bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly stable charge generation layers using caesium phosphate as n-dopants and inserting interlayers
Authors: Diez Carola , Reusch Thilo C. G. , Lang Erwin , Dobbertin Thomas , Brütting Wolfgang
Published: May 2012

Highly stable and efficient charge generation layers (CGLs) comprising caesium phosphate (Cs3PO4) doped 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (BCP) as n-type organic semiconductor and molybdenum trioxide (MoO3) doped N,N′-di-(naphthalen-1-yl)-N,N′-diphenyl-benzidine (α-NPD) as p-type organic semiconductor, respectively, are presented. By inserting narrow-gap organic copper-phthalocyanine (CuPc) and wide-gap insulating aluminum oxide (Al2O3) as interlayer (IL), we show that the long-term stability of the CGL can be improved. The variation of the CuPc IL thickness yields an optimum of 8 nm as a trade-off between minimal operating voltage and maximum voltage stability of the CGL. Luminance-current density-voltage characteristics and lifetime measurements of stacked green organic light emitting diodes (OLEDs) confirm the functionality and high voltage stability of the presented CGL. The luminous efficacy of the stacked OLED compared to the non-stacked reference device is nearly unchanged. However, the lifetime of the stacked device is enhanced by a factor of 3.5. Consistent with our experimental findings, we propose a model of the energy-level diagram of a fully doped CGL with IL based on a field-assisted tunneling mechanism.
Effect of precipitate-dislocation interactions on generation of nonlinear Lamb waves in creep-damaged metallic alloys
Authors: Xiang Yanxun , Deng Mingxi , Xuan Fu-Zhen , Liu Chang-Jun
Published: May 2012

An analytical model is presented for the effect of the interactions of dislocations with precipitate coherency strains on the generation of second-harmonic of Lamb waves in metallic alloys. The cumulative second-harmonic of Lamb wave propagation is shown to depend dominantly on the dislocation density, pinning dislocation length, internal stress due to the coherency strain, volume fraction of the precipitates, and the phase matching degree between the primary Lamb wave and the double frequency Lamb wave (DFLW). Experiments were carried out to introduce controlled levels of creep-induced damage to determine the nonlinear response of Lamb waves in titanium alloy Ti60 plates. A like mountain-shape change in the normalized acoustic nonlinearity of Lamb wave versus the creep loading time has been observed. Microscopic image analyses were performed to interpret the variation of the measured acoustic nonlinearity and to obtain the microstructure parameters of the Ti60 specimens with different creep damages. The analytical model was applied to these creep damaged Ti60 specimens, which revealed a good accordance with the measured results of the nonlinear Lamb waves. These results indicate that the acoustic nonlinearity of Lamb wave increases due to the rising of the precipitation volume fraction and the dislocation density in the early stage, and it decreases as a combined result of the reduction of the precipitation volume fraction and the dislocation density and the increasing mismatch of the phase velocity between the primary Lamb wave and the DFLW after a further creep loading.
Ultrafast optical response originating from carrier-transport processes in undoped GaAs/n-type GaAs epitaxial structures
Authors: Hasegawa Takayuki , Takagi Yoshihiro , Takeuchi Hideo , Yamada Hisashi , Hata Masahiko , Nakayama Masaaki
Published: May 2012

We have investigated ultrafast optical responses of undoped GaAs/n-type GaAs (i-GaAs/n-GaAs) epitaxial structures at room temperature using a reflection-type pump-probe technique. The built-in electric field in the i-GaAs layer is controlled by its thickness. It is found that the decay time of a photoexcitation-induced reflectivity change in a sub-picosecond range decreases with an increase in the built-in electric field strength. The observed optical response is related to the transport process of photogenerated carriers from the i-GaAs layer to the n-GaAs layer. The shortest response time about 60 fs demonstrates that the i-GaAs/n-GaAs structure is useful for ultrafast optical applications.
Dielectric relaxation and electrical conductivity in ferroelectric ceramic/polymer composites around the glass transition
Authors: Peláiz-Barranco A.
Published: May 2012

The electrical conductivity behavior of the [(Pb0.88Sm0.08)(Ti0.99Mn0.01)O3]/polyetherketoneketone ceramic/polymer composite is studied in a wide temperature and frequency ranges around the glass transition of the polymer phase (Tg). The universal relaxation law is applied to model the experimental response. The dc conductivity (σdc) and the hopping frequency (ωH) follow an Arrhenius dependence. The activation energy values for σdc are associated to oxygen migration. The contribution of the conductive processes to the dielectric relaxation is analyzed, considering the oxygen vacancies concentration in the ceramic phase. It is also considered the structural change around Tg and its influence on the dielectric relaxation.
Yielding and plastic slip in ZnO
Authors: Sung T. H. , Huang J. C. , Hsu J. H. , Jian S. R. , Nieh T. G.
Published: May 2012

The mechanical properties of ZnO were examined using nanoindentation and microcompression. The modulus, hardness, onset of yielding, and shear strength of the as-grown wafer measured by nanoindentation are 140, 7.1, 12, and 3.6 GPa. The onset of shearing (3.6 GPa) corresponds to the theoretical shear strength. Young’s modulus and yield strength measured from micropillar samples were 123 and 3 GPa. The primary slip plane forms an acute angle of 62° with respect to the basal planes, indicting it is pyramidal. Thermal annealing does not affect the residual stresses but can reduce the defect concentration, thus improves the ZnO luminescent properties.
Parity oscillations of Kondo temperature in a single molecule break junction
Authors: de Resende B. M. F. , Vernek E.
Published: May 2012

We study the Kondo temperature (TK) of a single molecule break junction. By employing a numerical renormalization group calculations we have found that TK depends dramatically upon the position of the molecule in the wire formed between the contacts. We show that TK exhibits strong oscillations when the parity of the left and/or right number of atomic sites (NL,NR) is changed. For a given set of parameters, the maximum value of TK occurs for (odd, odd) combination, while its minimum value is observed for (even, even). These oscillations are fully understood in terms of the effective hybridization function.
Fluorescence quenching near small metal nanoparticles
Authors: Pustovit V. N. , Shahbazyan T. V.
Published: May 2012

We develop a microscopic model for fluorescence of a molecule (or semiconductor quantum dot) near a small metal nanoparticle. When a molecule is situated close to metal surface, its fluorescence is quenched due to energy transfer to the metal. We perform quantum-mechanical calculations of energy transfer rates for nanometer-sized Au nanoparticles and find that nonlocal and quantum-size effects significantly enhance dissipation in metal as compared to those predicted by semiclassical electromagnetic models. However, the dependence of transfer rates on molecule's distance to metal nanoparticle surface, d, is significantly weaker than the d−4 behavior for flat metal surface with a sharp boundary predicted by previous calculations within random phase approximation.
Charge dynamics of a single donor coupled to a few-electron quantum dot in silicon
Authors: Mazzeo G. , Prati E. , Belli M. , Leti G. , Cocco S. , Fanciulli M. , Guagliardo F. , Ferrari G.
Published: May 2012

We report on the charge transfer dynamics between a silicon quantum dot and an individual phosphorous donor extracted from the current through the quantum dot as a probe for the donor ionization state. We employ a silicon n-metal-oxide-semiconductor field-effect transistor (MOSFET) with two side gates at a single metallization level to control both the device conductance and the donor charge. The elastic nature of the process is demonstrated by temperature and magnetic field independent tunneling times. The Fano factor approaches 1/2 revealing that the process is sub-poissonian.
Accurate calculation of field and carrier distributions in doped semiconductors
Authors: Yang Wenji , Tang Jianping , Yu Hongchun , Wang Yanguo
Published: May 2012

We use the numerical squeezing algorithm(NSA) combined with the shooting method to accurately calculate the built-in fields and carrier distributions in doped silicon films (SFs) in the micron and sub-micron thickness range and results are presented in graphical form for variety of doping profiles under different boundary conditions. As a complementary approach, we also present the methods and the results of the inverse problem (IVP) - finding out the doping profile in the SFs for given field distribution. The solution of the IVP provides us the approach to arbitrarily design field distribution in SFs - which is very important for low dimensional (LD) systems and device designing. Further more, the solution of the IVP is both direct and much easy for all the one-, two-, and three-dimensional semiconductor systems. With current efforts focused on the LD physics, knowing of the field and carrier distribution details in the LD systems will facilitate further researches on other aspects and hence the current work provides a platform for those researches.
Mechanisms of damage to corals exposed to sedimentation
Authors: Weber Miriam , de Beer Dirk , Lott Christian , Polerecky Lubos , Kohls Katharina , Abed Raeid M. M. , Ferdelman Timothy G. , Fabricius Katharina E.
Published: May 2012

We investigated the mechanisms leading to rapid death of corals when exposed to runoff and resuspended sediments, postulating that the killing was microbially mediated. Microsensor measurements were conducted in mesocosm experiments and in naturally accumulated sediment on corals. In organic-rich, but not in organic-poor sediment, pH and oxygen started to decrease as soon as the sediment accumulated on the coral. Organic-rich sediments caused tissue degradation within 1 d, whereas organic-poor sediments had no effect after 6 d. In the harmful organic-rich sediment, hydrogen sulfide concentrations were low initially but increased progressively because of the degradation of coral mucus and dead tissue. Dark incubations of corals showed that separate exposures to darkness, anoxia, and low pH did not cause mortality within 4 d. However, the combination of anoxia and low pH led to colony death within 24 h. When hydrogen sulfide was added after 12 h of anoxia and low pH, colonies died after an additional 3 h. We suggest that sedimentation kills corals through microbial processes triggered by the organic matter in the sediments, namely respiration and presumably fermentation and desulfurylation of products from tissue degradation. First, increased microbial respiration results in reduced O
2
and pH, initiating tissue degradation. Subsequently, the hydrogen sulfide formed by bacterial decomposition of coral tissue and mucus diffuses to the neighboring tissues, accelerating the spread of colony mortality. Our data suggest that the organic enrichment of coastal sediments is a key process in the degradation of coral reefs exposed to terrestrial runoff.
Weak electron–phonon coupling contributing to high thermoelectric performance in n-type PbSe
Authors: Wang Heng , Pei Yanzhong , LaLonde Aaron D. , Snyder G. Jeffrey
Published: May 2012

PbSe is a surprisingly good thermoelectric material due, in part, to its low thermal conductivity that had been overestimated in earlier measurements. The thermoelectric figure of merit,
zT
, can exceed 1 at high temperatures in both p-type and n-type PbSe, similar to that found in PbTe. While the p-type lead chalcogenides (PbSe and PbTe) benefit from the high valley degeneracy (12 or more at high temperature) of the valence band, the n-type versions are limited to a valley degeneracy of 4 in the conduction band. Yet the n-type lead chalcogenides achieve a
zT
nearly as high as the p-type lead chalcogenides. This effect can be attributed to the weaker electron–phonon coupling (lower deformation potential coefficient) in the conduction band as compared with that in the valence band, which leads to higher mobility of electrons compared to that of holes. This study of PbSe illustrates the importance of the deformation potential coefficient of the charge-carrying band as one of several key parameters to consider for band structure engineering and the search for high performance thermoelectric materials.
Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1
Authors: Wu Hong , Moshkina Natasha , Min Jinrong , Zeng Hong , Joshua Jennifer , Zhou Ming-Ming , Plotnikov Alexander N.
Published: May 2012

Histone acetyltransferase 1 is the founding member of the histone acetyltransferase superfamily and catalyzes lysine acetylation of newly synthesized histone H4. Here we report a 1.9-Å resolution crystal structure of human histone acetyltransferase 1 in complex with acetyl coenzyme A and histone H4 peptide. The crystal structure reveals that the cofactor and the side chain of lysine 12 of histone H4 peptide are placed in the canyon between the central and C-terminal domains. Histone H4 peptide adopts a well-defined conformation and establishes an extensive set of interactions with the enzyme including invariant residues Glu64 and Trp199, which together govern substrate-binding specificity of histone acetyltransferase 1. Our structure-guided enzyme kinetic study further demonstrates a cumulative effect of the active-site residues Glu187, Glu276, and Asp277 on deprotonation of the ɛ-amino group of reactive Lys12 for direct attack of the acetyl group of the cofactor.
K-RAS GTPase- and B-RAF kinase–mediated T-cell tolerance defects in rheumatoid arthritis
Authors: Singh Karnail , Deshpande Pratima , Li Guangjin , Yu Mingcan , Pryshchep Sergey , Cavanagh Mary , Weyand Cornelia M. , Goronzy Jörg J.
Published: May 2012

Autoantibodies to common autoantigens and neoantigens, such as IgG Fc and citrullinated peptides, are immunological hallmarks of rheumatoid arthritis (RA). We examined whether a failure in maintaining tolerance is mediated by defects in T-cell receptor activation threshold settings. RA T cells responded to stimulation with significantly higher ERK phosphorylation (
P
< 0.001). Gene expression arrays of ERK pathway members suggested a higher expression of
KRAS
and
BRAF
, which was confirmed by quantitative PCR (
P
= 0.003), Western blot, and flow cytometry (
P
< 0.01). Partial silencing of
KRAS
and
BRAF
lowered activation-induced phosphorylated ERK levels (
P
< 0.01). In individual cells, levels of these signaling molecules correlated with ERK phosphorylation, attesting that their concentrations are functionally important. In confocal studies, B-RAF/K-RAS clustering was increased in RA T cells 2 min after T-cell receptor stimulation (
P
< 0.001). Overexpression of B-RAF and K-RAS in normal CD4 T cells amplified polyclonal T-cell proliferation and facilitated responses to citrullinated peptides. We propose that increased expression of B-RAF and K-RAS lowers T-cell activation thresholds in RA T cells, enabling responses to autoantigens.
Theoretical study of catalytic mechanism for single-site water oxidation process
Authors: Lin Xiangsong , Hu Xiangqian , Concepcion Javier J. , Chen Zuofeng , Liu Shubin , Meyer Thomas J. , Yang Weitao
Published: May 2012

Water oxidation is a linchpin in solar fuels formation, and catalysis by single-site ruthenium complexes has generated significant interest in this area. Combining several theoretical tools, we have studied the entire catalytic cycle of water oxidation for a single-site catalyst starting with [Ru
II
(tpy)(bpm)(OH
2
)]
2+
(i.e., [Ru
II
-OH
2
]
2+
; tpy is 2,2
′
∶6
′
,2
′′
-terpyridine and bpm is 2,2′-bypyrimidine) as a representative example of a new class of single-site catalysts. The redox potentials and p
K
a
calculations for the first two proton-coupled electron transfers (PCETs) from [Ru
II
-OH
2
]
2+
to [Ru
IV
 = O]
2+
and the following electron-transfer process to [Ru
V
 = O]
3+
suggest that these processes can proceed readily in acidic or weakly basic conditions. The subsequent water splitting process involves two water molecules, [Ru
V
 = O]
3+
to generate [Ru
III
-OOH]
2+
, and H
3
O
+
with a low activation barrier (∼10 kcal/mol). After the key O---O bond forming step in the single-site Ru catalysis, another PECT process oxidizes [Ru
III
-OOH]
2+
to [Ru
IV
-OO]
2+
when the pH is lower than 3.7. Two possible forms of [Ru
IV
-OO]
2+
, open and closed, can exist and interconvert with a low activation barrier (< 7 kcal/mol) due to strong spin-orbital coupling effects. In Pathway 1 at pH = 1.0, oxygen release is rate-limiting with an activation barrier ∼12 kcal/mol while the electron-transfer step from [Ru
IV
-OO]
2+
to [Ru
V
 - OO]
3+
becomes rate-determining at pH = 0 (Pathway 2) with Ce(IV) as oxidant. The results of these theoretical studies with atomistic details have revealed subtle details of reaction mechanisms at several stages during the catalytic cycle. This understanding is helpful in the design of new catalysts for water oxidation.
Direct chemical evidence for eumelanin pigment from the Jurassic period
Authors: Glass Keely , Ito Shosuke , Wilby Philip R. , Sota Takayuki , Nakamura Atsushi , Bowers C. Russell , Vinther Jakob , Dutta Suryendu , Summons Roger , Briggs Derek E. G. , Wakamatsu Kazumasa , Simon John D.
Published: May 2012

Melanin is a ubiquitous biological pigment found in bacteria, fungi, plants, and animals. It has a diverse range of ecological and biochemical functions, including display, evasion, photoprotection, detoxification, and metal scavenging. To date, evidence of melanin in fossil organisms has relied entirely on indirect morphological and chemical analyses. Here, we apply direct chemical techniques to categorically demonstrate the preservation of eumelanin in two > 160 Ma Jurassic cephalopod ink sacs and to confirm its chemical similarity to the ink of the modern cephalopod,
Sepia officinalis
. Identification and characterization of degradation-resistant melanin may provide insights into its diverse roles in ancient organisms.
Different glutamate receptors convey feedforward and recurrent processing in macaque V1
Authors: Self Matthew W. , Kooijmans Roxana N. , Supèr Hans , Lamme Victor A. , Roelfsema Pieter R.
Published: May 2012

Neurons in the primary visual cortex (V1) receive feedforward input from the thalamus, which shapes receptive-field properties. They additionally receive recurrent inputs via horizontal connections within V1 and feedback from higher visual areas that are thought to be important for conscious visual perception. Here, we investigated what roles different glutamate receptors play in conveying feedforward and recurrent inputs in macaque V1. As a measure of recurrent processing, we used figure–ground modulation (FGM), the increased activity of neurons representing figures compared with background, which depends on feedback from higher areas. We found that feedforward-driven activity was strongly reduced by the AMPA receptor antagonist 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), whereas this drug had no effect on FGM. In contrast, blockers of the NMDA receptor reduced FGM, whereas their effect on visually driven activity varied with the subunit specificity of the drug. The NMDA receptor blocker 2-amino-5-phosphonovalerate (APV) caused a slight reduction of the visual response, whereas ifenprodil, which targets NMDA receptors containing the NMDA receptor NR2B subunit, increased the visual response. These findings demonstrate that glutamate receptors contribute differently to feedforward and recurrent processing in V1 and suggest ways to selectively disrupt recurrent processing so that its role in visual perception can be elucidated.
Thrips pollination of Mesozoic gymnosperms
Authors: Peñalver Enrique , Labandeira Conrad C. , Barrón Eduardo , Delclòs Xavier , Nel Patricia , Nel André , Tafforeau Paul , Soriano Carmen
Published: May 2012

Within modern gymnosperms, conifers and
Ginkgo
are exclusively wind pollinated whereas many gnetaleans and cycads are insect pollinated. For cycads, thrips are specialized pollinators. We report such a specialized pollination mode from Early Cretaceous amber of Spain, wherein four female thrips representing a genus and two species in the family Melanthripidae were covered by abundant
Cycadopites
pollen grains. These females bear unique ring setae interpreted as specialized structures for pollen grain collection, functionally equivalent to the hook-tipped sensilla and plumose setae on the bodies of bees. The most parsimonious explanation for this structure is parental food provisioning for larvae, indicating subsociality. This association provides direct evidence of specialized collection and transportation of pollen grains and likely gymnosperm pollination by 110–105 million years ago, possibly considerably earlier.
Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize
Authors: Riedelsheimer Christian , Lisec Jan , Czedik-Eysenberg Angelika , Sulpice Ronan , Flis Anna , Grieder Christoph , Altmann Thomas , Stitt Mark , Willmitzer Lothar , Melchinger Albrecht E.
Published: May 2012

The diversity of metabolites found in plants is by far greater than in most other organisms. Metabolic profiling techniques, which measure many of these compounds simultaneously, enabled investigating the regulation of metabolic networks and proved to be useful for predicting important agronomic traits. However, little is known about the genetic basis of metabolites in crops such as maize. Here, a set of 289 diverse maize inbred lines was genotyped with 56,110 SNPs and assayed for 118 biochemical compounds in the leaves of young plants, as well as for agronomic traits of mature plants in field trials. Metabolite concentrations had on average a repeatability of 0.73 and showed a correlation pattern that largely reflected their functional grouping. Genome-wide association mapping with correction for population structure and cryptic relatedness identified for 26 distinct metabolites strong associations with SNPs, explaining up to 32.0% of the observed genetic variance. On nine chromosomes, we detected 15 distinct SNP–metabolite associations, each of which explained more then 15% of the genetic variance. For lignin precursors, includingp-coumaric acid and caffeic acid, we found strong associations (Pvaluesto) with a region on chromosome 9 harboring cinnamoyl-CoA reductase, a key enzyme in monolignol synthesis and a target for improving the quality of lignocellulosic biomass by genetic engineering approaches. Moreover, lignin precursors correlated significantly with lignin content, plant height, and dry matter yield, suggesting that metabolites represent promising connecting links for narrowing the genotype–phenotype gap of complex agronomic traits.
Methylation of CenH3 arginine 37 regulates kinetochore integrity and chromosome segregation
Authors: Samel Anke , Cuomo Alessandro , Bonaldi Tiziana , Ehrenhofer-Murray Ann E.
Published: May 2012

Centromeres of eukaryotic chromosomes mark the site for kinetochore formation and microtubule attachment and are essential for accurate chromosome segregation. Although centromere identity is defined by the presence of the histone H3 variant CenH3/centromere protein A (CENP-A), little is known about how epigenetic modifications on CenH3 might regulate kinetochore assembly and centromere function. Here we show that CENP-A from
Saccharomyces cerevisiae
, termed Cse4, is methylated on arginine 37 (R37) and that this methylation regulates the recruitment of kinetochore components to centromeric sequences. The absence of Cse4 R37 methylation caused a growth defect in cells lacking the centromere binding factor Cbf1 and synthetic lethality when combined with mutations in components of the Ctf19 linker complex that connects the inner kinetochore to microtubule-binding proteins. The cells showed a cell-cycle arrest in G2/M phase and defects in plasmid and chromosome segregation. Furthermore, the levels of Mtw1/MIND (Mtw1 including Nnf1-Nsl1-Dsn1) and Ctf19 components at the centromere, but not of Cse4 itself, were reduced in the absence of Cse4 R37 methylation, thus showing that this modification regulates the recruitment of linker components to the centromere. Altogether, our data identify a unique regulatory principle on centromeric chromatin by posttranslational modification of the amino terminus of CenH3.
Frequent skipped spawning in the world’s largest cod population
Authors: Skjæraasen Jon Egil , Nash Richard D. M. , Korsbrekke Knut , Fonn Merete , Nilsen Trygve , Kennedy James , Nedreaas Kjell H. , Thorsen Anders , Witthames Peter R. , Geffen Audrey J. , Høie Hans , Kjesbu Olav Sigurd
Published: May 2012

Life-history theory suggests that animals may skip reproductive events after initial maturation to maximize lifetime fitness. In iteroparous teleosts, verifying past spawning history is particularly difficult; the degree of skipped spawning at the population level therefore remains unknown. We unequivocally show frequent skipped spawning in Northeast Arctic cod (NEAC) in a massive field and laboratory effort from 2006 to 2008. This was verified by postovulatory follicles in temporarily arrested ovaries close to the putative spawning period. At the population level, “skippers” were estimated to be approximately equally abundant as spawning females in 2008, constituting ∼24% of the females 60–100 cm. These females never truly started vitellogenesis and principally remained on the feeding grounds when spawners migrated southward, avoiding any migration costs. The proximate cause of skipping seems to be insufficient energy to initiate oocyte development, indicating that skipped spawning may partly be a density-dependent response important in population regulation. Our data also indicate more skipping among smaller females and potential tradeoffs between current and future reproductive effort. We propose that skipped spawning is an integral life-history component for NEAC, likely varying annually, and it could therefore be an underlying factor causing some of the currently unexplained large NEAC recruitment variation. The same may hold for other teleosts.
Empoasca
leafhoppers attack wild tobacco plants in a jasmonate-dependent manner and identify jasmonate mutants in natural populations
Authors: Kallenbach Mario , Bonaventure Gustavo , Gilardoni Paola A. , Wissgott Antje , Baldwin Ian T.
Published: May 2012

Choice of host plants by phytophagous insects is essential for their survival and reproduction. This choice involves complex behavioral responses to a variety of physical and chemical characteristics of potential plants for feeding. For insects of the order Hemiptera, these behavioral responses involve a series of steps including labial dabbing and probing using their piercing mouthparts. These initial probing and feeding attempts also elicit a rapid accumulation of phytohormones, such as jasmonic acid (JA), and the induced defense metabolites they mediate. When
Nicotiana attenuata
plants are rendered JA deficient by silencing the initial committed step of the JA biosynthesis pathway, they are severely attacked in nature by hemipteran leafhoppers of the genus
Empoasca
. By producing
N. attenuata
plants silenced in multiple steps of JA biosynthesis and perception and in the biosynthesis of the plant’s three major classes of JA-inducible insecticidal defenses, we demonstrate that the choice of plants for feeding by
Empoasca
leafhoppers in both nature and the glasshouse is independent of the accumulation of major insecticidal molecules. Moreover, this choice is independent of the presence of
Candidatus Phytoplasma
spp. and is not associated with detectable changes in plant volatiles but instead depends on the plant´s capacity to mediate JA signaling. We exploited this trait and used
Empoasca
leafhoppers to reveal genetic variation in JA accumulation and signaling hidden in
N. attenuata
natural populations.
Structural basis for homeodomain recognition by the cell-cycle regulator Geminin
Authors: Zhou Bo , Liu Changdong , Xu Zhiwen , Zhu Guang
Published: May 2012

Homeodomain-containing transcription factors play a fundamental role in the regulation of numerous developmental and cellular processes. Their multiple regulatory functions are accomplished through context-dependent inputs of target DNA sequences and collaborating protein partners. Previous studies have well established the sequence-specific DNA binding to homeodomains; however, little is known about how protein partners regulate their functions through targeting homeodomains. Here we report the solution structure of the Hox homeodomain in complex with the cell-cycle regulator, Geminin, which inhibits Hox transcriptional activity and enrolls Hox in cell proliferative control. Side-chain carboxylates of glutamates and aspartates in the C terminus of Geminin generate an overall charge pattern resembling the DNA phosphate backbone. These residues provide electrostatic interactions with homeodomain, which combine with the van der Waals contacts to form the stereospecific complex. We further showed that the interaction with Geminin is homeodomain subclass-selective and Hox paralog-specific, which relies on the stapling role of residues R43 and M54 in helix III and the basic amino acid cluster in the N terminus. Interestingly, we found that the C-terminal residue Ser184 of Geminin could be phosphorylated by Casein kinase II, resulting in the enhanced binding to Hox and more potent inhibitory effect on Hox transcriptional activity, indicating an additional layer of regulation. This structure provides insight into the molecular mechanism underlying homeodomain-protein recognition and may serve as a paradigm for interactions between homeodomains and DNA-competitive peptide inhibitors.
Contribution of cryoelectron microscopy of vitreous sections to the understanding of biological membrane structure
Authors: Leforestier Amélie , Lemercier Nicolas , Livolant Françoise
Published: May 2012

Using cryoelectron microscopy of vitreous sections, we investigated in situ the ultrastructure of biological membranes, selected from several cell types for their diverse biological functions. Here we describe how to visualize the two membrane leaflets and tightly apposed membranes, lying as close as 1.1 nm apart, by tuning the imaging conditions. We show how defects in membrane stacks may be clues to resolving their structure. Details of membrane proteins are also resolved, as well as protein lattices with correlations between stacked membranes. Imaging the cell in its native hydrated state can now be done in the nanometer resolution range, which should open unique routes for investigating structure–function relationships.
Global analysis of chaperone effects using a reconstituted cell-free translation system
Authors: Niwa Tatsuya , Kanamori Takashi , Ueda Takuya , Taguchi Hideki
Published: May 2012

Protein folding is often hampered by protein aggregation, which can be prevented by a variety of chaperones in the cell. A dataset that evaluates which chaperones are effective for aggregation-prone proteins would provide an invaluable resource not only for understanding the roles of chaperones, but also for broader applications in protein science and engineering. Therefore, we comprehensively evaluated the effects of the major
Escherichia coli
chaperones, trigger factor, DnaK/DnaJ/GrpE, and GroEL/GroES, on ∼800 aggregation-prone cytosolic
E. coli
proteins, using a reconstituted chaperone-free translation system. Statistical analyses revealed the robustness and the intriguing properties of chaperones. The DnaK and GroEL systems drastically increased the solubilities of hundreds of proteins with weak biases, whereas trigger factor had only a marginal effect on solubility. The combined addition of the chaperones was effective for a subset of proteins that were not rescued by any single chaperone system, supporting the synergistic effect of these chaperones. The resource, which is accessible via a public database, can be used to investigate the properties of proteins of interest in terms of their solubilities and chaperone effects.
Asymmetric forest transition driven by the interaction of socioeconomic development and environmental heterogeneity in Central America
Authors: Redo Daniel J. , Grau H. Ricardo , Aide T. Mitchell , Clark Matthew L.
Published: May 2012

Forest transitions (FT) have been observed in many developed countries and more recently in the developing world. However, our knowledge of FT from tropical regions is mostly derived from case studies from within a particular country, making it difficult to generalize findings across larger regions. Here we overcome these difficulties by conducting a recent (2001–2010) satellite-based analysis of trends in forest cover across Central America, stratified by biomes, which we related to socioeconomic variables associated with human development. Results show a net decrease of woody vegetation resulting from 12,201 km2of deforestation of moist forests and 6,825 km2of regrowth of conifer and dry forests. The Human Development Index was the socioeconomic variable best associated with forest cover change. The least-developed countries, Nicaragua and Guatemala, experienced both rapid deforestation of moist forests and significant recovery of conifer and dry forests. In contrast, the most developed countries, Panama and Costa Rica, had net woody vegetation gain and a more stable forest cover configuration. These results imply a good agreement with FT predictions of forest change in relation to socioeconomic development, but strong asymmetry in rates and directions of change largely dependent upon the biome where change is occurring. The FT model should be refined by incorporating ecological and socioeconomic heterogeneity, particularly in multicountry and regional studies. These asymmetric patterns of forest change should be evaluated when developing strategies for conserving biodiversity and environmental services.
Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy
Authors: Siebrasse Jan Peter , Kaminski Tim , Kubitscheck Ulrich
Published: May 2012

Nuclear export of mRNA is a key transport process in eukaryotic cells. To investigate it, we labeled native mRNP particles in living
Chironomus tentans
salivary gland cells with fluorescent hrp36, the hnRNP A1 homolog, and the nuclear envelope by fluorescent NTF2. Using light sheet microscopy, we traced single native mRNA particles across the nuclear envelope. The particles were observed to often probe nuclear pore complexes (NPC) at their nuclear face, and in only 25% of the cases yielded actual export. The complete export process took between 65 ms up to several seconds. A rate-limiting step was observed, which could be assigned to the nuclear basket of the pore and might correspond to a repositioning and unfolding of mRNPs before the actual translocation. Analysis of single fluorescent Dbp5 molecules, the RNA helicase essential for mRNA export, revealed that Dbp5 most often approached the cytoplasmic face of the NPC, and exhibited a binding duration of approximately 55 ms. Our results have allowed a refinement of the current models for mRNA export.
Reprogramming of proline and glutamine metabolism contributes to the proliferative and metabolic responses regulated by oncogenic transcription factor c-MYC
Authors: Liu Wei , Le Anne , Hancock Chad , Lane Andrew N. , Dang Chi V. , Fan Teresa W.-M. , Phang James M.
Published: May 2012

In addition to glycolysis, the oncogenic transcription factor c-MYC (MYC) stimulates glutamine catabolism to fuel growth and proliferation of cancer cells through up-regulating glutaminase (GLS). Glutamine is converted to glutamate by GLS, entering the tricarboxylic acid cycle as an important energy source. Less well-recognized, glutamate can also be converted to proline through Δ
1
-pyrroline-5-carboxylate (P5C) and vice versa. This study suggests that some MYC-induced cellular effects are due to MYC regulation of proline metabolism. Proline oxidase, also known as proline dehydrogenase (POX/PRODH), the first enzyme in proline catabolism, is a mitochondrial tumor suppressor that inhibits proliferation and induces apoptosis. MiR-23b* mediates POX/PRODH down-regulation in human kidney tumors. MiR-23b* is processed from the same transcript as miR-23b; the latter inhibits the translation of GLS. Using MYC-inducible human Burkitt lymphoma model P493 and PC3 human prostate cancer cells, we showed that MYC suppressed POX/PRODH expression primarily through up-regulating miR-23b*. The growth inhibition in the absence of MYC was partially reversed by POX/PRODH knockdown, indicating the importance of suppression of POX/PRODH in MYC-mediated cellular effects. Interestingly, MYC not only inhibited POX/PRODH, but also markedly increased the enzymes of proline biosynthesis from glutamine, including P5C synthase and P5C reductase 1. MYC-induced proline biosynthesis from glutamine was directly confirmed using
13
C,
15
N-glutamine as a tracer. The metabolic link between glutamine and proline afforded by MYC emphasizes the complexity of tumor metabolism. Further studies of the relationship between glutamine and proline metabolism should provide a deeper understanding of tumor metabolism while enabling the development of novel therapeutic strategies.
Intron-mediated alternative splicing of
Arabidopsis P5CS1
and its association with natural variation in proline and climate adaptation
Authors: Kesari Ravi , Lasky Jesse R. , Villamor Joji Grace , Des Marais David L. , Chen Ying-Jiun C. , Liu Tzu-Wen , Lin Wendar , Juenger Thomas E. , Verslues Paul E.
Published: May 2012

Drought-induced proline accumulation is widely observed in plants but its regulation and adaptive value are not as well understood. Proline accumulation of the
Arabidopsis
accession Shakdara (Sha) was threefold less than that of Landsberg
erecta
(L
er
) and quantitative trait loci mapping identified a reduced function allele of the proline synthesis enzyme

Δ
1
-pyrroline-5-carboxylate synthetase1

(
P5CS1
) as a basis for the lower proline of Sha. Sha
P5CS1
had additional TA repeats in intron 2 and a G-to-T transversion in intron 3 that were sufficient to promote alternative splicing and production of a nonfunctional transcript lacking exon 3 (exon 3-skip
P5CS1
). In Sha, and additional accessions with the same intron polymorphisms, the nonfunctional exon 3-skip
P5CS1
splice variant constituted as much as half of the total
P5CS1
transcript. In a larger panel of
Arabidopsis
accessions, low water potential-induced proline accumulation varied by 10-fold and variable production of exon 3-skip
P5CS1
among accessions was an important, but not the sole, factor underlying variation in proline accumulation. Population genetic analyses suggest that
P5CS1
may have evolved under positive selection, and more extensive correlation of exon 3-skip
P5CS1
production than proline abundance with climate conditions of natural accessions also suggest a role of
P5CS1
in local adaptation to the environment. These data identify a unique source of alternative splicing in plants, demonstrate a role of exon 3-skip
P5CS1
in natural variation of proline metabolism, and suggest an association of
P5CS1
and its alternative splicing with environmental adaptation.
Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases
Authors: Zamft Bradley , Bintu Lacramioara , Ishibashi Toyotaka , Bustamante Carlos
Published: May 2012

RNA polymerase pausing represents an important mechanism of transcriptional regulation. In this study, we use a single-molecule transcription assay to investigate the effect of template base-pair composition on pausing by RNA polymerase II and the evolutionarily distinct mitochondrial polymerase Rpo41. For both enzymes, pauses are shorter and less frequent on GC-rich templates. Significantly, incubation with RNase abolishes the template dependence of pausing. A kinetic model, wherein the secondary structure of the nascent RNA poses an energetic barrier to pausing by impeding backtracking along the template, quantitatively predicts the pause densities and durations observed. The energy barriers extracted from the data correlate well with RNA folding energies obtained from cotranscriptional folding simulations. These results reveal that RNA secondary structures provide a
cis
-acting mechanism by which sequence modulates transcriptional elongation.
Stress-induced epigenetic regulation of κ-opioid receptor gene involves transcription factor c-Myc
Authors: Flaisher-Grinberg Shlomit , Persaud Shawna D. , Loh Horace H. , Wei Li-Na
Published: May 2012

Exposure to stress is associated with adverse emotional and behavioral responses. Whereas the κ-opioid receptor (KOR) system is known to mediate some of the effects, it is unclear whether and how stress affects epigenetic regulation of this gene. Because the KOR gene can use two promoters (Pr1 and Pr2) and two polyadenylation signals (PA1 and PA2), it is also interesting whether and how these distinct regulatory mechanisms are differentially modulated by stress. The current study examined the effects of stress on these different regulatory mechanisms of the KOR gene. Results showed that stress selectively increased the expression of KOR mRNA isoforms controlled by Pr1 and terminated at PA1 in specific brain areas including the medial–prefrontal cortex, hippocampus, brainstem, and sensorimotor cortex, but not in the amygdala or hypothalamus. These effects correlated with altered epigenetic state of KOR Pr1 chromatin, as well as elevation and increased recruitment of the principal transcription factor c-Myc, which could activate Pr1. Stress-induced modulation of Pr1 was further validated using glutamate-sensitive murine hippocampal cell line, HT22. The results revealed a common molecular mechanism underlying the effect of stress on selected chromatin regions of this gene at the cellular level and in the context of whole animal and identified a critical role for c-Myc in stress-triggered epigenetic regulation of the KOR gene locus. This study sheds light on the mechanisms of stress-induced epigenetic regulation that targets specific chromatin segments and suggests certain KOR transcripts and its principal transcription factor c-Myc as potential targets for brain-area–specific intervention.
Mgr2 promotes coupling of the mitochondrial presequence translocase to partner complexes
Authors: Gebert Michael , Schrempp Sandra G. , Mehnert Carola S. , Heißwolf Anna K. , Oeljeklaus Silke , Ieva Raffaele , Bohnert Maria , von der Malsburg Karina , Wiese Sebastian , Kleinschroth Thomas , Hunte Carola , Meyer Helmut E. , Haferkamp Ilka , Guiard Bernard , Warscheid Bettina , Pfanner Nikolaus , van der Laan Martin
Published: May 2012

Many mitochondrial proteins are synthesized with N-terminal presequences in the cytosol. The presequence translocase of the inner mitochondrial membrane (TIM23) translocates preproteins into and across the membrane and associates with the matrix-localized import motor. The TIM23 complex consists of three core components and Tim21, which interacts with the translocase of the outer membrane (TOM) and the respiratory chain. We have identified a new subunit of the TIM23 complex, the inner membrane protein Mgr2. Mitochondria lacking Mgr2 were deficient in the Tim21-containing sorting form of the TIM23 complex. Mgr2 was required for binding of Tim21 to TIM23CORE, revealing a binding chain of TIM23CORE-Mgr2/Tim21–respiratory chain. Mgr2-deficient yeast cells were defective in growth at elevated temperature, and the mitochondria were impaired in TOM-TIM23 coupling and the import of presequence-carrying preproteins. We conclude that Mgr2 is a coupling factor of the presequence translocase crucial for cell growth at elevated temperature and for efficient protein import.
DNA polymerase ζ generates tandem mutations in immunoglobulin variable regions
Authors: Saribasak Huseyin , Maul Robert W. , Cao Zheng , Yang William W. , Schenten Dominik , Kracker Sven , Gearhart Patricia J.
Published: May 2012

Low-fidelity DNA polymerases introduce nucleotide substitutions in immunoglobulin variable regions during somatic hypermutation. Although DNA polymerase (pol) η is the major low-fidelity polymerase, other DNA polymerases may also contribute. Existing data are contradictory as to whether pol ζ is involved. We reasoned that the presence of pol η may mask the contribution of pol ζ, and therefore we generated mice deficient for pol η and heterozygous for pol ζ. The frequency and spectra of hypermutation was unaltered between Polζ+/− Polη−/− and Polζ+/+ Polη−/− clones. However, there was a decrease in tandem double-base substitutions in Polζ+/− Polη−/− cells compared with Polζ+/+ Polη−/− cells, suggesting that pol ζ generates tandem mutations. Contiguous mutations are consistent with the biochemical property of pol ζ to extend a mismatch with a second mutation. The presence of this unique signature implies that pol ζ contributes to mutational synthesis in vivo. Additionally, data on tandem mutations from wild type, Polζ+/−, Polζ−/−, Ung−/−, Msh2−/−, Msh6−/−, and Ung−/− Msh2−/− clones suggest that pol ζ may function in the MSH2–MSH6 pathway.
Spectral characteristics of amplified spontaneous emission in a semiconductor disc laser
Authors: Zhang Peng , Dai Teli , Liang Yiping , Fan Siqiang , Song Yanrong , Zhang Xinping
Published: May 2012

In an optically pumped semiconductor disc laser, which is always with a multiple layer active region and a large spot size, the spontaneous emission of quantum wells will be trapped by the waveguide caused by the multiple layer, travel a long excited distance relative to the surface-emitting mode and be subsequently amplified. Here we demonstrate a new mechanism for the amplified spontaneous emission (ASE): the etalon effect of the sub-cavity formed by the bottom distributed Bragg reflector and the top air–semiconductor interface. The spectral characteristics of this ASE including its temperature dependence, pump power dependence and observing angle dependence are experimentally studied, and the results are in good agreement with the theoretical model.
Optical and electrical Kerr effects in polydiacetylene nanoparticle submonolayer probed by surface plasmon resonance spectroscopy
Authors: Kuraishi Oki , Tanaka Daisuke , Shimojo Masayuki , Kajikawa Kotaro
Published: May 2012

Optical and electrical Kerr effects in a polydiacetylene (PDA) nanoparticle (NP) submonolayer film formed on a gold substrate were investigated. The third-order nonlinear susceptibilities of the PDA NPs at an off-resonance wavelength of 1064 nm were χ(3) = (−7.6 + 6.6i) × 10−9 esu (optical Kerr effect) and χ(3) = (−1.2 + 0.39i) × 10−9 esu (electrical Kerr effect), which are an order of magnitude larger than the value reported. We observed a reflectivity change of 5% with an illumination intensity of 9.3 MW cm−2 in the attenuated total reflection geometry, as a result of the refractive index change of 0.001 on the basis of the optical Kerr effect. The results indicate that the PDA NPs are promising materials for optical switching using plasmonic waveguides.
Study of the electro-optic effect in new organic nonlinear optical polymeric materials
Authors: Mahmood M H , Saadon H L
Published: May 2012

The electro-optic (EO) coefficients of two new organic nonlinear optical (NLO) guest–host poly(N-vinylcarbazole)/Disperse Orange 25 (PVK/DO25) and NLO side-chain poly(Disperse Orange 3 methacrylamide) (PDO3MAA) systems were determined and compared through a modified reflection technique. In order to obtain the maximum EO activity, the poling temperature and chromophore (dye) concentration were investigated. At ambient temperature, the degree of poling was stable over months. Moreover, it was found that the side-chain PDO3MAA system has a temporal stability slightly higher than or comparable to that of the guest–host PVK/DO25 system. In addition to that, figures of merit were defined and calculated from the experimental data and we used these figures to compare with those of an inorganic Z-cut LiTaO3 (LT) plate.