bluuebunny/crossref_metadata_2025 huggingface dataset:
Increase in exhaled nitric oxide and protective role of the nitric oxide system in experimental pulmonary embolism
Authors: Nilsson K F , Gustafsson L E , Adding L C , Linnarsson D , Agvald P
Published: January 2007

Background and purpose:

Pulmonary embolism (PE) represents a real diagnostic challenge. PE is associated with pulmonary hypertension due to pulmonary vascular obstruction and vasoconstriction. We recently reported that pulmonary gas embolism transiently increases exhaled nitric oxide (FENO), but it is not known whether solid emboli may alter FENO, and whether an intact endogenous NO synthesis has a beneficial effect in experimental solid pulmonary embolism.

Experimental approach:

We used anaesthetised and ventilated rabbits in these experiments. To mimic PE, a single intravenous infusion of homogenized autologous skeletal muscle tissue (MPE) was given to rabbits with intact NO production (MPE of 60, 15, or 7.5 mg kg−1; group 1) and to another group (group 2) with inhibited NO synthesis (L‐NAME 30 mg kg−1; MPE of 7.5, 15 or 30 mg kg−1).

Key results:

In group 1, after MPE, FENO increased rapidly and dose‐dependently and FENO was still significantly elevated after 60 min with the two highest emboli doses. All these animals survived more than 60 min after embolization. In group 2, MPE of 7.5, 15 and 30 mg kg−1, in combination with NO synthesis inhibition, resulted in 67%, 50% and 25% survival at 60 min respectively, representing a statistically significant decrease in survival. Cardiovascular and blood‐gas changes after MPE were intensified by pre‐treatment with NO synthesis inhibitor.

Conclusions and implications:

We conclude that solid PE causes a sustained, dose‐dependent increase in FENO, giving FENO a diagnostic potential in PE. Furthermore, intact NO production appears critical for tolerance to acute PE.

British Journal of Pharmacology (2007) 150, 494–501. doi:10.1038/sj.bjp.0707001
Acceleration of R5 HIV replication by polymorphonuclear neutrophils in cultures of macrophages
Authors: Yoshida Tsuyoshi , Jones Vickie C , Kobayashi Makiko , Li Xiao‐Dong , Pollard Richard B , Suzuki Fujio
Published: January 2007

Cell‐to‐cell contact between monocyte‐derived macrophages (MDM) and endothelial cells has resulted in the increased proliferation of CC chemokine receptor 5/M‐tropic (R5) human immunodeficiency virus (HIV) in MDM. In the present study, R5 HIV replication was shown to be increased by polymorphonuclear neutrophils (PMN) in MDM cultures through the soluble factors released from these PMN. The replication of R5 HIV in MDM was greatly enhanced when PMN were added to cultures. An increase in the replication of R5 HIV was also demonstrated when the virus was replicated in MDM cultured in a double chamber transwell with PMN. Chemokine ligand (CCL) 2 and interleukin (IL)‐10 were detected in culture fluids of PMN exposed to R5 HIV. The replication of R5 HIV was not accelerated in cultures of MDM and PMN in a double chamber transwell supplemented with a mixture of monoclonal antibodies directed against CCL2 and IL‐10. Similarly, the replication of R5 HIV was accelerated in MDM cultures supplemented with a mixture of recombinant CCL2 and IL‐10. These results indicated that, in response to the viral stimulation, PMN produce CCL2 and IL‐10 and enhance the replication of R5 HIV in MDM cultures.
Multiphase growth in Bi-Mn-O thin films
Authors: Fujino S. , Murakami M. , Lim S.-H. , Salamanca-Riba L. G. , Wuttig M. , Takeuchi I.
Published: January 2007

We report on multiphase thin film growth of the Bi-Mn-O system on SrTiO3 (100) substrates. By varying the deposition oxygen partial pressure, the dominant phase formed in the film can be continuously changed from single phase epitaxal multiferroic BiMnO3 to epitaxally grown ferromagnetic Mn3O4. X-ray diffraction and transmission electron microscopy revealed that epitaxial multiferroic nanocomposites consisting of BiMnO3 and Mn3O4 form when the deposition pressure is ≈10 mTorr. The magnetic properties of the films were found to change as a function deposition pressure in a manner consistent with the variation in the nanocomposite microstructure.
Synthesis of confined electrically conducting carbon nanowires by heavy ion irradiation of fullerene thin film
Authors: Kumar Amit , Avasthi D. K. , Tripathi A. , Kabiraj D. , Singh F. , Pivin J. C.
Published: January 2007

Conducting nanowires parallel to each other, embedded in fullerene matrix are synthesized by high energy heavy ion irradiation of thin fullerene film at low fluence (up to 5×1011ions∕cm2). The conductivity of the conducting zone is about seven orders of magnitude higher than that of the fullerene matrix. The conducting nanowires are evidenced by conducting atomic force microscopy. The typical diameter of the conducting tracks is observed to be about 40–100nm. The creation of conducting wires is explained by transformation of fullerene to conducting form of carbon in the ion track, surrounded by the polymerized zone. The polymerization of fullerene is evidenced by Fourier transform infrared spectroscopy.
Improving mechanical properties of amorphous carbon nitride films by titanium doping
Authors: Xu P. , Li J. J. , Wang Q. , Wang Z. L. , Gu C. Z. , Cui Z.
Published: January 2007

Titanium doped amorphous carbon nitride (a-CNx) films with a nitrogen content of ∼24at.% were synthesized by radio frequency magnetron sputtering method. The effects of incorporating Ti on the mechanical properties of a-CNx films were investigated by nanoindentation, scanning electron microscope, x-ray diffraction spectra, and x-ray photoelectron spectroscopy, respectively. It was found that nanometer sized TiN crystallites were formed and embedded in the a-CNx matrix, causing an enhancement of hardness from ∼28to∼40GPa in the a-CNx films. The improved mechanical properties with addition of Ti are attributed to the densified microstructure due to the development of fine grain size of TiN and sp3 C–N bonds. These TiN nanocrystal grains are separated by an amorphous phase, preventing dislocation movement and hence enhancing the hardness of the film. The increased sp3 C–N bond fraction induced by incorporation of Ti also plays an important role in the enhancement of hardness.
Contactless electroreflectance of InAs∕In0.53Ga0.23Al0.24As quantum dashes grown on InP substrate: Analysis of the wetting layer transition
Authors: Kudrawiec R. , Motyka M. , Misiewicz J. , Somers A. , Schwertberger R. , Reithmaier J. P. , Forchel A. , Sauerwald A. , Kümmell T. , Bacher G.
Published: January 2007

Contactless electroreflectance (CER) spectroscopy has been applied to study optical transitions in InAs∕In0.53Ga0.23Al0.24As quantum dashes (QDashes) grown on an InP substrate by molecular beam epitaxy. CER resonances related to optical transitions in all relevant parts of the structure, i.e., InAs coverage, In0.53Ga0.23Al0.24As barriers, and the cap layer, have been clearly observed at room temperature. The signal, which is associated with light absorption in the InAs coverage, has been carefully analyzed, and the optical transitions in the wetting layer (WL) quantum well (QW) and QDashes have been identified in CER spectra. It has been shown that measurements of WL transitions and analysis of their energies allow us to determine the band gap discontinuity for the QDash/QDash-barrier interface. It has been found that the conduction band offset for the InAs∕In0.53Ga0.23Al0.24As interface is close to ∼70%. Moreover, it has been observed that the intensity of the WL transition varies with the cap layer which was used to terminate the QDash structure. The conditions for the observation of WL transitions are discussed in this work.
A new glance at HCl-monohydrate spectroscopy, using on-the-fly dynamics
Authors: Buch V. , Mohamed F. , Parrinello M. , Devlin J. P.
Published: January 2007

On-the-fly dynamics is used to analyze the remarkably anharmonic infrared spectroscopy of crystalline HCl monohydrate, an ionic solid composed of H3O+ and Cl−. The dominant intense infrared feature is shown to originate from specific sections of the hydronium trajectory, in which one of the H-atoms interacts strongly with a neighboring Cl−.
Formulation and numerical analysis of diatomic molecular dissociation using Boltzmann kinetic equation
Authors: Yano Ryosuke , Suzuki Kojiro , Kuroda Hisayasu
Published: January 2007

The direct description of chemical reactions by the Boltzmann equation still involves some difficulties in the kinetic theory. In this paper, we describe diatomic molecular dissociation due to transitions of vibrational quantum states resulting from inelastic collisions. These can be described by the Wang Chang-Uhlenbeck (WCU) equation. To avoid direct evaluation of the strong nonlinear collision kernel of the WCU equation, we used a kinetic equation. For accurate description of the dissociation process, we describe improvements we made to the conventional inelastic collision model (the so-called Morse model). Combining this inelastic collision model with the gas mixture model by Oguchi, we formulated a model for representing diatomic molecular dissociations. We validated this model by simulating a hypersonic shock layer with diatomic molecular dissociation.
One photon two electron excitations between doubly excited states of helium
Authors: Bhattacharyya S. , Sil A. N. , Mukherjee T. K. , Mukherjee P. K.
Published: January 2007

Variational calculations using Hylleraas coordinates have been performed for the first time for estimating the energies of 3dnf(Do1,3) state of helium for n=4,5,6. We predict absorption peaks at 12.219, 12.647, and 12.857eV for the Do3 series converging to N=3 ionization threshold of He+ which can be expected to be observed in the experiment of single photon double excitation of lowest Pe3 state of helium placed in synchrotron radiation.
Phonon characteristics and photoluminescence of bamboo structured silicon-doped boron nitride multiwall nanotubes
Authors: Xu Shifeng , Fan Yi , Luo Jingsong , Zhang Ligong , Wang Wenquan , Yao Bin , An Linan
Published: January 2007

Bamboo structured silicon-doped boron nitride multiwall nanotubes are synthesized via catalyst-assisted pyrolysis of a boron-containing polymeric precursor. The nanotubes are characterized using transmission electron microscopy, x-ray diffraction, Raman, and Fourier-transformed infrared spectroscope. The results suggest that the Si dopants cause significant changes in the structure and phonon characteristics of the nanotubes as compared to pure boron nitride nanotubes. A broad photoluminescence band ranging between 500 and 800nm is observed from the nanotubes, which is attributed to Si dopants. Study on temperature dependence of emission intensity suggests that the thermal activation energy of the nonradiative recombination process is 35meV.
Elongated grains in textured substrate tapes and their effect on transport currents in superconductor layers
Authors: Eickemeyer J. , Selbmann D. , Hühne R. , Wendrock H. , Hänisch J. , Güth A. , Schultz L. , Holzapfel B.
Published: January 2007

The development of cube textured flexible metallic substrate tapes is of basic interest for the economic production of YBa2Cu3Ox (YBCO) coated superconductors. Nickel tapes microalloyed with silver were prepared with the specific feature of an elongated grain structure. Cube textured NiO films were grown by surface oxidation epitaxy on these tapes retaining the elongated grains. Further, buffer layers and YBCO were deposited thereon. The YBCO layer transports an up to four times higher critical current density (Jc=2.35MA∕cm2) in the direction of grain elongation compared to the transversal one (Jc=0.55MA∕cm2).
Temperature-dependent photoluminescence of quasialigned Al-doped ZnO nanorods
Authors: He H. P. , Tang H. P. , Ye Z. Z. , Zhu L. P. , Zhao B. H. , Wang L. , Li X. H.
Published: January 2007

Temperature-dependent photoluminescence (PL) properties of quasialigned Al-doped ZnO nanorods grown by thermal evaporation method were investigated. The ionization energy of the Al donor was determined to be ∼90meV. A PL peak at 3.315eV was observed at low temperature and was tentatively related to excitons bound to surface defects. The emission, along with its first longitudinal optical phonon replica, persists up to room temperature and dominates the near band edge (NBE) emission of the nanorods. The doping of Al results in a redshift of ∼0.04eV of the room-temperature NBE emission of the ZnO nanorods.
High power 2.4μm heavily strained type-I quantum well GaSb-based diode lasers with more than 1W of continuous wave output power and a maximum power-conversion efficiency of 17.5%
Authors: Shterengas L. , Belenky G. , Kisin M. V. , Donetsky D.
Published: January 2007

The authors demonstrate a double quantum well GaSb-based diode laser operating at 2.4μm with a room-temperature cw output power of 1050mW and a maximum power-conversion efficiency of 17.5%. Laser differential gain with respect to current increases by a factor of 2 and laser threshold current is nearly halved when the compressive strain in the quantum wells is increased from 1.2% to 1.6%. This improvement is due to substantially improved hole confinement in the heavily compressively strained active region.
Influence of the AlN interlayer crystal quality on the strain evolution of GaN layer grown on Si (111)
Authors: Liu W. , Zhu J. J. , Jiang D. S. , Yang H. , Wang J. F.
Published: January 2007

The strain evolution in metal organic chemical vapor deposition growth of GaN on Si (111) substrate with an AlN interlayer is studied. During the growth of GaN film on AlN interlayer, the growth stress changes from compression to tension. The study shows that the density of V trenches in the AlN interlayer surface and the threading dislocations generated in the AlN interlayer have a significant influence on this strain evolution process. The dislocations generated in AlN interlayer may thread across the interface and play a key role in the strain evolution process of the GaN layer grown on AlN interlayer.
Atomic ordering effect of quantum dots embedded in InGaN∕GaN multiquantum well structures
Authors: Kim Keunjoo
Published: January 2007

The authors have studied the micro-Raman analysis on the InGaN∕GaN multiquantum well structures grown by metal organic chemical vapor deposition. For the quantum well structure with the trapezoidal-type, Raman vibration modes at the region of 610.4–640.6cm−1 on the c(0001) plane and 210cm−1 on the a(0001) plane were observed. These modes provide the atomically ordered superlattice structures of InGaN quantum dot formation of the wurtzite structures of Ga1In2N3 alloys corresponding to the In composition of x=0.67. The formation of quantum dots around the quantum well region was observed in the highly resolved transmission electron microscopic image.
Planar metal heterostructures for nanoplasmonic waveguides
Authors: Wang Bing , Wang Guo Ping
Published: January 2007

The authors propose and numerically demonstrate a planar metal heterostructure for guiding surface plasmon polaritons (SPPs). By the analysis of the effective index method and finite-difference time-domain numerical simulations, they reveal that the planar metal heterostructure created by inlaying a Ag film, on which SPPs show a lower phase velocity, into an Al film and coating them with a uniform dielectric layer can strongly confine SPPs in the Ag region of the waveguide with 171×33nm2 cross section and 1.76μm propagation length. The planar metal heterostructures provide a way for constructing various nanoscale counterparts of conventional planar integrated devices such as splitters, resonators, sensors, optical switches, logical circuit, etc.
Improved metrological characteristics of a carbon-nanotube-based ionization gauge
Authors: Choi In-Mook , Woo Sam-Yong , Song Han-Wook
Published: January 2007

A low-pressure detection technology utilizing the field emission of carbon nanotubes (CNTs) is introduced and its performance is characterized. To overcome the limitations of conventional ionization gauges, the CNTs had been proposed as an electron source. However, the simple triode structure of previous CNT pressure sensor not only has suffered from a limited measurement range but is also subject to a serious CNT array degradation problem. In this letter, the authors report the characterization results of an improved CNT-based pressure gauge, which is implemented by a screen-printing method, a modified mesh structure, and a pulse width modulation signal.
Repeatability of laboratory measurements for maternally derived yolk carotenoid concentrations in bird eggs
Authors: Cassey Phillip , Ewen John G. , Karadas Filiz , Hauber Mark E.
Published: January 2007

We describe a source of variability in maternally derived yolk carotenoids that is not routinely calculated in published studies. We quantify the measurement error in yolk carotenoid concentrations that may accrue during the analysis of yolk contents from repeat extractions and repeat high performance liquid chromatography (HPLC) runs of the same egg yolk sample from free range clutches of four farm bird species in New Zealand. We show that the variability between different eggs is substantially greater than the variability between replicate yolk extractions and HPLC analyses. Importantly, our results provide confidence to researchers that technical repeatability is a lesser concern when studying the biological differences between yolk samples.
Photoselected electron transfer pathways in DNA photolyase
Authors: Prytkova Tatiana R. , Beratan David N. , Skourtis Spiros S.
Published: January 2007

Cyclobutane dimer photolyases are proteins that bind to UV-damaged DNA containing cyclobutane pyrimidine dimer lesions. They repair these lesions by photo-induced electron transfer. The electron donor cofactor of a photolyase is a two-electron-reduced flavin adenine dinucleotide (FADH
−
). When FADH
−
is photo-excited, it transfers an electron from an excited π → π* singlet state to the pyrimidine dimer lesion of DNA. We compute the lowest excited singlet states of FADH
−
using ab initio (time-dependent density functional theory and time-dependent Hartree–Fock), and semiempirical (INDO/S configuration interaction) methods. The calculations show that the two lowest π → π* singlet states of FADH
−
are localized on the side of the flavin ring that is proximal to the dimer lesion of DNA. For the lowest-energy donor excited state of FADH
−
, we compute the conformationally averaged electronic coupling to acceptor states of the thymine dimer. The coupling calculations are performed at the INDO/S level, on donor–acceptor cofactor conformations obtained from molecular dynamics simulations of the solvated protein with a thymine dimer docked in its active site. These calculations demonstrate that the localization of the
1
FADH
−
* donor state on the flavin ring enhances the electronic coupling between the flavin and the dimer by permitting shorter electron-transfer pathways to the dimer that have single through-space jumps. Therefore, in photolyase, the photo-excitation itself enhances the electron transfer rate by moving the electron towards the dimer.
Role of SUMO in the dynamics of telomere maintenance in fission yeast
Authors: Xhemalce Blerta , Riising Eva Madi , Baumann Peter , Dejean Anne , Arcangioli Benoît , Seeler Jacob-S.
Published: January 2007

The sheltering of chromosome ends from illegitimate DNA repair reactions and telomere length homeostasis are critical for preserving genomic integrity. Growing evidence implicates covalent protein modification by SUMO (small ubiquitin-like modifier) (sumoylation) in the regulation of numerous DNA transactions, including DNA repair and transcription, as well as heterochromatin formation and maintenance. We have recently shown that fission yeast Pli1p is a SUMO E3 ligase and that
pli1
mutants, which are impaired for global sumoylation, are viable, but exhibit de-regulated homologous recombination and marked defects in chromosome segregation and centromeric silencing, as well as a consistent increase in telomere length. In this work, we explore the mechanisms underlying sumoylation-dependent telomere maintenance. We show that Pli1p, but not the related Nse2p, is the principal SUMO E3 ligase enzyme involved. Using both a
pli1
mutation and a physiological “knockdown” of sumoylation, achieved by inducible expression of a dominant negative form of the conjugating enzyme Ubc9p, we further show that telomere lengthening induced by lack of sumoylation is not due to unscheduled telomere–telomere recombination. Instead, sumoylation increases telomerase activity, therefore suggesting that this modification controls the activity of a positive or negative regulator of telomerase.
HIV-susceptible transgenic rats allow rapid preclinical testing of antiviral compounds targeting virus entry or reverse transcription
Authors: Goffinet Christine , Allespach Ina , Keppler Oliver T.
Published: January 2007

The current testing of anti-HIV drugs is hampered by the lack of a small animal that is readily available and easy to handle; can be infected systemically with HIV type 1 (HIV-1); harbors the major HIV-1 target cells in a physiological frequency, organ distribution, and activation state; and is established as a pharmacological model. Here, we explored the potential of outbred Sprague–Dawley rats that transgenically express the HIV-1 receptor complex on CD4 T cells and macrophages as a model for the preclinical evaluation of inhibitors targeting virus entry or reverse transcription. The concentrations of the peptidic fusion inhibitor enfuvirtide or the nonnucleoside reverse transcriptase inhibitor efavirenz required to inhibit HIV-1 infection of cultured primary CD4 T cells and macrophages from human CD4 and CCR5-transgenic rats differed by no more than 3-fold from those required for human reference cultures. Prophylactic treatment of double-transgenic rats with a weight-adapted pediatric dosing regimen for either enfuvirtide (s.c., twice-daily) or efavirenz (oral, once-daily) achieved a 92.5% or 98.8% reduction, respectively, of the HIV-1 cDNA load in the spleen 4 days after i.v. HIV-1 challenge. Notably, a once-daily dosing regimen for enfuvirtide resulted in a ≈5-fold weaker inhibition of infection, unmasking the unfavorable pharmacokinetic characteristics of the synthetic peptide in the context of an efficacy trial. This work provides proof of principle that HIV-susceptible transgenic rats can allow a rapid and predictive preclinical evaluation of the inhibitory potency and of the pharmacokinetic properties of antiviral compounds targeting early steps in the HIV replication cycle.
Epigenetic memory at malaria virulence genes
Authors: Chookajorn Thanat , Dzikowski Ron , Frank Matthias , Li Felomena , Jiwani Alisha Z. , Hartl Daniel L. , Deitsch Kirk W.
Published: January 2007

During its red blood cell stage, the malaria parasite
Plasmodium falciparum
can switch its variant surface proteins (
P. falciparum
erythrocyte membrane protein 1) to evade the host immune response. The
var
gene family encodes
P. falciparum
erythrocyte membrane protein 1, different versions of which have unique binding specificities to various human endothelial surface molecules. Individual parasites each contain ≈60
var
genes at various locations within their chromosomes; however, parasite isolates contain different complements of
var
genes, thus, the gene family is enormous with a virtually unlimited number of members. A single
var
gene is expressed by each parasite in a mutually exclusive manner. We report that control of
var
gene transcription and antigenic variation is associated with a chromatin memory that includes methylation of histone H3 at lysine K9 as an epigenetic mark. We also discuss how gene transcription memory may affect the mechanism of pathogenesis and immune evasion.
Biological control of pests in Ukraine: legacy from the past and challenges for the future.
Authors: Stefanovska T. R. , Pidlisnyuk V. V. , Kaya H. K.
Published: January 2007

Biological control has a long and rich history in Ukraine which is closely linked with other countries of the Former Soviet Union, and some relevant studies from these countries are also included in this review. The use of natural enemies against Ukrainian insect pests demonstrates that biological control approaches have enjoyed a degree of success. The release of
Aphelinus mali
in a classical biological control programme against the woolly apple aphid,
Eriosoma lanigerum
, was successful. In contrast, the release of the hemipterans,
Perillus bioculatus
and
Podisus maculiventris
, against the Colorado potato beetle,
Leptinotarsa decemlineata
, was not successful, and studies in the use of these hemipterans as biological control agents continue. Conservation biological control is practised in apple and cereal cropping systems resulting in a number of predators and parasitoids being preserved. Augmentation of natural enemies, especially predatory mites against the spider mite
Tetranychus urticae
in greenhouse cucumber and tomato production, has provided suppression of this pest. Various strains of
Bacillus thuringiensis
are being used inundatively against Lepidopteran, coleopteran and mosquito pests. A granulovirus has been studied for use against the codling moth (
Cydia pomonella
), and the fungus,
Beauveria bassiana
, is being evaluated against several insect pests. Entomopathogenic nematodes have generated some interest for future use in Ukraine as potential biological control agents against soil-inhabiting pests. Although biological control programmes have been practised for many years, the agricultural sector in Ukraine is moving from a command to a market economy. The latter economy is profit-driven and relies more on chemical pesticide usage. The challenge is to integrate biological control programmes into the market economy.
The predatory stinkbug
Podisus nigrispinus
: biology, ecology and augmentative releases for lepidoperan larval control in
Eucalyptus
forests in Brazil.
Authors: Torres J. B. , Zanuncio J. C. , Moura M. A.
Published: January 2007

Podisus nigrispinus
feeds primarily on insect larvae. It has been reared and released in Brazil to control lepidopterous larvae, particularly defoliators of
Eucalyptus
trees, but inoculative releases and conservation of natural populations in other crops have also been attempted. Aspects favouring the use of
P. nigrispinus
as a biocontrol agent include: (i) cost-effective mass-rearing capabilities with alternative prey or artificial diets; (ii) compatibility of the predator with some insecticides and forest production practices; (iii) natural occurrence in diverse habitats associated with lepidopteran outbreaks. The biology and ecology of
P. nigrispinus
and its mass production and use to control defoliating lepidopteran larvae in
Eucalyptus
plantations are discussed, and research needs to expand its use in pest management are outlined.
Functional, developmental and clinical anatomy of the bovine penis and prepuce.
Authors: Ashdown R. R.
Published: January 2007

Several changes in nomenclature from that of the Nomina Anatomica Veterinaria (4th edition) are suggested. The neuromuscular mechanisms of erection and ejaculation involve activity of both smooth and striated penile muscles. Functional and clinical anatomy of the penis and prepuce are considered for these five main stages of service performance: sexual arousal (which prepares for erection and ejaculation); penile erection and also its failure (impotence); intromission and its failure; ejaculation and associated clinical problems; detumescence and repositioning of the penis after service. Preputial mobility and injuries are also discussed. Anatomical changes of the corpus cavernosum penis during erection are described and related clinical problems are discussed, under three headings: Penile elongation and distension; Straightening of the sigmoid flexure; and Spiraldeviation of the penis. Prenatal development of penis and prepuce is described. Postnatal development is then considered with special emphasis on clinical problems in the young bull.
Multifunctional agriculture and the economic future of EU farming.
Authors: Moran D.
Published: January 2007

Multifunctional agriculture is the rubric that defines a policy to reorient farming to be consistent with sustainable development. In essence, the European agricultural sector is to be liberalized with support and preferential tariff arrangements either removed or redirected towards environmental and social goals. Farmers are to be rewarded more by the market, with public intervention increasingly reserved for areas where public good issues are at stake. This transition marks a new direction for farm enterprises that are now forced to find new niches in which to operate. The wider environmental and social impacts of this transition remain to be determined.
T-DNA mutagenesis in the model plant
Medicago truncatula
: is it efficient enough for legume molecular genetics?
Authors: Brocard L. , Schultze M. , Kondorosi A. , Ratet P.
Published: January 2007

The development of efficient transformation protocols in several legume species has opened the possibility to use T-DNA insertional mutagenesis to investigate legume-specific processes such as symbiosis. A T-DNA mutagenesis approach was initiated in the model legume
Medicago truncatula
by constructing a small collection of 1000
M. truncatula
T-DNA lines, using in vitro-mediated transformation-regeneration protocols. In this T-DNA collection, mutant phenotypes were observed but generally did not result from the disruption of genes by the T-DNA but most probably from somaclonal mutations induced by the in vitro regeneration process or by unsuccessful T-DNA integration events resulting in small (undetectable) insertions or deletions in the genome of the regenerated plants. In addition, a promoter trap approach was also not very successful for gene discovery because aberrant gene fusions were observed in this collection. Therefore, the T-DNA mutagenesis approach in
M. truncatula
seems to be limited by the lack of an efficient in planta transformation protocol that would allow the generation of a large mutant collection suitable for reverse genetic studies. Thus, there is a need for the development of alternative tools for efficient gene disruption in legumes.
The ecology of non-native invasive plant species: are there consistent patterns?
Authors: Inderjit Inderjit , Drake J. A.
Published: January 2007

Non-native invasive species are defined as those naturalized species that are new to a particular region and produce reproductive offspring at considerable distance from their native land. Invasive plants can be introduced accidentally (e.g.
Parthenium hysterophorus
and
Chromolaena odorata
) or deliberately (e.g.
Lantana camara
and
Prosopis juliflora
) and can have profound population, community and ecosystem-level effects. The aim of this paper is to examine how ecological attributes such as disturbance, species diversity and species richness influence invasion patterns. Are there parameters that retrospectively explain a significant amount of variation in invasion outcome? How often do the same parameters correlate with invasion success or failure among different communities, and can these variables be implemented in general models that aim to predict the likelihood of plant invasions? We feel that the chances of detecting any broadly applicable relationship (i.e. general factors that governs habitat invasibility or invasive success) are remote given contemporary approaches to biological invasions. Our conclusion is based on the nature of complex dynamical systems, where generality is possible at some levels of organization and observation but not others. Precise prediction requires a case-by-case study, and even then the outcome of biological invasions can be surprising.
Conversion of CT numbers into tissue parameters for Monte Carlo dose calculations: a multi-centre study
Authors: Vanderstraeten Barbara , Chin Pik Wai , Fix Michael , Leal Antonio , Mora Grisel , Reynaert Nick , Seco Joao , Soukup Martin , Spezi Emiliano , De Neve Wilfried , Thierens Hubert
Published: January 2007

The conversion of computed tomography (CT) numbers into material composition and mass density data influences the accuracy of patient dose calculations in Monte Carlo treatment planning (MCTP). The aim of our work was to develop a CT conversion scheme by performing a stoichiometric CT calibration. Fourteen dosimetrically equivalent tissue subsets (bins), of which ten bone bins, were created. After validating the proposed CT conversion scheme on phantoms, it was compared to a conventional five bin scheme with only one bone bin. This resulted in dose distributions D14and D5for nine clinical patient cases in a European multi-centre study. The observed local relative differences in dose to medium were mostly smaller than 5%. The dose–volume histograms of both targets and organs at risk were comparable, although within bony structures D14was found to be slightly but systematically higher than D5. Converting dose to medium to dose to water (D14to D14watand D5to D5wat) resulted in larger local differences as D5watbecame up to 10% higher than D14wat. In conclusion, multiple bone bins need to be introduced when Monte Carlo (MC) calculations of patient dose distributions are converted to dose to water.
A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
Authors: Tenney Aaron E. , Wu Jia Qian , Langton Laura , Klueh Paul , Quatrano Ralph , Brent Michael R.
Published: January 2007

Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template sequence is then inferred from this alignment. This technique makes possible many exciting biological applications. Here we present two such applications, alternate splice finding and elucidation of multiple insertion sites in a random insertional mutagenesis library. Our results demonstrate that RT–PCR followed by Trace Recalling is a more efficient and cost effective way to find alternate splices than traditional methods. We also present a method for mapping double-insertion events in a random insertional-mutagenesis library.
Conservation, Convergence, and Divergence of Light-Responsive, Circadian-Regulated, and Tissue-Specific Expression Patterns during Evolution of the Arabidopsis GATA Gene Family
Authors: Manfield Iain W. , Devlin Paul F. , Jen Chih-Hung , Westhead David R. , Gilmartin Philip M.
Published: January 2007

In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.
Abscisic Acid and Stress Signals InduceViviparous1Expression in Seed and Vegetative Tissues of Maize
Authors: Cao Xueyuan , Costa Liliana M. , Biderre-Petit Corinne , Kbhaya Bouchab , Dey Nrisingha , Perez Pascual , McCarty Donald R. , Gutierrez-Marcos Jose F. , Becraft Philip W.
Published: January 2007

Viviparous1 (Vp1) encodes a B3 domain-containing transcription factor that is a key regulator of seed maturation in maize (Zea mays). However, the mechanisms of Vp1 regulation are not well understood. To examine physiological factors that may regulate Vp1 expression, transcript levels were monitored in maturing embryos placed in culture under different conditions. Expression of Vp1 decreased after culture in hormone-free medium, but was induced by salinity or osmotic stress. Application of exogenous abscisic acid (ABA) also induced transcript levels within 1 h in a dose-dependent manner. The Vp1 promoter fused to β-glucuronidase or green fluorescent protein reproduced the endogenous Vp1 expression patterns in transgenic maize plants and also revealed previously unknown expression domains of Vp1. The Vp1 promoter is active in the embryo and aleurone cells of developing seeds and, upon drought stress, was also found in phloem cells of vegetative tissues, including cobs, leaves, and stems. Sequence analysis of the Vp1 promoter identified a potential ABA-responsive complex, consisting of an ACGT-containing ABA response element (ABRE) and a coupling element 1-like motif. Electrophoretic mobility shift assay confirmed that the ABRE and putative coupling element 1 components specifically bound proteins in embryo nuclear protein extracts. Treatment of embryos in hormone-free Murashige and Skoog medium blocked the ABRE-protein interaction, whereas exogenous ABA or mannitol treatment restored this interaction. Our data support a model for a VP1-dependent positive feedback mechanism regulating Vp1 expression during seed maturation.
Cold Nights Impair Leaf Growth and Cell Cycle Progression in Maize through Transcriptional Changes of Cell Cycle Genes
Authors: Rymen Bart , Fiorani Fabio , Kartal Fatma , Vandepoele Klaas , Inzé Dirk , Beemster Gerrit T.S.
Published: January 2007

Low temperature inhibits the growth of maize (Zea mays) seedlings and limits yield under field conditions. To study the mechanism of cold-induced growth retardation, we exposed maize B73 seedlings to low night temperature (25°C /4°C, day/night) from germination until the completion of leaf 4 expansion. This treatment resulted in a 20% reduction in final leaf size compared to control conditions (25°C/18°C, day/night). A kinematic analysis of leaf growth rates in control and cold-treated leaves during daytime showed that cold nights affected both cell cycle time (+65%) and cell production (−22%). In contrast, the size of mature epidermal cells was unaffected. To analyze the effect on cell cycle progression at the molecular level, we identified through a bioinformatics approach a set of 43 cell cycle genes and analyzed their expression in proliferating, expanding, and mature cells of leaves exposed to either control or cold nights. This analysis showed that: (1) the majority of cell cycle genes had a consistent proliferation-specific expression pattern; and (2) the increased cell cycle time in the basal meristem of leaves exposed to cold nights was associated with differential expression of cell cycle inhibitors and with the concomitant down-regulation of positive regulators of cell division.
Rice SCAMP1 Defines Clathrin-Coated,trans-Golgi–Located Tubular-Vesicular Structures as an Early Endosome in Tobacco BY-2 Cells
Authors: Lam Sheung Kwan , Siu Ching Lung , Hillmer Stefan , Jang Seonghoe , An Gynheung , Robinson David G. , Jiang Liwen
Published: January 2007

We recently identified multivesicular bodies (MVBs) as prevacuolar compartments (PVCs) in the secretory and endocytic pathways to the lytic vacuole in tobacco (Nicotiana tabacum) BY-2 cells. Secretory carrier membrane proteins (SCAMPs) are post-Golgi, integral membrane proteins mediating endocytosis in animal cells. To define the endocytic pathway in plants, we cloned the rice (Oryza sativa) homolog of animal SCAMP1 and generated transgenic tobacco BY-2 cells expressing yellow fluorescent protein (YFP)–SCAMP1 or SCAMP1-YFP fusions. Confocal immunofluorescence and immunogold electron microscopy studies demonstrated that YFP-SCAMP1 fusions and native SCAMP1 localize to the plasma membrane and mobile structures in the cytoplasm of transgenic BY-2 cells. Drug treatments and confocal immunofluorescence studies demonstrated that the punctate cytosolic organelles labeled by YFP-SCAMP1 or SCAMP1 were distinct from the Golgi apparatus and PVCs. SCAMP1-labeled organelles may represent an early endosome because the internalized endocytic markers FM4-64 and AM4-64 reached these organelles before PVCs. In addition, wortmannin caused the redistribution of SCAMP1 from the early endosomes to PVCs, probably as a result of fusions between the two compartments. Immunogold electron microscopy with high-pressure frozen/freeze-substituted samples identified the SCAMP1-positive organelles as tubular-vesicular structures at the trans-Golgi with clathrin coats. These early endosomal compartments resemble the previously described partially coated reticulum and trans-Golgi network in plant cells.
Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development
Authors: Evans Matthew M.S.
Published: January 2007

Angiosperm embryo sac development begins with a phase of free nuclear division followed by cellularization and differentiation of cell types. The indeterminate gametophyte1 (ig1) gene of maize (Zea mays) restricts the proliferative phase of female gametophyte development. ig1 mutant female gametophytes have a prolonged phase of free nuclear divisions leading to a variety of embryo sac abnormalities, including extra egg cells, extra polar nuclei, and extra synergids. Positional cloning of ig1 was performed based on the genome sequence of the orthologous region in rice. ig1 encodes a LATERAL ORGAN BOUNDARIES domain protein with high similarity to ASYMMETRIC LEAVES2 of Arabidopsis thaliana. A second mutant allele of ig1 was identified in a noncomplementation screen using active Mutator transposable element lines. Homozygous ig1 mutants have abnormal leaf morphology as well as abnormal embryo sac development. Affected leaves have disrupted abaxial–adaxial polarity and fail to repress the expression of meristem-specific knotted-like homeobox (knox) genes in leaf primordia, causing a proliferative, stem cell identity to persist in these cells. Despite the superficial similarity of ig1-O leaves and embryo sacs, ectopic knox gene expression cannot be detected in ig1-O embryo sacs.
Evidence for Increased Neuropeptide Y Synthesis in Mediobasal Hypothalamus in Relation to Parental Hyperphagia and Gonadal Activation in Breeding Ring Doves
Authors: Ramakrishnan S. , Strader A. D. , Wimpee B. , Chen P. , Smith M. S. , Buntin J. D.
Published: January 2007

Like lactating mammals, male and female ring dove parents increase their food consumption to meet the energetic challenges of provisioning their young. To clarify the neurochemical mechanisms involved, the present study investigated the relationship between parental hyperphagia and changes in activity of the potent orexigen neuropeptide Y (NPY) in the hypothalamus of breeding doves. Changes in NPY‐immunoreactive (NPY‐ir) cell numbers in the tuberal hypothalamus of male and female doves were examined by immunocytochemistry at six stages of the breeding cycle. Parallel NPY mRNA measurements were recorded in mediobasal hypothalamus (which includes the tuberal hypothalamus) by semiquantitative reverse transcription‐polymerase chain reaction using 18S rRNA as the internal standard. NPY mRNA changes were also measured in the mediobasal hypothalamus of nonbreeding doves following intracranial administration of prolactin, an orexigenic hormone that is elevated in the plasma of parent doves, and in response to food deprivation, which mimics the negative energy state that develops in parents as they provision their growing young. NPY‐ir cell numbers in the tuberal hypothalamus and NPY mRNA levels in the mediobasal hypothalamus were significantly higher in breeding males and females during the period of parental hyperphagia after hatching than during the late incubation period when food intake remains unchanged. In nonbreeding doves, food deprivation and prolactin treatment increased NPY mRNA in this region by two‐ to three‐fold, which suggests that NPY expression is sensitive to hormonal and metabolic signals associated with parenting. We conclude that NPY synthesis is increased in the mediobasal hypothalamus during the posthatching period, which presumably supports increased NPY release and resulting parental hyperphagia. NPY‐ir and mRNA were also high in the mediobasal hypothalamus prior to egg laying when food intake remained unchanged. Several lines of evidence suggest that this elevation in NPY supports the increased gonadal activity that accompanies intense courtship and nest building interactions in breeding doves.
Intracerebroventricular Administration of Corticotrophin‐Releasing Hormone Receptor Antagonists Produces Different Effects on Hypothalamic Pituitary Adrenal Responses to Novel Restraint Depending on the Stress History of the Animal
Authors: Vining C. , Iyer V. , Bhatnagar S.
Published: January 2007

Corticotrophin‐releasing hormone (CRH) regulates acute stress‐induced changes in neuroendocrine function and behaviour. However, little is known about CRH functions in animals that have prior experience with repeated stress. Repeatedly‐stressed rats exhibit a habituated hypothalamic‐pituitary‐adrenal (HPA) response to a familiar, homotypic stressor but exhibit maintained or enhanced HPA responses to a novel, heterotypic stressor. We examined the effects of intracerebroventricular (i.c.v.) administration of two different nonselective CRH receptor antagonists, alpha‐helical CRH(9‐41) (ahCRH) or D‐Phe CRH(12‐41) (D‐PheCRH), on HPA responses to acute restraint in rats previously exposed to repeated cold stress (i.e. facilitated responses). Antagonists were administered as single i.c.v. injections prior to restraint to provide a general index of CRH function in control versus repeatedly‐stressed rats. CRH receptor blockade with either ahCRH or D‐PheCRH produced different effects on HPA responses to novel restraint depending on whether the animal had been previously cold stressed or not. Interestingly, some agonist‐type effects were observed but only in repeatedly‐stressed rats. In summary, these results indicate that manipulations of the CRH receptor have different effects on HPA activity depending on the stress history of the animal.