bluuebunny/crossref_metadata_2025 huggingface dataset:
Nitrogen cycling during the Cretaceous, Cenomanian‐Turonian Oceanic Anoxic Event II
Authors: Junium Christopher K. , Arthur Michael A.
Published: March 2007

Low δ15N values, ranging from +1.2‰ to −3.9‰, and atomic carbon/nitrogen (C/N) ratios of 25–50 are characteristic of “black shales” deposited during the Cenomanian‐Turonian boundary interval and Oceanic Anoxic Event II (OAE II). An observed antithetic relationship between C/N ratios and δ15N could suggest a predominance of terrestrially derived organic matter or a diagenetic control on δ15N variability shifting bulk δ15N values lower. However, Hydrogen Indices (HI) generally >450, and a positive correlation of HI with C/N mitigates against a significant terrestrial organic matter fraction. High C/N values are likely the result preferential degradation of labile, N‐rich compounds during early diagenesis and loss of N as ammonium from sediments through time. A hypothetical model that considers the degradation of a 15N‐enriched labile protein fraction yields only small, 1–2‰ negative shifts in δ15N. However, 15N depletion during diagenesis is contrary to normal isotope kinetics which should result in 15N enrichment of bulk organic matter. Therefore we conclude that the bulk δ15N values in this study reflect primary changes in the nitrogen cycle. The δ15N data support the hypothesis of expanded nitrogen fixation driven by upwelling of nutrient‐nitrogen poor, phosphorus replete waters during OAE II and from the mid‐Cenomanian to Santonian at Demerara Rise. The low δ15N values, which are significantly lower than bulk δ15N values in modern regions where nitrogen fixation is known to be important, probably result from a more significant fraction of dissolved inorganic nitrogen being produced by nitrogen fixation. During the peak of OAE II a marked shift to lower δ15N values is observed. This shift possibly reflects greater utilization of 15N‐depleted ammonium during a chemocline upward excursion (CUE). Dominance of low δ15N values from other periods of more widespread marine anoxia is likely the result of similar processes.
A wavelet investigation of possible orbital influences on past geomagnetic field intensity
Authors: Heslop D.
Published: March 2007

A number of sedimentary records of relative paleointensity have been reported to contain modes of variability that could have been driven by changes in the Earth's orbital or climatic state. Proposed relationships are often based on visual correlation in the time domain or the presence of peaks in relative paleointensity frequency spectra close to those of the orbital components. When discussing hypothesized connections, it is not common for the phase relationship between paleointensity and orbital change to be addressed, so a true mechanistic link cannot be confirmed. The existence of a direct link between records of paleointensity and orbital/climatic variation is tested using the cross‐wavelet transform and squared wavelet coherence. It is found that while all the records show common power at certain periods, the geomagnetic and orbital variations do not exhibit a consistent phase relationship, suggesting there is no direct physical link between them. This interpretation is supported by a lack of significant correlation in the time‐frequency plane between the studied records as measured by the squared wavelet coherence.
Effect of air‐sea coupling in the assessment of CO2‐induced intensification of tropical cyclone activity
Authors: Hasegawa Akira , Emori Seita
Published: March 2007

We compared the CCSR/NIES/FRCGC coupled general circulation model (GCM) with the atmospheric GCM under control and future warmed conditions to investigate the effects of air‐sea coupling on tropical cyclone properties, such as intensity and precipitation. Air‐sea coupling suppresses tropical cyclone activity, because water vapor supply is reduced by sea surface temperature (SST) decrease due to the cold wakes under the tropical cyclones. Air‐sea coupling tends to suppress tropical cyclone activity to a greater extent in a warmer world, because of the higher base SST and a larger decrease in SST due to the enhanced thermal stratification of the upper ocean. The overestimation of tropical cyclone activity in atmospheric models is more significant for extreme variables such as maximum precipitation than for averaged variables. Therefore, changes in tropical cyclone activity due to global warming based on atmosphere‐only models may be overestimated, especially for extreme events.
Vertical distribution of hydrogen at high northern latitudes on Mars: The Mars Odyssey Neutron Spectrometer
Authors: Feldman W. C. , Mellon M. T. , Gasnault O. , Diez B. , Elphic R. C. , Hagerty J. J. , Lawrence D. J. , Maurice S. , Prettyman T. H.
Published: March 2007

Neutron leakage currents measured using the Mars Odyssey Neutron Spectrometer are used to develop a two‐layer model of the distribution of hydrogen (here parameterized as water‐equivalent hydrogen, WEH) at high northern latitudes. The WEH abundance in the upper layer, Wup, was found to range between 1% and about 5%. The maximum value of the apparent thickness, D, of this upper layer peaks at about 60° latitude, giving the appearance of zonal bands of enhanced D in both hemispheres. This maximum is consistent with an expected transition from WEH contained solely in hydrous minerals at lower latitudes, to WEH contained both in the forms of water ice and water of hydration at high latitudes. A strong anti‐correlation between the WEH concentration in the lower layer and apparent depth, D, at high latitudes is observed and may provide clues to the origin of these deposits.
Energetic electron acceleration in the downstream reconnection outflow region
Authors: Imada S. , Nakamura R. , Daly P. W. , Hoshino M. , Baumjohann W. , Mühlbachler S. , Balogh A. , Rème H.
Published: March 2007

Energetic electrons in an earthward reconnection outflow region have been observed by Cluster/Research with Adaptive Particle Imaging Detectors. We found a good correlation between the energetic electron enhancement and a normal magnetic field (Bz) enhancement within a 0.25‐s time resolution. The large normal magnetic field is thought to be associated with magnetic reconnection because the negative/positive Bz reversal observed during the fast proton tailward/earthward flow reversal is a good indicator of magnetic reconnection. Using the four‐spacecraft Cluster, we can clearly see that this large positive Bz structure propagates in the earthward direction. Furthermore, we find that the energy spectrum of the energetic electrons becomes harder toward the downstream region. A negative Bz enhancement is also observed. The intensity of energetic electron enhancement associated with the negative Bz enhancement is weaker than that associated with the positive one. To discuss the temporal and spatial profile of energetic electron acceleration in the magnetic reconnection region, we determined the spacecraft position in the temporally evolving magnetic structures of reconnection. Our observation clearly indicates second‐step acceleration, in addition to X line acceleration, of energetic electrons in the downstream reconnection outflow region.
Erosive dynamics of channels incised by subsurface water flow
Authors: Lobkovsky Alexander E. , Smith Braunen E. , Kudrolli Arshad , Mohrig David C. , Rothman Daniel H.
Published: March 2007

We propose a dynamical model for channels incised into an erodible bed by subsurface water flow. The model is validated by the time‐resolved topographic measurements of channel growth in a laboratory‐scale experiment. Surface heights in the experiment are measured via a novel laser‐aided imaging technique. The erosion rate in the model is composed of diffusive and advective components as well as a simple driving term due to the seeping water. Steady driving conditions may exist whenever channels are incised into a flat and level erodible bed by a water table replenished via steady (on average) rainfall. Under such steady driving conditions, the model predicts an asymptotically self‐similar growing shape for the channel transects. Conversely, given a transect shape that evolved under steady driving conditions and an estimate of the erosion rate at the bottom of the channel, granular transport coefficients can be inferred from the static channel shape. We report an estimate of these transport coefficients for a system of ravines incised into unconsolidated sand in the Apalachicola River basin, Florida.
IUPAC-NIST Solubility Data Series. 82: Alcohols with Water—Revised and Updated: Part 2. C5 Alcohols with Water
Authors: Goral Marian , Wisniewska-Goclowska Barbara
Published: March 2007

The mutual solubility and related liquid–liquid equilibria of C5 alcohols with water are exhaustively and critically reviewed. Reports of experimental determination of solubility in ten chemically distinct binary systems for which data appeared in the primary literature prior to the end of 2004 are compiled. For eight systems sufficient data are available to allow critical evaluation. All data are expressed as mass percent and mole fraction as well as the originally reported units. In addition to the standard evaluation criteria used throughout the Solubility Data Series, a new method based on the simultaneous evaluation of the all experimental data, which includes liquid–liquid equilibrium correlation and prediction.
The effect of particle size on the effective thermal conductivity of Al2O3-water nanofluids
Authors: Li Calvin H. , Peterson G. P.
Published: March 2007

A steady-state method was used to evaluate the effective thermal conductivity of Al2O3∕distilled water nanofluids with nanoparticle diameters of 36 and 47nm. Tests were conducted over a temperature range of 27–37°C for volume fractions ranging from 0.5% to 6.0%. The thermal conductivity enhancement of the two nanofluids demonstrated a nonlinear relationship with respect to temperature, volume fraction, and nanoparticle size, with increases in the volume fraction, temperature, and particle size all resulting in an increase in the measured enhancement. The most significant finding was the effect that variations in particle size had on the effective thermal conductivity of the Al2O3∕distilled water nanofluids. The largest enhancement difference observed occurred at a temperature of approximately 32°C and at a volume fraction of between 2% and 4%. The experimental results exhibited a peak in the enhancement factor in this range of volume fractions for the temperature range evaluated, which implies that an optimal size exists for different nanoparticle and base fluid combinations. This phenomenon can be neither predicted nor explained using the theoretical models currently available in the literature.
Exotic affinities under Debye plasma
Authors: Bhattacharyya S. , Sil A. N. , Mukherjee T. K. , Mukherjee P. K.
Published: March 2007

Muonic affinities of the exotic system π+μ− have been calculated variationally using a general three-body formalism. The system is found to be stable in the ground state under Coulomb coupling. The stability of this system under an external plasma environment has been analyzed using multiterm correlated basis sets of Hylleraas type. The effect of external plasma has been incorporated using the standard Debye screening model. The system tends toward gradual instability under the increased strength of the plasma, and the affinities have been found to decrease gradually and systematically. The effect of correlation on the exotic affinities has been analyzed in detail. The effect of angular correlation on exotic affinities is found to be around 40–80%.
Multipactor in rectangular waveguides
Authors: Semenov V. E. , Rakova E. I. , Anderson D. , Lisak M. , Puech J.
Published: March 2007

Multipactor inside a rectangular waveguide is studied using both an analytical approach and numerical simulations. Particular attention is given to an analysis of the role of such effects as the velocity spread of secondary emitted electrons and the action of the rf magnetic field on the electron motion. Conventional resonance theory is shown to give correct predictions for the multipactor threshold in cases where the height of the waveguide is very small and first order resonance multipactor dominates. In cases of higher order resonances, an accurate prediction of the multipactor threshold requires that the spread of the normal component of the electron emission velocity is taken into account. Furthermore, the spread of the tangential component of the electron emission velocity and the action of the rf magnetic field are shown to be very important when the waveguide height exceeds a certain critical value, which depends on the waveguide width. A new theory is developed for predicting the multipactor threshold at higher order resonances and this theory is confirmed by numerical simulations.
Direct measurement of slip length in electrolyte solutions
Authors: Huang Peter , Breuer Kenneth S.
Published: March 2007

Electrokinetic effects and electrostatic repulsion between tracer particles and glass surface have both been proposed as possible sources that would lead to false slip results obtained from velocimetry-based measurements. Using a three-dimensional total internal reflection velocimetry technique, we address such a concern by comparing the measured slip lengths between nonionic solutions and electrolyte solutions whose ionic concentrations have been predicted to reduce the electricity-induced slip effect to a submolecular level. It is observed that the presence of electrolytes has no effect on the measured slip lengths, suggesting that the observed slip velocities are most likely not due to electrostatic and electrokinetic effects, but are consequences of true boundary slip.
Predissociation of Bi2 A(u+), v′=21–39
Authors: Dolezal Michael W. , Perram Glen P.
Published: March 2007

Collisionless lifetimes for Bi2 A(0u+), v′=20–39, J′⩽105 have been measured using pulsed laser induced fluorescence techniques to investigate the effects of predissociation. The observed predissociation rates, Γ=kpd(v′)J(J+1), are quite rapid, ranging from kpd=1.53×102s−1 for v′=21to1.5×105s−1 for v′=39. The dense Bi2(A→X) spectrum required both traditional lifetime measurements and synthetic spectrum fits to laser excitation spectra to determine the full range of observed rates. A single, repulsive potential responsible for the observed A-state predissociation could not be identified to adequately describe the vibrational dependence of the predissociation rates.
New instrument for tribocharge measurement due to single particle impacts
Authors: Watanabe Hideo , Ghadiri Mojtaba , Matsuyama Tatsushi , Long Ding Yu , Pitt Kendal G.
Published: March 2007

During particulate solid processing, particle-particle and particle-wall collisions can generate electrostatic charges. This may lead to a variety of problems ranging from fire and explosion hazards to segregation, caking, and blocking. A fundamental understanding of the particle charging in such situations is therefore essential. For this purpose we have developed a new device that can measure charge transfer due to impact between a single particle and a metal plate. The device consists of an impact test system and two sets of Faraday cage and preamplifier for charge measurement. With current amplifiers, high-resolution measurements of particle charges of approximately 1 and 10fC have been achieved before and after the impact, respectively. The device allows charge measurements of single particles with a size as small as ∼100μm impacting on the target at different incident angles with a velocity up to about 80m∕s. Further analyses of the charge transfer as a function of particle initial charge define an equilibrium charge, i.e., an initial charge level prior to impact for which no net charge transfer would occur as a result of impact.
Ferroelectric and switching behavior of poly(vinylidene fluoride-trifluoroethylene) copolymer ultrathin films with polypyrrole interface
Authors: Xu Haisheng , Zhong Juhua , Liu Xiaobing , Chen Jianhua , Shen Dong
Published: March 2007

Thin polypyrrole-poly(styrene sulfonate) acid film is employed as interface layers between both bottom and top metal electrodes of a ferroelectric polymer, poly(vinylidene fluoride-trifluoroethylene) copolymer capacitor. The sandwiched structure Titanium∕polypyrrole-poly(styrene sulfonate)∕poly(vinylidene fluoride-trifluoroethylene)∕polypyrrole-poly(styrene sulfonate)∕titanium shows prominent ferroelectric properties even as the thickness of P(VDF-TrFE) film is down to 500Å. The coercive voltage as low as 2.6V is obtained with a remanent polarization of 86mC∕m2 and a switching time of 30μs. The cell remains good ferroelectric properties at 60°C, which is the operating temperature for many electronics. Moreover, the sandwiched structure shows excellent data retention, after more than 1×107 of switching cycles, the remanent polarization remains as high as 69mC∕m2. The soft conductive polymer electrodes not only increase the crystallinity but also enhance the crystal dipole orientation comparing with the conventionally used metal electrodes.
Low-threshold and high efficiency lasing upon band-edge excitation in a cholesteric liquid crystal
Authors: Matsuhisa Yuko , Huang Yuhua , Zhou Ying , Wu Shin-Tson , Ozaki Ryotaro , Takao Yuuki , Fujii Akihiko , Ozaki Masanori
Published: March 2007

A low threshold and high efficiency laser based on dye-doped cholesteric liquid crystals (CLCs) is demonstrated using an input excitation with the same handedness of circular polarization as the helical structure of the sample at the shorter wavelength band edge of the reflection band. The responsible mechanism originates from the dramatic increase of the optical density of state (DOS) at the band edges. The calculated DOS of the CLC system confirms the authors’ experimental results.
Continuous-wave terahertz imaging with a hybrid system
Authors: Löffler Torsten , May Thilo , am Weg Christian , Alcin Ali , Hils Bernd , Roskos Hartmut G.
Published: March 2007

The authors have developed a hybrid system for coherent raster-scan imaging at 0.6THz. It combines a high-power electronic source (a multiplied Gunn emitter) with a femtosecond Ti:sapphire laser in order to achieve a high dynamic range via electro-optic detection. The single-scan dynamic range of 60db at a lock-in time constant of 10ms is sufficient to permit detection of scattered terahertz radiation in addition to specularly reflected/transmitted light. Active synchronization of the electronic source and the laser is not needed because of the remarkably low jitter between the two radiation sources.
Drug target interaction energies by the kernel energy method in aminoglycoside drugs and ribosomal A site RNA targets
Authors: Huang Lulu , Massa Lou , Karle Jerome
Published: March 2007

It is possible to use the full power of
ab initio
quantum mechanics in application to the interaction of drugs and their molecular targets. This idea had barely been realized until recently, because of the well known growth in computational difficulty of the use of quantum mechanics, with the number of atoms in the molecule to be studied. Because the biochemical molecules of medicinal chemistry are so often large, containing thousands or even tens of thousands of atoms, the computational difficulty of the full quantum problem had been prohibitive. Two things have happened, however, that change this perspective: (
i
) the advances of parallel supercomputers, and (
ii
) the discovery of a quantum formalism called quantum crystallography and the use of quantum kernels, a method that is well suited for parallel computation. Such advances would allow the quantum mechanical
ab initio
calculation of the molecular energy of peptides, proteins, DNA, and RNA, obtaining results of high accuracy. In this approach the computational difficulty of representing a molecule increases only modestly with the number of atoms. The calculations are simplified by adopting an acceptable approximation that allows a full biological molecule to be represented by smaller “kernels” of atoms. These results suggest that problems of medicinal chemistry, such as the rational design of drugs, may be illuminated by quantum mechanical analysis. The general case is illustrated by specific examples, namely, the HF/STO-3G calculations of three aminoglycoside drugs that attach to ribosomal A-site RNA nucleotide targets.
Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same molecular signaling module
Authors: Wylie Dennis C. , Das Jayajit , Chakraborty Arup K.
Published: March 2007

Activation of T helper cells is necessary for the adaptive immune response to pathogens, and spurious activation can result in organ-specific autoimmunity (e.g., multiple sclerosis). T cell activation is initiated by membrane-proximal signaling that is predicated on the binding of the T cell receptor expressed on the T cell surface to peptide major histocompatibility complex (pMHC) molecules presented on the surface of antigen-presenting cells. These signaling processes regulate diverse outcomes, such as the ability of T cells to discriminate sensitively between stimulatory pMHC molecules and those that are characteristic of “self,” and the phenomenon of antagonism (wherein the presence of certain pMHC molecules impairs T cell receptor signaling). We describe a molecular model for membrane-proximal signaling in T cells from which these disparate observations emerge as two sides of the same coin. This development of a unified mechanism that is consistent with diverse data would not have been possible without explicit consideration of the stochastic nature of the pertinent biochemical events. Our studies also reveal that certain previously proposed concepts are not dueling ideas but rather are different stimuli-dependent manifestations of a unified molecular model for membrane-proximal signaling. This model may provide a conceptual framework for further investigations of early events that regulate T cell activation in response to self and foreign antigens and for the development of intervention protocols to inhibit aberrant signaling.
Inorganic nitrogen availability after severe stand-replacing fire in the Greater Yellowstone ecosystem
Authors: Turner Monica G. , Smithwick Erica A. H. , Metzger Kristine L. , Tinker Daniel B. , Romme William H.
Published: March 2007

Understanding ecosystem processes as they relate to wildfire and vegetation dynamics is of growing importance as fire frequency and extent increase throughout the western United States. However, the effects of severe, stand-replacing wildfires are poorly understood. We studied inorganic nitrogen pools and mineralization rates after stand-replacing wildfires in the Greater Yellowstone Ecosystem, Wyoming. After fires that burned in summer 2000, soil ammonium concentration peaked in 2001 (33 mg NH4-N· kgsoil−1); soil nitrate increased subsequently (2.7 mg NO3-N·kgsoil−1in 2003) but was still low. However, annual net ammonification rates were largely negative from 2001 to 2004, indicating ammonium depletion. Thus, although net nitrification rates were positive, annual net nitrogen mineralization (net ammonification plus net nitrification) remained low. Aboveground net primary production (ANPP) increased from 0.25 to 1.6 Mg·ha−1·yr−1from 2001 to 2004, but variation in ANPP among stands was not related to net nitrogen mineralization rates. Across a broader temporal gradient (stand age zero to >250 yr), negative rates of net annual ammonification were especially pronounced in the first postfire year. Laboratory incubations using15N isotope pool dilution revealed that gross production of ammonium was reduced and ammonium consumption greatly exceeded gross production during the initial postfire years. Our results suggest a microbial nitrogen sink for several years after severe, stand-replacing fire, confirming earlier hypotheses about postdisturbance succession and nutrient cycling in cold, fire-dominated coniferous forests. Postfire forests in Yellowstone seem to be highly conservative for nitrogen, and microbial immobilization of ammonium plays a key role during early succession.
Spliced leader RNA trans-splicing in dinoflagellates
Authors: Zhang Huan , Hou Yubo , Miranda Lilibeth , Campbell David A. , Sturm Nancy R. , Gaasterland Terry , Lin Senjie
Published: March 2007

Through the analysis of hundreds of full-length cDNAs from fifteen species representing all major orders of dinoflagellates, we demonstrate that nuclear-encoded mRNAs in all species, from ancestral to derived lineages, are trans-spliced with the addition of the 22-nt conserved spliced leader (SL), DCCGUAGCCAUUUUGGCUCAAG (D = U, A, or G), to the 5′ end. SL trans-splicing has been documented in a limited but diverse number of eukaryotes, in which this process makes it possible to translate polycistronically transcribed nuclear genes. In SL trans-splicing, SL-donor transcripts (SL RNAs) contain two functional domains: an exon that provides the SL for mRNA and an intron that contains a spliceosomal (Sm) binding site. In dinoflagellates, SL RNAs are unusually short at 50–60 nt, with a conserved Sm binding motif (AUUUUGG) located in the SL (exon) rather than the intron. The initiation nucleotide is predominantly U or A, an unusual feature that may affect capping, and hence the translation and stability of the recipient mRNA. The core SL element was found in mRNAs coding for a diverse array of proteins. Among the transcripts characterized were three homologs of Sm-complex subunits, indicating that the role of the Sm binding site is conserved, even if the location on the SL is not. Because association with an Sm-complex often signals nuclear import for U-rich small nuclear RNAs, it is unclear how this Sm binding site remains on mature mRNAs without impeding cytosolic localization or translation of the latter.
Evolving the lock to fit the key to create a family of G protein-coupled receptors potently activated by an inert ligand
Authors: Armbruster Blaine N. , Li Xiang , Pausch Mark H. , Herlitze Stefan , Roth Bryan L.
Published: March 2007

We evolved muscarinic receptors in yeast to generate a family of G protein-coupled receptors (GPCRs) that are activated solely by a pharmacologically inert drug-like and bioavailable compound (clozapine-
N
-oxide). Subsequent screening in human cell lines facilitated the creation of a family of muscarinic acetylcholine GPCRs suitable for
in vitro
and
in situ
studies. We subsequently created lines of telomerase-immortalized human pulmonary artery smooth muscle cells stably expressing all five family members and found that each one faithfully recapitulated the signaling phenotype of the parent receptor. We also expressed a G
i
-coupled designer receptor in hippocampal neurons (hM
4
D) and demonstrated its ability to induce membrane hyperpolarization and neuronal silencing. We have thus devised a facile approach for designing families of GPCRs with engineered ligand specificities. Such reverse-engineered GPCRs will prove to be powerful tools for selectively modulating signal-transduction pathways
in vitro
and
in vivo
.
M-Cadherin Activates Rac1 GTPase through the Rho-GEF Trio during Myoblast Fusion
Authors: Charrasse Sophie , Comunale Franck , Fortier Mathieu , Portales-Casamar Elodie , Debant Anne , Gauthier-Rouvière Cécile
Published: March 2007

Cadherins are transmembrane glycoproteins that mediate Ca2+-dependent homophilic cell–cell adhesion and play crucial role during skeletal myogenesis. M-cadherin is required for myoblast fusion into myotubes, but its mechanisms of action remain unknown. The goal of this study was to cast some light on the nature of the M-cadherin–mediated signals involved in myoblast fusion into myotubes. We found that the Rac1 GTPase activity is increased at the time of myoblast fusion and it is required for this process. Moreover, we showed that M-cadherin–dependent adhesion activates Rac1 and demonstrated the formation of a multiproteic complex containing M-cadherin, the Rho-GEF Trio, and Rac1 at the onset of myoblast fusion. Interestingly, Trio knockdown efficiently blocked both the increase in Rac1-GTP levels, observed after M-cadherin–dependent contact formation, and myoblast fusion. We conclude that M-cadherin–dependent adhesion can activate Rac1 via the Rho-GEF Trio at the time of myoblast fusion.
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
Authors: Parra Genis , Bradnam Keith , Korf Ian
Published: March 2007

Motivation: The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge. Obtaining a set of well-characterized genes is a basic requirement in the initial steps of any genome annotation process. An accurate set of genes is needed in order to learn about species-specific properties, to train gene-finding programs, and to validate automatic predictions. Unfortunately, many new genome projects lack comprehensive experimental data to derive a reliable initial set of genes.

Results: In this study, we report a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data. We define a set of conserved protein families that occur in a wide range of eukaryotes, and present a mapping procedure that accurately identifies their exon–intron structures in a novel genomic sequence. CEGMA includes the use of profile-hidden Markov models to ensure the reliability of the gene structures. Our procedure allows one to build an initial set of reliable gene annotations in potentially any eukaryotic genome, even those in draft stages.

Availability: Software and data sets are available online at http://korflab.ucdavis.edu/Datasets.

Contact:  ifkorf@ucdavis.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
rh_tsp_map3.0: end-to-end radiation hybrid mapping with improved speed and quality control
Authors: Schäffer Alejandro A. , Rice Edward Stallknecht , Cook William , Agarwala Richa
Published: March 2007

Summary:  rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps.

Availability:  rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm

Contact:  richa@helix.nih.gov, FAX: 301-480-2288. (Please send email concurrently with any fax.)
Participation of Endomembrane Cation/H+ Exchanger AtCHX20 in Osmoregulation of Guard Cells
Authors: Padmanaban Senthilkumar , Chanroj Salil , Kwak June M. , Li Xiyan , Ward John M. , Sze Heven
Published: March 2007

Guard cell movement is induced by environmental and hormonal signals that cause changes in turgor through changes in uptake or release of solutes and water. Several transporters mediating these fluxes at the plasma membrane have been characterized; however, less is known about transport at endomembranes. CHX20, a member of a poorly understood cation/H+ exchanger gene family in Arabidopsis (Arabidopsis thaliana), is preferentially and highly expressed in guard cells as shown by promoter∷β-glucuronidase activity and by whole-genome microarray. Interestingly, three independent homozygous mutants carrying T-DNA insertions in CHX20 showed 35% reduction in light-induced stomatal opening compared to wild-type plants. To test the biochemical function of CHX20, cDNA was expressed in a yeast (Saccharomyces cerevisiae) mutant that lacks Na+(K+)/H+ antiporters (Δnhx1 Δnha1 Δkha1) and plasma membrane Na+ pumps (Δena1-4). Curiously, CHX20 did not enhance tolerance of mutants to moderate Na+ or high K+ stress. Instead, it restored growth of the mutant on medium with low K+ at slightly alkaline pH, but had no effect on growth at acidic pH. Green fluorescent protein-tagged CHX20 expressed in mesophyll protoplasts was localized mainly to membranes of the endosomal system. Furthermore, light-induced stomatal opening of the Arabidopsis mutants was insensitive to external pH and was impaired at high KCl. The results are consistent with the idea that, in exchanging K+ for H+, CHX20 maintains K+ homeostasis and influences pH under certain conditions. Together, these results provide genetic and biochemical evidence that one CHX protein plays a critical role in osmoregulation through K+ fluxes and possibly pH modulation of an active endomembrane system in guard cells.
Molecular Modeling and Site-Directed Mutagenesis Reveal the Benzylisoquinoline Binding Site of the Short-Chain Dehydrogenase/Reductase Salutaridine Reductase
Authors: Geissler René , Brandt Wolfgang , Ziegler Jörg
Published: March 2007

Recently, the NADPH-dependent short-chain dehydrogenase/reductase (SDR) salutaridine reductase (E.C. 1.1.1.248) implicated in morphine biosynthesis was cloned from Papaver somniferum. In this report, a homology model of the Papaver bracteatum homolog was created based on the x-ray structure of human carbonyl reductase 1. The model shows the typical α/β-folding pattern of SDRs, including the four additional helices αF′-1 to αF′-4 assumed to prevent the dimerization of the monomeric short-chain dehyrogenases/reductases. Site-directed mutagenesis of asparagine-152, serine-180, tyrosine-236, and lysine-240 resulted in enzyme variants with strongly reduced performance or inactive enzymes, showing the involvement of these residues in the proton transfer system for the reduction of salutaridine. The strong preference for NADPH over NADH could be abolished by replacement of arginine residues 44 and 48 by glutamic acid, confirming the interaction between the arginines and the 2′-phosphate group. Docking of salutaridine into the active site revealed nine amino acids presumably responsible for the high substrate specificity of salutaridine reductase. Some of these residues are arranged in the right position by an additional αE′ helix, which is not present in SDRs analyzed so far. Enzyme kinetic data from mutagenic replacement emphasize the critical role of these residues in salutaridine binding and provide the first data on the molecular interaction of benzylisoquinoline alkaloids with enzymes.
PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins
Authors: Richardt Sandra , Lang Daniel , Reski Ralf , Frank Wolfgang , Rensing Stefan A.
Published: March 2007

Diversification of transcription-associated protein (TAP) families during land plant evolution is a key process yielding increased complexity of plant life. Understanding the evolutionary relationships between these genes is crucial to gain insight into plant evolution. We have determined a substantial set of TAPs that are focused on, but not limited to, land plants using PSI-BLAST searches and subsequent filtering and clustering steps. Phylogenies were created in an automated way using a combination of distance and maximum likelihood methods. Comparison of the data to previously published work confirmed their accuracy and usefulness for the majority of gene families. Evidence is presented that the flowering plant apical stem cell regulator WUSCHEL evolved from an ancestral homeobox gene that was already present after the water-to-land transition. The presence of distinct expanded gene families, such as COP1 and HIT in moss, is discussed within the evolutionary backdrop. Comparative analyses revealed that almost all angiosperm transcription factor families were already present in the earliest land plants, whereas many are missing among unicellular algae. A global analysis not only of transcription factors but also of transcriptional regulators and novel putative families is presented. A wealth of data about plant TAP families and all data accrued throughout their automated detection and analysis are made available via the PlanTAPDB Web interface. Evolutionary relationships of these genes are readily accessible to the nonexpert at a mouse-click. Initial analyses of selected gene families revealed that PlanTAPDB can easily be exerted for knowledge discovery.
The N-Terminal Double-Stranded RNA Binding Domains ofArabidopsisHYPONASTIC LEAVES1 Are Sufficient for Pre-MicroRNA Processing
Authors: Wu Feijie , Yu Lin , Cao Wenguang , Mao Yanfei , Liu Zhongyuan , He Yuke
Published: March 2007

Arabidopsis thaliana HYPONASTIC LEAVES1 (HYL1) is a microRNA (miRNA) biogenesis protein that contains two N-terminal double-stranded RNA binding domains (dsRBDs), a putative nuclear localization site (NLS), and a putative protein–protein interaction domain. The interaction of HYL1 with DICER-LIKE1 is important for the efficient and precise processing of miRNA primary transcripts in plant miRNA biogenesis. To define the roles of the various domains of HYL1 in miRNA processing and the miRNA-directed phenotype, we transferred a series of HYL1 deletion constructs into hyl1 null mutants. The N-terminal region containing dsRBD1 and dsRBD2 completely rescued the mutant phenotype of hyl1, triggering the accumulation of miR166 and miR160 and resulting in reduced mRNA levels of the targeted genes. In vivo biochemical analysis of the HYL1-containing complexes from the transgenic plants revealed that the N-terminal dsRBDs of HYL1 were sufficient for processing miRNA precursors and the generation of mature miRNA. Transient and stable expression analysis demonstrated that the putative NLS domain was indeed the nuclear localization signal, whereas the N-terminal region containing the dsRBDs was not restricted to the nucleus. We suggest that the N-terminal dsRBDs fulfill the function of the whole HYL1 and thus play an essential role in miRNA processing and miRNA-directed silencing of targeted genes.
Single Gene–Mediated Shift in Pollinator Attraction inPetunia
Authors: Hoballah Maria Elena , Gübitz Thomas , Stuurman Jeroen , Broger Larissa , Barone Mario , Mandel Therese , Dell'Olivo Alexandre , Arnold Maeva , Kuhlemeier Cris
Published: March 2007

Animal-mediated pollination is essential in plant reproductive biology and is often associated with pollination syndromes, sets of floral traits, such as color, scent, shape, or nectar content. Selection by pollinators is often considered a key factor in floral evolution and plant speciation. Our aim is the identification and characterization of the genetic changes that caused the evolution of divergent pollination syndromes in closely related plant species. We focus on ANTHOCYANIN2 (AN2), a well-defined myb-type transcription factor that is a major determinant of flower color variation between Petunia integrifolia and Petunia axillaris. Analysis of sequence variation in AN2 in wild P. axillaris accessions showed that loss-of-function alleles arose at least five times independently. DNA sequence analysis was complemented by functional assays for pollinator preference using genetic introgressions and transgenics. These results show that AN2 is a major determinant of pollinator attraction. Therefore, changes in a single gene cause a major shift in pollination biology and support the notion that the adaptation of a flowering plant to a new pollinator type may involve a limited number of genes of large effect. Gene identification and analysis of molecular evolution in combination with behavioral and ecological studies can ultimately unravel the evolutionary genetics of pollination syndromes.
Modern management of haemophilic arthropathy
Authors: Leslie Raffini , Catherine Manno
Published: March 2007

Currently available factor concentrates for treatment of patients with haemophilia are virally inactivated or are made by recombinant technology and their broad use in developed nations has resulted in the dramatic elimination of the treatment‐related viral illnesses that decimated the haemophilia community in the late 20th century. The major morbidity experienced by patients with haemophilia today is joint disease, a result of repeated bleeding episodes into joint spaces. Although administration of factor concentrates to prevent bleeding has been demonstrated to prevent haemophilic joint disease when applied assiduously, repeated bleeding episodes induce synovitis that is irreversible and may progress despite subsequent prophylaxis. Surgical and nuclear medicine interventions are available to reduce the pain of haemophilic arthropathy and to reduce further bleeding episodes. Patients with high titre inhibitors are at great risk for the development of joint disease and present the greatest therapeutic challenges when joint surgery is needed.
The pathogenesis of transfusion‐related acute lung injury (TRALI)
Authors: Bux Jürgen , Sachs Ulrich J. H.
Published: March 2007

In recent years, transfusion‐related acute lung injury (TRALI) has developed from an almost unknown transfusion reaction to the most common cause of transfusion‐related major morbidities and fatalities. A clinical definition of TRALI was established in 2004, based on acute respiratory distress, non‐cardiogenic lung oedema temporal association with transfusion and hypoxaemia. Histological findings reveal lung oedema, capillary leucostasis and neutrophil extravasation. However, the pathogenesis of TRALI remains controversial. Leucocyte antibodies, present in fresh frozen plasma and platelet concentrates from multiparous donors, and neutrophil priming agents released in stored cellular blood components have been considered to be causative. As neutrophils and endothelial cells are pivotal in the pathogenesis of TRALI, a threshold model was established to try to unify the various reported findings on pathogenesis. This model comprises the priming of neutrophils and/or endothelium by the patient's co‐morbidity, neutrophil and/or endothelial cell activation by the transfused blood component, and the severity of the TRALI reaction.
Unexplained anaemia in older persons is characterised by low erythropoietin and low levels of pro‐inflammatory markers
Authors: Ferrucci Luigi , Guralnik Jack M. , Bandinelli Stefania , Semba Richard D. , Lauretani Fulvio , Corsi Annamaria , Ruggiero Carmelinda , Ershler William B. , Longo Dan L.
Published: March 2007

Epidemiological studies report that a third of the cases of anaemia in older persons is unexplained. We compared erythropoietin (EPO), inflammatory markers and major comorbidities between older subjects with normal haemoglobin levels and those with different aetiologic forms of anaemia, including unexplained anaemia. Participants were a representative sample of 964 persons aged ≥65 years, with no evidence of bleeding, complete blood tests, and a complete blood count within 6 h of phlebotomy. Anaemia was defined as haemoglobin <130 g/l in men and 120 g/l in women, and classified as a result of chronic kidney disease, iron deficiency, chronic disease and B12/folate deficiency anaemia, or unexplained anaemia based on standard criteria. Of the 124 anaemic participants, 42 (36·8%) had unexplained anaemia. Participants with anaemia of chronic diseases had significantly higher interleukin‐6 (IL‐6) and C‐reactive protein (CRP) levels, while those with unexplained anaemia had significantly lower CRP than non‐anaemic controls. Iron deficiency anaemia was characterised by significantly higher EPO levels compared with other types of anaemia and normal haemoglobin, B12 and/or folate deficiency. Unexplained anaemia was characterised by unexpectedly low EPO and low lymphocyte count. Unexplained anaemia is associated with reduced kidney EPO response, low levels of pro‐inflammatory markers and low lymphocyte counts.
An interphase fluorescence in situ hybridisation assay for the detection of 3q26.2/EVI1 rearrangements in myeloid malignancies
Authors: Bobadilla Dolores , Enriquez Elmon L. , Alvarez Georgina , Gaytan Popsie , Smith David , Slovak Marilyn L.
Published: March 2007

Chromosome rearrangements involving band 3q26.2 are associated with myeloid malignancies, aberrant expression of the human ecotropic virus integration site‐1 (EVI1) gene, an unfavourable prognosis and an aggressive clinical course. The 3q26.2 rearrangements are characteristically heterogeneous and typically difficult to detect in poor quality metaphases. To develop a dual‐colour fluorescence in situ hybridisation (FISH) assay for the detection of 3q26.2/EVI1 aberrations, a series of 10 BAC clones corresponding to the EVI1 gene region were systematically evaluated and narrowed down to two probe sets; one probe set encompassed the EVI1 gene extending centromeric, while the second probe set covered the EVI1 gene and extends telomeric. Both probe sets were evaluated on 35 patient samples with cytogenetically defined 3q26.2 rearrangements collected at various treatment time points, the inv(3)(q21q26.2) Kasumi‐4 cell line, and 10 known negative samples. The two‐probe set strategy identified all samples, despite the vast breakpoint heterogeneity observed. In samples from acute myeloid leukaemia and myelodysplastic syndrome cases, the majority of inversion breakpoints were 3′ to EVI1 whereas 3q26.2 translocation breakpoints frequently mapped 5′ to EVI1. However, two 3q26.2 translocation samples had breakpoints 3′ to EVI1. Most inv(3q) chronic myeloid leukaemia samples showed breakpoints within the EVI1 gene. This study demonstrated that, despite the extensive breakpoint heterogeneity observed with 3q26.2 aberrations, this FISH strategy is effective for the detection of 3q26.2 abnormalities in myeloid malignancies.
A dose‐response study of hormone replacement in young hypogonadal women: effects on intima media thickness and metabolism
Authors: Ostberg Julia E. , Storry Clare , Donald Ann E. , Attar M Javad Hosseinzadeh , Halcox Julian P. J. , Conway Gerard S.
Published: March 2007

Objective  Young hypogonadal women appear to have an increased risk of cardiovascular disease. We studied the influence of increasing doses of hormone replacement therapy (HRT) on markers of metabolism and vascular physiology.

Design  Nine‐month sequential dose‐ranging study.

Patients  A total of 25 young hypogonadal women (Turner Syndrome, n = 14; 46,XX gonadal dysgenesis, n = 9), hypogonadotrophic hypogonadism (n = 2), mean age 31·9 years (range 18·5–42·2). All subjects sequentially received oral 17β‐oestradiol 1,2 and 4 mg daily in a cyclical formulation for 12 weeks each.

Measurements  Metabolic markers and vascular physiology measurements to assess intima media thickness (IMT); arterial stiffness: pulse wave velocity (PWV) and augmentation index (AIx); endothelial function: flow‐mediated dilatation (FMD).

Results  Increasing doses of oestrogen resulted in a reduction in IMT (0·63 ± 0·06 vs. 0·58 ± 0·06 vs. 0·56 ± 0·06 mm at 1 mg, 2 mg and 4 mg 17β‐oestradiol, respectively, P = 0·001). Results were similar in women with Turner Syndrome and normal karyotype. High‐density lipoprotein (HDL) cholesterol concentrations increased (1·9 ± 0·4 vs. 2·0 ± 0·5 vs. 2·2 ± 0·4 mmol/l, P = 0·001) and plasma glucose (4·8 ± 0·4 vs. 4·7 ± 0·3 vs. 4·6 ± 0·6 mmol/l, P = 0·038) decreased slightly with the increasing dose of HRT. There was no correlation between the changes in IMT and HDL. Increasing HRT dose had no significant impact on blood pressure, weight, other lipid parameters, insulin, C‐reactive protein, interleukin‐6 and fibrinogen concentrations or FMD, PWV and AIx.

Conclusions  Increasing doses of HRT result in a reduction in carotid IMT in young hypogonadal women, along with increased serum HDL and decreased plasma glucose. This study raises the possibility that exogenous oestrogen may be cardioprotective in young women, but this observation needs to be balanced against a prothrombotic effect which is predominant in postmenopausal women.