bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of intermolecular interaction of poly(N-isopropylacrylamide) solution with attenuated total reflectance terahertz spectroscopy
Authors: Naito H. , Ogawa Y. , Hoshina H. , Sultana S. , Kondo N.
Published: May 2012

The terahertz attenuated total reflectance spectra of Poly(N-isopropylacrylamide) (P-NIPAAm) solutions were measured in the range of 26.5–47.3 °C. The phase-change in P-NIPAAm was observed via the temperature dependence of the spectra. The collapse of hydrogen bonds in solution was confirmed by the decrease in the signal intensities around 62 cm−1, which corresponds to fast dielectric relaxation by rotation and collision of molecules, and around 166 cm−1, which corresponds to the stretching mode of the intermolecular vibration of water molecules.
Photo-induced changes in fundamental properties of organic solar cells
Authors: Bhattacharya J. , Mayer R. W. , Samiee M. , Dalal V. L.
Published: May 2012

We report on the measurement of fundamental properties such as deep defects and hole mobility in poly-3-hexyl-thiophene (P3HT)/[6,6]-phenyl-C60-butyric acid methyl ester(PCBM) solar cells when the cells are exposed to solar radiation without any atmospheric exposure. It is found that the midgap defect density in P3HT and the interface density between P3HT and PCBM increase significantly upon light soaking along with a reduction in hole mobility in P3HT. The increase in defect density leads to a corresponding increase in reverse saturation current of the diode, and the corresponding decrease in open circuit voltage of the cell upon light soaking.
Stochastic processes in light-assisted nanoparticle formation
Authors: Naruse Makoto , Liu Yang , Nomura Wataru , Yatsui Takashi , Aida Masaki , Kish Laszlo B. , Ohtsu Motoichi
Published: May 2012

Recently, light-assisted nanofabrication have been introduced, such as the synthesis of quantum dots using photo-induced desorption that yields reduced size fluctuations or metal sputtering under light illumination resulting in self-organized, nanoparticle chains. The physical mechanisms have originally been attributed to material desorption or plasmon resonance effects. However, significant stochastic phenomena are also present that have not been explained yet. We introduce stochastic models taking account of the light-assisted processes that reproduce phenomenological characteristics consistent with the experimental observations.
From A to B: A ride in the free energy surfaces of protein G domains suggests how new folds arise
Authors: Sutto Ludovico , Camilloni Carlo
Published: May 2012

Metamorphic proteins are an extremely intriguing case of protein evolution and a golden opportunity to challenge the current simplified models. In a recent work, we showed that a coarse-grained Gō model can be used to study the thermodynamics of lymphotactin, a naturally occurring metamorphic protein. Here, we extend such model by including the necessary atomic detail to study the effects of the single mutations that artificially bring the GA domain of protein G to fold into the GB domain of the same protein. The results of this all-atom Gō model show how the residual structure of the denatured state is an early indicator of a forthcoming fold and function switch. These findings reconcile the results of previous studies on similar systems highlighting the different role played by secondary and tertiary interactions and suggesting a possible way for new folds to arise.
Reduction of spectral phonon relaxation times from suspended to supported graphene
Authors: Qiu Bo , Ruan Xiulin
Published: May 2012

We have performed molecular dynamics simulations with phonon spectral analysis to predict the mode-wise phonon relaxation times (RT) of suspended and supported graphene at room temperature, and the findings are consistent with recent optical measurements. For acoustic phonons, RTs reduce from up to 50 ps to less than 5 ps when graphene is put on silicon dioxide substrate. Similarly, optical phonon RTs reduce by half when supported. Stronger interfacial bonding is found to result in more RT reduction. Our results provide a fundamental understanding at the spectral phonon property level for the observed thermal conductivity reduction in supported graphene.
Method to determine hkl strains and shear moduli under torsion using neutron diffraction
Authors: Woracek R. , Bunn J. R. , Penumadu D. , Hubbard C. R.
Published: May 2012

An experimental method, using in-situ neutron diffraction for the measurement of shear strain, based on (hkl) lattice spacing changes under torsional loading, is described. This method provides the ability to probe the response of crystallographic planes to application of shear stress, inside the bulk of samples that are subjected to torsion. To demonstrate the method, shear moduli corresponding to bcc (211), (200), and (110) were experimentally determined for a solid cylinder of ferritic alloy 12L14 under elastic loading. Results indicate that the elastic constants determined under torsional shear show a different degree of anisotropy than those obtained from tensile loading.
Precision equation-of-state measurements on National Ignition Facility ablator materials from 1 to 12 Mbar using laser-driven shock waves
Authors: Barrios M. A. , Boehly T. R. , Hicks D. G. , Fratanduono D. E. , Eggert J. H. , Collins G. W. , Meyerhofer D. D.
Published: May 2012

A large uncertainty in the design of ignition capsules for use in the National Ignition Campaign (NIC) is the ablator equation of state. In this article, we report equation-of-state measurements for two candidate NIC ablator materials, glow-discharge polymer (GDP), and germanium-doped GDP. These materials were driven to pressures of 1 to 12 Mbar using laser-driven shock waves. Hugoniot measurements were obtained using the impedance matching technique with an α-quartz standard. This article presents the first kinematic measurements in the high-pressure fluid regime for these materials, which show to be in close agreement with Livermore equation-of-state model predictions.
Hydrogen release from Li alanates originates in molecular lattice instability emerging at ∼100 K
Authors: Tomiyasu K. , Sato T. , Horigane K. , Orimo S. , Yamada K.
Published: May 2012

Lattice vibrations from 20 K to room temperature in lithium alanates LiAlH4 and Li3AlH6, which decompose to release hydrogen over 423 K, were investigated by neutron spectroscopy. For both alanates, the overall spectra already start to broaden at 100–150 K with increasing temperature. The spectral lines assigned to the librational (rotational) modes of the polyhedral Al hydrido complexes, [AlH4]− and [AlH6]3−, exhibit not only broadening but also softening at around 250–300 K. These results suggest that the decomposition stems from low-temperature bulk lattice instability/anharmonicity, in particular, due to the weakening of binding between the complexes and their surroundings.
Sustainable heat extraction from abandoned mine tunnels: A numerical model
Authors: Ghoreishi Madiseh S. A. , Ghomshei Mory M. , Hassani F. P. , Abbasy F.
Published: May 2012

Abandoned mines are often associated with enduring liabilities, which involve significant costs for decades after the decommissioning of the mine. Using a decommissioned mine as a geothermal resource can offset the environmental costs by supplying green heat to the communities living in and around the mine area. In this paper, a numerical assessment of geothermal heat extraction from underground mine workings using an open loop geothermal system is carried out. In this study, our focus is on fully flooded mines where the heat flow from the rock mass to the mine cavities is dominantly controlled by conduction in the rock mass. The sustainable heat flux into the mine workings is assessed using a transient two-dimensional axisymmetric heat transfer model. Finite volume method is applied to solve the model and simulate the transient temperature fields in the rock mass and within the water (flowing through cavities). The model is capable of controlling the rate of heat extraction through continuous adjustment of the rate of water flow through the mine. Sustainable rate of heat extraction is calculated for seasonally varied heat loads and for different project life cycles. It is shown that, with proper resource management, each kilometre of a typical deep underground mine tunnel, can produce about 150 kW of usable heat in a sustainable manner. The model is validated by comparing its results with other published models and realistic data available from Springhill mine, Nova Scotia, Canada. It is found that the sustainable heat extraction is controlled dominantly by virgin rock temperature, thermal conductivity of the rock mass, and seasonal heat load variations.
Defect and adsorbate induced ferromagnetic spin-order in magnesium oxide nanocrystallites
Authors: Kumar Ashok , Kumar Jitendra , Priya Shashank
Published: May 2012

We report the correlation between d0 ferromagnetism, photoluminescence (PL), and adsorbed hydrogen (H−) species in magnesium oxide (MgO) nanocrystallites. Our study suggests that the oxygen vacancies, namely singly ionized anionic vacancies (F+) and dimers (F22+) induce characteristic photoluminescence and the room-temperature ferromagnetic spin-order. Nanocrystallites with low population of oxygen vacancies have revealed diamagnetic behavior. Intriguingly, on adsorption of hydrogen (H−) species in the MgO nanocrystallites, ferromagnetic behavior was either enhanced (in the case of highly oxygen deficient nanocrystallites) or begun to percolate (in the case of nanocrystallite with low population density of oxygen vacancies).
Real-time x-ray diffraction of metastable phases during solidification from the undercooled LuFeO3 melt by two-dimensional detector at 1 kHz
Authors: Vijaya Kumar Malahalli , Kuribayashi K. , Nagashio K. , Ishikawa T. , Okada J. , Yu J. , Yoda S. , Katayama Y.
Published: May 2012

In-situ identification of metastable phases formed from the undercooled LuFeO3 melt under controlled oxygen partial pressure Po2 was studied by x-ray diffraction measurements at a synchrotron radiation source. Real-time observation of the formation and growth of individual phases during the single recalescence of Lu3Fe2O7 and LuFe2O4 phases at Po2 of 1 × 103 Pa has been revealed by a high speed imaging system at 1 kHz. The obtained diffraction pattern of the metastable phase in the LuFeO3 system was consistent with that of the metastable and stable phases reported in the Lu-Fe-O system.
Rate dependence of the serrated flow in Ni-10Pd during high temperature instrumented microindentation
Authors: Gan Bin , Tin Sammy
Published: May 2012

Instrumented indentation tests were conducted on a pure nickel and a Ni-10Pd solid solution at 450 °C with loading rates varying from 62.5 to 1000 mN/s. The load–depth curves from the pure nickel exhibited a smooth and continuous transition; while the load–depth curves from the Ni-10Pd were initially smooth and then became serrated after reaching a critical load. Increases in loading rates resulted in an earlier occurrence of the serrated flow with a higher load threshold. The mechanism responsible for the serration was delineated by accounting for the reconfiguration of dislocation substructures and the interactions between solutes and forest dislocations.
Transport properties of high-performance all-Heusler Co2CrSi/Cu2CrAl/Co2CrSi giant magnetoresistance device
Authors: Bai Z. Q. , Lu Y. H. , Shen L. , Ko V. , Han G. C. , Feng Y. P.
Published: May 2012

Transport properties of giant magnetoresistance (MR) junction consisting of trilayer Co2CrSi/Cu2CrAl/Co2CrSi Heusler alloys (L21) are studied using first-principles approach based on density functional theory and the non-equilibrium Green's function method. Highly conductive channels are found in almost the entire k-plane when the magnetizations of the electrodes are parallel, while they are completely blocked in the antiparallel configuration, which leads to a high magnetoresistance ratio (the pessimistic MR ratio is nearly 100%). Furthermore, the calculated I-V curve shows that the device behaves as a good spin valve with a considerable disparity in currents under the parallel and antiparallel magnetic configurations of the electrodes. The Co2CrSi/Cu2CrAl/Co2CrSi junction could be useful for high-performance all-metallic current-perpendicular-to-plane giant magnetoresistance reading head for the next generation high density magnetic storage.
Improvement in rectification ratio of an Al-based bulk thermal rectifier working at high temperatures
Authors: Takeuchi Tsunehiro , Goto Hiroki , Nakayama Ryu-suke , Terazawa Yu-ichi , Ogawa Koto , Yamamoto Akio , Itoh Takashi , Mikami Masashi
Published: May 2012

In this study, we attempted to improve the thermal rectification ratio (TRR = (JAB – JBA)/JBA) of a thermal rectifier consisting of two Al-based alloys, Al72.6Re17.4Si10 and Al71.6Mn17.4Si11, both of which are known to be the 1/1-cubic approximant of icosahedral quasicrystal. In order to estimate the thermal rectification ratio obtainable for a thermal rectifier made from two given materials, we employed a simple method of TRR calculation using the classical Fourier-law of heat conduction. The largest TRR, which exceeded 0.12 for the thermal reservoirs kept at TH = 500 K and TL = 300 K, was experimentally obtained, coinciding with what the calculations predicted. By using the experimentally determined thermal conductivity and the calculation method employed in this study, we show the potential of an Al62Cu25.5Fe12.5 icosahedral quasicrystal as one of the constituent materials of thermal rectifier possessing a TRR magnitude in excess of unity.
Correlation between the thermodynamic stability of austenite and the shear modulus of polycrystalline steel alloy
Authors: Terasaki H. , Yamagishi H. , Moriguchi K. , Tomio Y. , Komizo Y.
Published: May 2012

Elastic moduli in steel alloys with different martensitic start temperatures were measured during the cooling cycle by using the ultrasonic pulse sing-around method. Our findings show that the shear modulus governs austenite stability prior to martensitic transformation in polycrystalline steel alloys. A non-linear increase in shear modulus is also observed during the cooling cycle. The correlation between elastic modulus and austenite stability in polycrystalline steel alloys is discussed, and the compatibility of the results obtained in this study with the stability theory analyzed in a single crystal is also discussed.
Low temperature fabrication and characterization of nickel germanide Schottky source/drain contacts for implant-less germanium p-channel metal-oxide-semiconductor field-effect transistors
Authors: Gajula D. R. , McNeill D. W. , Coss B. E. , Dong H. , Jandhyala S. , Kim J. , Wallace R. M. , Armstrong B. M.
Published: May 2012

In this work, nickel germanide Schottky contacts have been fabricated on n-type germanium (n-Ge) with an optimum barrier height of 0.63 eV. For rapid thermal annealing (RTA) temperatures above 300  °C, all phases of nickel and germanium convert to nickel mono-germanide (NiGe). However, higher RTA temperatures are also found to cause agglomeration of the NiGe phase and higher leakage current. So, the optimum temperature for Schottky-based source/drain contact formation on n-Ge is ∼300 °C, where the nickel mono-germanide phase is formed but without phase agglomeration.
Spin-polarization of VGaON center in GaN and its application in spin qubit
Authors: Wang Xiaopeng , Zhao Mingwen , Wang Zhenhai , He Xiujie , Xi Yan , Yan Shishen
Published: May 2012

VGaON center in cubic gallium nitride is a defect complex composing of a substitutional oxygen atom at nitrogen site (ON) and an adjacent gallium vacancy (VGa). Based on first-principles calculations, we predicted that this VGaON center has much in common with the famous nitrogen-vacancy center in diamond, but the excitation energy is very low. The electron spin-polarization of the centers can be tuned by changing the charge states. The neutral ONVGa center has the v↓ and exy↓ states being well isolated from the bulk bands with appropriate spacing which are suitable for achieving spin qubit operation with low excitation energy.
Raman analysis of monoclinic Cu2SnS3 thin films
Authors: Berg Dominik M. , Djemour Rabie , Gütay Levent , Siebentritt Susanne , Dale Phillip J. , Fontane Xavier , Izquierdo-Roca Victor , Pérez-Rodriguez Alejandro
Published: May 2012

Secondary phases like Cu2SnS3 are major obstacles for kesterite thin film solar cell applications. We prepare Cu2SnS3 using identical annealing conditions as used for the kesterite films. By x-ray diffraction, the crystal structure of Cu2SnS3 was identified as monoclinic. Polarization-dependent Raman investigations allowed the identification of the dominant peaks at 290 cm−1 and 352 cm−1 with the main A′ symmetry vibrational modes from the monoclinic Cu2SnS3 phase. Furthermore, micro-resolved Raman investigations revealed local variations in the spectra that are attributed to a secondary phase (possibly Cu2Sn3S7). This exemplifies the abilities of micro-resolved Raman measurements in the detection of secondary phases.
Co-occurrence of linguistic and biological diversity in biodiversity hotspots and high biodiversity wilderness areas
Authors: Gorenflo L. J. , Romaine Suzanne , Mittermeier Russell A. , Walker-Painemilla Kristen
Published: May 2012

As the world grows less biologically diverse, it is becoming less linguistically and culturally diverse as well. Biologists estimate annual loss of species at 1,000 times or more greater than historic rates, and linguists predict that 50–90% of the world’s languages will disappear by the end of this century. Prior studies indicate similarities in the geographic arrangement of biological and linguistic diversity, although conclusions have often been constrained by use of data with limited spatial precision. Here we use greatly improved datasets to explore the co-occurrence of linguistic and biological diversity in regions containing many of the Earth’s remaining species: biodiversity hotspots and high biodiversity wilderness areas. Results indicate that these regions often contain considerable linguistic diversity, accounting for 70% of all languages on Earth. Moreover, the languages involved are frequently unique (endemic) to particular regions, with many facing extinction. Likely reasons for co-occurrence of linguistic and biological diversity are complex and appear to vary among localities, although strong geographic concordance between biological and linguistic diversity in many areas argues for some form of functional connection. Languages in high biodiversity regions also often co-occur with one or more specific conservation priorities, here defined as endangered species and protected areas, marking particular localities important for maintaining both forms of diversity. The results reported in this article provide a starting point for focused research exploring the relationship between biological and linguistic–cultural diversity, and for developing integrated strategies designed to conserve species and languages in regions rich in both.
Monomeric site-specific nucleases for genome editing
Authors: Kleinstiver Benjamin P. , Wolfs Jason M. , Kolaczyk Tomasz , Roberts Alanna K. , Hu Sherry X. , Edgell David R.
Published: May 2012

Targeted manipulation of complex genomes often requires the introduction of a double-strand break at defined locations by site-specific DNA endonucleases. Here, we describe a monomeric nuclease domain derived from GIY-YIG homing endonucleases for genome-editing applications. Fusion of the GIY-YIG nuclease domain to three-member zinc-finger DNA binding domains generated chimeric GIY-zinc finger endonucleases (GIY-ZFEs). Significantly, the I-TevI-derived fusions (Tev-ZFEs) function in vitro as monomers to introduce a double-strand break, and discriminate in vitro and in bacterial and yeast assays against substrates lacking a preferred 5′-CNNNG-3′ cleavage motif. The Tev-ZFEs function to induce recombination in a yeast-based assay with activity on par with a homodimeric Zif268 zinc-finger nuclease. We also fused the I-TevI nuclease domain to a catalytically inactive LADGLIDADG homing endonuclease (LHE) scaffold. The monomeric Tev-LHEs are active in vivo and similarly discriminate against substrates lacking the 5′-CNNNG-3′ motif. The monomeric Tev-ZFEs and Tev-LHEs are distinct from the FokI-derived zinc-finger nuclease and TAL effector nuclease platforms as the GIY-YIG domain alleviates the requirement to design two nuclease fusions to target a given sequence, highlighting the diversity of nuclease domains with distinctive biochemical properties suitable for genome-editing applications.
Visible light generation of I–I bonds by Ru-tris(diimine) excited states
Authors: Farnum Byron H. , Jou Jeffrey J. , Meyer Gerald J.
Published: May 2012

Seven Ru-tris(diimine) compounds were prepared to study the photooxidation of iodide. Iodide oxidation results in the formation of I–I bonds, and it is therefore relevant to the conversion and storage of solar energy. Iodide oxidation is also a key step for electrical power generation in dye-sensitized solar cells. The mechanistic details of iodide oxidation and I–I bond formation were elucidated through time-resolved spectroscopic measurements. Bimolecular electron-transfer reactions between Ru-tris(diimine) excited states and iodide first yielded the iodine atom that subsequently reacted with excess I
-
to yield the I–I bond of diiodide (

). An important finding was that excited-state iodide oxidation was rapid (
k
 > 10
9
 M
-1
 s
-1
) even for thermodynamically uphill reactions. These results indicated that iodide oxidation to the iodine atom may account for a significant fraction of sensitizer regeneration within dye-sensitized solar cells.
Further constraints on the Chauvet cave artwork elaboration
Authors: Sadier Benjamin , Delannoy Jean-Jacques , Benedetti Lucilla , Bourlès Didier L. , Jaillet Stéphane , Geneste Jean-Michel , Lebatard Anne-Elisabeth , Arnold Maurice
Published: May 2012

Since its discovery, the Chauvet cave elaborate artwork called into question our understanding of Palaeolithic art evolution and challenged traditional chronological benchmarks [Valladas H et al. (2001)
Nature
413:419–479]. Chronological approaches revealing human presences in the cavity during the Aurignacian and the Gravettian are indeed still debated on the basis of stylistic criteria [Pettitt P (2008)
J Hum Evol
55:908–917]. The presented
36
Cl Cosmic Ray Exposure ages demonstrate that the cliff overhanging the Chauvet cave has collapsed several times since 29 ka until the sealing of the cavity entrance prohibited access to the cave at least 21 ka ago. Remarkably agreeing with the radiocarbon dates of the human and animal occupancy, this study confirms that the Chauvet cave paintings are the oldest and the most elaborate ever discovered, challenging our current knowledge of human cognitive evolution.
Bisphenol A alters the development of the rhesus monkey mammary gland
Authors: Tharp Andrew P. , Maffini Maricel V. , Hunt Patricia A. , VandeVoort Catherine A. , Sonnenschein Carlos , Soto Ana M.
Published: May 2012

The xenoestrogen bisphenol A (BPA) used in the manufacturing of various plastics and resins for food packaging and consumer products has been shown to produce numerous endocrine and developmental effects in rodents. Exposure to low doses of BPA during fetal mammary gland development resulted in significant alterations in the gland’s morphology that varied from subtle ones observed during the exposure period to precancerous and cancerous lesions manifested in adulthood. This study assessed the effects of BPA on fetal mammary gland development in nonhuman primates. Pregnant rhesus monkeys were fed 400 μg of BPA per kg of body weight daily from gestational day 100 to term, which resulted in 0.68 ± 0.312 ng of unconjugated BPA per mL of maternal serum, a level comparable to that found in humans. At birth, the mammary glands of female offspring were removed for morphological analysis. Morphological parameters similar to those shown to be affected in rodents exposed prenatally to BPA were measured in whole-mounted glands; estrogen receptor (ER) α and β expression were assessed in paraffin sections. Student'sttests for equality of means were used to assess differences between exposed and unexposed groups. The density of mammary buds was significantly increased in BPA-exposed monkeys, and the overall development of their mammary gland was more advanced compared with unexposed monkeys. No significant differences were observed in ER expression. Altogether, gestational exposure to the estrogen-mimic BPA altered the developing mammary glands of female nonhuman primates in a comparable manner to that observed in rodents.
Mutation at the circadian clock gene
EARLY MATURITY 8
adapts domesticated barley (
Hordeum vulgare
) to short growing seasons
Authors: Faure Sebastien , Turner Adrian S. , Gruszka Damian , Christodoulou Vangelis , Davis Seth J. , von Korff Maria , Laurie David A.
Published: May 2012

The circadian clock is an autonomous oscillator that produces endogenous biological rhythms with a period of about 24 h. This clock allows organisms to coordinate their metabolism and development with predicted daily and seasonal changes of the environment. In plants, circadian rhythms contribute to both evolutionary fitness and agricultural productivity. Nevertheless, we show that commercial barley varieties bred for short growing seasons by use of
early maturity 8
(
eam8
) mutations, also termed
mat-a
, are severely compromised in clock gene expression and clock outputs. We identified
EAM8
as a barley ortholog of the
Arabidopsis thaliana
circadian clock regulator
EARLY FLOWERING3
(
ELF3
) and demonstrate that
eam8
accelerates the transition from vegetative to reproductive growth and inflorescence development. We propose that
eam8
was selected as barley cultivation moved to high-latitude short-season environments in Europe because it allowed rapid flowering in genetic backgrounds that contained a previously selected late-flowering mutation of the photoperiod response gene
Ppd-H1
. We show that
eam8
mutants have increased expression of the floral activator
HvFT1
, which is independent of allelic variation at
Ppd-H1
. The selection of independent
eam8
mutations shows that this strategy facilitates short growth-season adaptation and expansion of the geographic range of barley, despite the pronounced clock defect.
Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration
Authors: Hatakeyama Tetsuhiro S. , Kaneko Kunihiko
Published: May 2012

Circadian clocks—ubiquitous in life forms ranging from bacteria to multicellular organisms—often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures, despite the expected Arrhenius form for the reaction coefficient. Observations have shown that the amplitude of the oscillation depends on the temperature but the period does not; this suggests that although not every reaction step is temperature independent, the total system comprising several reactions still exhibits compensation. Here we present a general mechanism for such temperature compensation. Consider a system with multiple activation energy barriers for reactions, with a common enzyme shared across several reaction steps. The steps with the highest activation energy rate-limit the cycle when the temperature is not high. If the total abundance of the enzyme is limited, the amount of free enzyme available to catalyze a specific reaction decreases as more substrates bind to the common enzyme. We show that this change in free enzyme abundance compensates for the Arrhenius-type temperature dependence of the reaction coefficient. Taking the example of circadian clocks with cyanobacterial proteins KaiABC, consisting of several phosphorylation sites, we show that this temperature compensation mechanism is indeed valid. Specifically, if the activation energy for phosphorylation is larger than that for dephosphorylation, competition for KaiA shared among the phosphorylation reactions leads to temperature compensation. Moreover, taking a simpler model, we demonstrate the generality of the proposed compensation mechanism, suggesting relevance not only to circadian clocks but to other (bio)chemical oscillators as well.
Diurnal, localized exposure of phosphatidylserine by rod outer segment tips in wild-type but notItgb5−/−orMfge8−/−mouse retina
Authors: Ruggiero Linda , Connor Mark P. , Chen Jeannie , Langen Ralf , Finnemann Silvia C.
Published: May 2012

In the mammalian retina, life-long renewal of light-sensitive photoreceptor outer segments (POS) involves circadian shedding of distal rod POS tips and their subsequent phagocytosis by the adjacent retinal pigment epithelium (RPE) every morning after light onset. Molecular mechanisms that promote or synchronize POS tip shedding have thus far remained unknown. Here we examined plasma membrane asymmetry of living POS by quantifying surface exposure of the membrane phospholipid phosphatidylserine (PS) using antibodies, annexin V, and pSIVA (polarity-sensitive indicator of viability and apoptosis), an annexin-based biosensor with switchable states of fluorescence. We found that isolated POS particles possess externalized PS, whose blockade or removal reduces their binding and engulfment by RPE in culture. Imaging of live photoreceptors in freshly dissected mouse retina detected PS externalization restricted to POS tips with discrete boundaries. In wild-type mice, frequency of rod tips exposing PS and length of tips with exposed PS peak shortly after light onset. In contrast, PS-marked POS tips do not vary in mice lacking the diurnal phagocytic rhythm of the RPE due to loss of either the phagocytosis receptor αvβ5 integrin, expressed by the RPE but not by photoreceptors, or its extracellular ligand milk fat globule-EGF factor 8 (MFG-E8). These data identify a molecular distinction, localized PS exposure, that is specific to the surface of rod POS tips. Enhanced PS exposure preceding rod shedding and phagocytosis suggests that surface PS promotes these processes. Moreover, our results demonstrate that the diurnal rhythm of PS demarcation of POS tips is not intrinsic to rod photoreceptors but requires activities of the RPE as well.
Rhizobium
–legume symbiosis shares an exocytotic pathway required for arbuscule formation
Authors: Ivanov Sergey , Fedorova Elena E. , Limpens Erik , De Mita Stephane , Genre Andrea , Bonfante Paola , Bisseling Ton
Published: May 2012

Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the
Rhizobium
–legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the
Rhizobium
–legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these
Medicago VAMP72
genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the
Rhizobium
–legume symbiosis.
Mixed-lineage kinase 3 phosphorylates prolyl-isomerase Pin1 to regulate its nuclear translocation and cellular function
Authors: Rangasamy Velusamy , Mishra Rajakishore , Sondarva Gautam , Das Subhasis , Lee Tae Ho , Bakowska Joanna C. , Tzivion Guri , Malter James S. , Rana Basabi , Lu Kun Ping , Kanthasamy Anumantha , Rana Ajay
Published: May 2012

Nuclear protein peptidyl-prolyl isomerase Pin1-mediated prolyl isomerization is an essential and novel regulatory mechanism for protein phosphorylation. Therefore, tight regulation of Pin1 localization and catalytic activity is crucial for its normal nuclear functions. Pin1 is commonly dysregulated during oncogenesis and likely contributes to these pathologies; however, the mechanism(s) by which Pin1 catalytic activity and nuclear localization are increased is unknown. Here we demonstrate that mixed-lineage kinase 3 (MLK3), a MAP3K family member, phosphorylates Pin1 on a Ser138 site to increase its catalytic activity and nuclear translocation. This phosphorylation event drives the cell cycle and promotes cyclin D1 stability and centrosome amplification. Notably, Pin1 pSer138 is significantly up-regulated in breast tumors and is localized in the nucleus. These findings collectively suggest that the MLK3-Pin1 signaling cascade plays a critical role in regulating the cell cycle, centrosome numbers, and oncogenesis.
Unraveling quantum mechanical effects in water using isotopic fractionation
Authors: Markland Thomas E. , Berne B. J.
Published: May 2012

When two phases of water are at equilibrium, the ratio of hydrogen isotopes in each is slightly altered because of their different phase affinities. This isotopic fractionation process can be utilized to analyze water’s movement in the world’s climate. Here we show that equilibrium fractionation ratios, an entirely quantum mechanical property, also provide a sensitive probe to assess the magnitude of nuclear quantum fluctuations in water. By comparing the predictions of a series of water models, we show that those describing the OH chemical bond as rigid or harmonic greatly overpredict the magnitude of isotope fractionation. Models that account for anharmonicity in this coordinate are shown to provide much more accurate results because of their ability to give partial cancellation between inter- and intramolecular quantum effects. These results give evidence of the existence of competing quantum effects in water and allow us to identify how this cancellation varies across a wide-range of temperatures. In addition, this work demonstrates that simulation can provide accurate predictions and insights into hydrogen fractionation.
Early evidence of the ballgame in Oaxaca, Mexico
Authors: Blomster Jeffrey P.
Published: May 2012

As a defining characteristic of Mesoamerican civilization, the ballgame has a long and poorly understood history. Because the ballgame is associated with the rise of complex societies, understanding its origins also illuminates the evolution of socio-politically complex societies. Although initial evidence, in the form of ceramic figurines, dates to 1700 BCE, and the oldest known ballcourt dates to 1600 BCE, the ritual paraphernalia and ideology associated with the game appear around 1400 BCE, the start of the so-called Early Horizon, defined by the spread of Olmec-style symbols across Mesoamerica. Early Horizon evidence of ballgame paraphernalia both identical to and different from that of the Gulf Coast Olmec can be seen on figurines from coastal Chiapas and the central highlands of Mexico, respectively. The Mexican state of Oaxaca, however, has yielded little data on early involvement in the ballgame. The discovery of a ballplayer figurine in the Mixteca Alta region of Oaxaca demonstrates the early participation of this region in the iconography and ideology of the ballgame. In lieu of an actual ballcourt, the focus may have been on the symbolic component of ballplayers and their association with supernatural forces, as part of emerging leaders’ legitimization strategies.
Probing isoform-specific functions of polypeptide GalNAc-transferases using zinc finger nuclease glycoengineered SimpleCells
Authors: Schjoldager Katrine T.-B. G. , Vakhrushev Sergey Y. , Kong Yun , Steentoft Catharina , Nudelman Aaron S. , Pedersen Nis B. , Wandall Hans H. , Mandel Ulla , Bennett Eric P. , Levery Steven B. , Clausen Henrik
Published: May 2012

Our knowledge of the O-glycoproteome [N-acetylgalactosamine (GalNAc) type] is highly limited. The O-glycoproteome is differentially regulated in cells by dynamic expression of a subset of 20 polypeptide GalNAc-transferases (GalNAc-Ts), and methods to identify important functions of individual GalNAc-Ts are largely unavailable. We recently introduced SimpleCells, i.e., human cell lines made deficient in O-glycan extension by zinc finger nuclease targeting of a key gene in O-glycan elongation (Cosmc), which allows for proteome-wide discovery of O-glycoproteins. Here we have extended the SimpleCell concept to include proteome-wide discovery of unique functions of individual GalNAc-Ts. We used the GalNAc-T2 isoform implicated in dyslipidemia and the human HepG2 liver cell line to demonstrate unique functions of this isoform. We confirm that GalNAc-T2–directed site-specific O-glycosylation inhibits proprotein activation of the lipase inhibitor ANGPTL3 in HepG2 cells and further identify eight O-glycoproteins exclusively glycosylated by T2 of which one, ApoC-III, is implicated in dyslipidemia. Our study supports an essential role for GalNAc-T2 in lipid metabolism, provides serum biomarkers for GalNAc-T2 enzyme function, and validates the use of
GALNT
gene targeting with SimpleCells for broad discovery of disease-causing deficiencies in O-glycosylation. The presented glycoengineering strategy opens the way for proteome-wide discovery of functions of GalNAc-T isoforms and their role in congenital diseases and disorders.
Environmental biodiversity, human microbiota, and allergy are interrelated
Authors: Hanski Ilkka , von Hertzen Leena , Fyhrquist Nanna , Koskinen Kaisa , Torppa Kaisa , Laatikainen Tiina , Karisola Piia , Auvinen Petri , Paulin Lars , Mäkelä Mika J. , Vartiainen Erkki , Kosunen Timo U. , Alenius Harri , Haahtela Tari
Published: May 2012

Rapidly declining biodiversity may be a contributing factor to another global megatrend—the rapidly increasing prevalence of allergies and other chronic inflammatory diseases among urban populations worldwide. According to the “biodiversity hypothesis,” reduced contact of people with natural environmental features and biodiversity may adversely affect the human commensal microbiota and its immunomodulatory capacity. Analyzing atopic sensitization (i.e., allergic disposition) in a random sample of adolescents living in a heterogeneous region of 100 × 150 km, we show that environmental biodiversity in the surroundings of the study subjects’ homes influenced the composition of the bacterial classes on their skin. Compared with healthy individuals, atopic individuals had lower environmental biodiversity in the surroundings of their homes and significantly lower generic diversity of gammaproteobacteria on their skin. The functional role of the Gram-negative gammaproteobacteria is supported by in vitro measurements of expression of IL-10, a key anti-inflammatory cytokine in immunologic tolerance, in peripheral blood mononuclear cells. In healthy, but not in atopic, individuals, IL-10 expression was positively correlated with the abundance of the gammaproteobacterial genus
Acinetobacter
on the skin. These results raise fundamental questions about the consequences of biodiversity loss for both allergic conditions and public health in general.
Stoichiometry for binding and transport by the twin arginine translocation system
Authors: Celedon Jose M. , Cline Kenneth
Published: May 2012

Twin arginine translocation (Tat) systems transport large folded proteins across sealed membranes. Tat systems accomplish this feat with three membrane components organized in two complexes. In thylakoid membranes, cpTatC and Hcf106 comprise a large receptor complex containing an estimated eight cpTatC-Hcf106 pairs. Protein transport occurs when Tha4 joins the receptor complex as an oligomer of uncertain size that is thought to form the protein-conducting structure. Here, binding analyses with intact membranes or purified complexes indicate that each receptor complex could bind eight precursor proteins. Kinetic analysis of translocation showed that each precursor-bound site was independently functional for transport, and, with sufficient Tha4, all sites were concurrently active for transport. Tha4 titration determined that ∼26 Tha4 protomers were required for transport of each OE17 (oxygen-evolving complex subunit of 17 kD) precursor protein. Our results suggest that, when fully saturated with precursor proteins and Tha4, the Tat translocase is an ∼2.2-megadalton complex that can individually transport eight precursor proteins or cooperatively transport multimeric precursors.
Female mouse fetal loss mediated by maternal autoantibody
Authors: Wang Li , Zhou Dun , Lee Ji , Niu Haitao , Faust Thomas W. , Frattini Stephen , Kowal Czeslawa , Huerta Patricio T. , Volpe Bruce T. , Diamond Betty
Published: May 2012

Systemic lupus erythematosus (SLE), a disease of women during childbearing years, is characterized by the production of double-stranded DNA antibodies. A subset of these antibodies, present in 40% of patients, cross-reacts with the NR2A and NR2B subunits of the N-methyl-d-aspartate receptor (NMDAR). In this study, we show that, in mouse models, these antibodies cause a loss of female fetus viability by inducing apoptosis of NR2A-expressing neurons within the brainstem late in fetal development; gender specificity derives from a time-dependent increased expression of NR2A in female brainstem or increased vulnerability of female fetal neurons to signaling through NR2A-containing NMDARs. This paradigm is consistent with available data on the sex ratio of live births of women with SLE. It represents a novel mechanism by which maternal autoantibodies can severely affect fetal health in a gender-specific fashion and raises the question of how many maternal antibodies affect brain development or exhibit gender-specific fetal effects.
Gray Mold of Green Shiso (Perilla frutescens), Caused by Botrytis cinerea, in California
Authors: Koike S. T. , Daugovish O.
Published: May 2012

Shiso (Perilla frutescens) is a leafy herb in the Lamiaceae family and is widely used in Japanese and other Asian cuisine for cooking, pickling, oil (from the seeds), and garnish. A number of shiso types are used, though the most common are green shiso (ao-shiso) and red shiso (aka-shiso). In the winter months of 2010 and early spring 2011, a foliar blight disease developed on greenhouse-grown green shiso produced in Ventura County, CA. Initial symptoms were angular, dull green leaf lesions on older foliage. Such lesions often were initiated along leaf edges. As the disease progressed, lesions turned gray green, expanded, and could affect most of the leaf surface. Lesion tissue became dry and papery in texture; signs of a pathogen were not present. Tests for bacterial agents were negative. However, a fungus was consistently isolated from symptomatic leaves. Isolates of this fungus were grown on potato dextrose agar (PDA) in petri plates incubated under fluorescent lights and were identified as Botrytis cinerea (1). On PDA, mycelial growth was gray brown and conidiophores measured 2 mm or longer and were branched at the terminals. Conidia were aseptate, hyaline, ellipsoidal, and measured (6.5–) 8.4 to 9.2 (–12.0) × (6.1–) 6.8 to 8.0 (–9.5) μm. Sclerotia were not present. Pathogenicity of four isolates was tested by spraying conidial suspensions (1 × 105 conidia/ml) until runoff onto sets of potted green and red shiso plants. Each set consisted of six wounded (leaf tips cut) and six unwounded plants. Plants were enclosed in plastic bags for 48 h and then maintained at 22 to 24°C in a greenhouse. After 4 days, leaf lesions developed on both wounded and unwounded leaves of green and red shiso. The resulting symptoms were similar to those observed in commercial production and B. cinerea was recovered from symptomatic tissue. Non-inoculated, wounded, and unwounded red and green shiso plants were sprayed with distilled water and did not develop symptoms. This experiment was conducted two times and results were the same. To our knowledge, this is the first report of gray mold of shiso in the United States caused by B. cinerea. The disease caused significant damage to the shiso crop because symptomatic leaves are unacceptable for market. In 2010, the greenhouse facility that contained the diseased shiso had numerous leaks in the roof; winter rains that occurred during this time therefore resulted in higher free moisture and humidity in the growing area, which likely provided optimum environmental conditions for the pathogen to infect and cause disease on shiso.

Reference: (1) M. B. Ellis and J. M. Waller. CMI Descriptions of Pathogenic Fungi and Bacteria. No. 431, 1974.
First Report of Gray Mold of Strawberry Caused by Botrytis caroliniana in North Carolina
Authors: Fernández-Ortuño D. , Li X. P. , Wang F. , Schnabel G.
Published: May 2012

Gray mold caused by Botrytis spp. is one of the most economically important diseases of cultivated strawberry (Fragaria × ananassa) worldwide. In June 2011, strawberry fruit that was symptomatic of gray mold disease was collected from High Point county in North Carolina. Fruit had brown lesions that enlarged quickly and were covered with green-gray masses of spores followed by a soft rot. To isolate the causal agent, conidia were scraped off the fruit, suspended in 1% Tween 20, spread on water agar amended with 0.1% lactic acid, and emerging colonies were then transferred onto potato dextrose agar (PDA) medium. All but one single-spore colony (designated HP33) were at first colorless and later became gray to brown when the conidiphores and conidia developed on PDA. Isolate HP33 was white to pale gray with short, tufted aerial mycelium, black sclerotia in concentric rings, and did not produce conidia on PDA. Conidia were subhyaline to light brown, smooth, ellipsoid, ovoid or obovoid, and were on average 11.7 × 8.6 μm. The conidiophores were erect, septate, and brown to subhyaline from the base to apex, with swollen basal cell and multiple inflated conidiogenous cells. These morphological features were consistent with Botrytis caroliniana X. P. Li & G. Schnabel sp. nov., a new species isolated recently from blackberry fruit in South Carolina (2). All other single-spore isolates were confirmed to be B. cinerea as described previously (1). To confirm the identity of isolate HP33 to the species level, the necrosis and ethylene-inducing protein 1 (NEP1) was PCR amplified and sequenced by primer pairs NEP1for/NEP1rev as described previously (3). The nucleotide sequence matched the ones published for B. caroliniana (GenBank Accession Nos. JF811593, JF811594, and JF811595). Pathogenicity tests were conducted by inoculating 10 surface-sterilized strawberry fruit with single agar plugs (6 mm in diameter) containing actively growing mycelium; 10 control fruit received agar plugs without mycelium. The inoculated fruit were incubated for 3 days at room temperature in airtight plastic bags and after that developed typical gray mold symptoms. Koch's postulates were fulfilled by the reisolation of B. caroliniana from symptomatic fruit. Control fruit remained healthy. To our knowledge, this is the first report of B. caroliniana on strawberry. It is uncertain whether the new species requires management strategies different from those that control gray mold caused by B. cinerea.

References: (1) D. Fernández-Ortuño et al. Plant Dis. 95:1482, 2011. (2) X. P. Li et al. Mycologia 2012, doi:10.3852/11-218. (3) M. Staats et al. Fungal Genet. Biol. 44:52, 2007.