer Frank , Östman Arne
Published: August 2010

Protein tyrosine phosphatases (PTPs) are regulated through reversible oxidation of the active-site cysteine. Previous studies have implied soluble reactive oxygen species (ROS), like H
2
O
2
, as the mediators of PTP oxidation. The potential role(s) of peroxidized lipids in PTP oxidation have not been described. This study demonstrates that increases in cellular lipid peroxides, induced by disruption of glutathione peroxidase 4, induce cellular PTP oxidation and reduce the activity of PDGF receptor targeting PTPs. These effects were accompanied by site-selective increased PDGF β-receptor phosphorylation, sensitive to 12/15-lipoxygenase (12/15-LOX) inhibitors, and increased PDGF-induced cytoskeletal rearrangements. Importantly, the 12/15-LOX–derived 15-OOH-eicosatetraenoic acid lipid peroxide was much more effective than H
2
O
2
in induction of in vitro PTP oxidation. Our study thus establishes that lipid peroxides are previously unrecognized inducers of oxidation of PTPs. This identifies a pathway for control of receptor tyrosine kinase signaling, which might also be involved in the etiology of diseases associated with increased lipid peroxidation.
Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities
Authors: Chisholm Ryan A. , Pacala Stephen W.
Published: August 2010

A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function.
Characterization ofProchlorococcusclades from iron-depleted oceanic regions
Authors: Rusch Douglas B. , Martiny Adam C. , Dupont Christopher L. , Halpern Aaron L. , Venter J. Craig
Published: August 2010

Prochlorococcusdescribes a diverse and abundant genus of marine photosynthetic microbes. It is primarily found in oligotrophic waters across the globe and plays a crucial role in energy and nutrient cycling in the ocean ecosystem. The abundance, global distribution, and availability of isolates makeProchlorococcusa model system for understanding marine microbial diversity and biogeochemical cycling. Analysis of 73 metagenomic samples from the Global Ocean Sampling expedition acquired in the Atlantic, Pacific, and Indian Oceans revealed the presence of two uncharacterizedProchlorococcusclades. A phylogenetic analysis using six different genetic markers places the clades close to known lineages adapted to high-light environments. The two uncharacterized clades consistently cooccur and dominate the surface waters of high-temperature, macronutrient-replete, and low-iron regions of the Eastern Equatorial Pacific upwelling and the tropical Indian Ocean. They are genetically distinct from each other and other high-lightProchlorococcusisolates and likely define a previously unrecognized ecotype. Our detailed genomic analysis indicates that these clades comprise organisms that are adapted to iron-depleted environments by reducing their iron quota through the loss of several iron-containing proteins that likely function as electron sinks in the photosynthetic pathway in otherProchlorococcusclades from high-light environments. The presence and inferred physiology of these clades may explain whyProchlorococcuspopulations from iron-depleted regions do not respond to iron fertilization experiments and further expand our understanding of how phytoplankton adapt to variations in nutrient availability in the ocean.