bluuebunny/crossref_metadata_2025 huggingface dataset:
Reactome - a knowledgebase of human biological pathways
Authors: D'Eustachio Peter , Croft David , de Bono Bernard , Gopinath Gopal , Gillespie Marc , Jassal Bijay , Matthews Lisa , Schmidt Esther , Vastrik Imre , Wu Guanming , Lewis Suzanna , Birney Ewan , Stein Lincoln
Published: October 2007

Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality control and peer review by a second expert. Reactome data are released quarterly. At release time, electronic orthology inference performed on human data produces reaction predictions in 22 species ranging from mouse to bacteria. Cross-references to a large number of publicly available databases are attached, providing multiple entry points into the database. The Reactome Mart allows query submission and data retrieval from Reactome and across other databases. The SkyPainter tool provides visualization and statistical analysis of user supplied data, e.g. from microarray experiments. Reactome data are freely available in a number of data formats (e.g. BioPax, SBML).
Is the infection/latency/reactivation cycle of viruses an oncogenic engine?
Authors: Ripalti Alessandro
Published: October 2007

Human oncogenic viruses are defined as necessary but not sufficient to initiate cancer. Experimental evidence suggests that the oncogenic potential of a virus is effective only in cells that have already accumulated a number of genetic mutations leading to cell cycle deregulation. Current models for viral driven oncogenesis cannot explain why tumor development in carriers of tumorigenic viruses is a very rare event, occurring decades after virus infection. Considering that viruses are mutagenic agents per se and human oncogenic viruses additionally establish latent and persistent infections, I attempt here to provide a mechanism of tumor initiation both for RNA and DNA viruses, suggesting viruses could be both necessary and sufficient in human tumorigenesis. I hypothesize a general, albeit inefficient hit and rest mechanism by which viruses may produce a limited reservoir of cells harbouring genetic damage that would be initiated when the virus first hits the cell, before latency is established. Cells surviving genetic damage would consequently become more sensitive to further damage mediated by the otherwise insufficient transforming activity of virus products expressed in latency, or upon episodic reactivations (viral persistence). Cells with a combination of genetic damage leading to a cancerous phenotype would emerge very rarely, as the probability of such an occurrence would be dependent on severity and frequency of consecutive hit and rest cycles due to viral reinfections and reactivations.
Direct, Live Imaging of Cortical Spreading Depression and Anoxic Depolarisation Using a Fluorescent, Voltage-Sensitive Dye
Authors: Farkas Eszter , Pratt Rosalind , Sengpiel Frank , Obrenovitch Tihomir P
Published: October 2007

Perilesion depolarisations, whether transient anoxic depolarisation (AD) or spreading depression (SD), occur in stroke models and in patients with acute brain ischaemia, but their contribution to lesion progression remains unclear. As these phenomena correspond to waves of cellular depolarisation, we have developed a technique for their live imaging with a fluorescent voltage-sensitive (VS) dye (RH-1838). Method development and validation were performed in two different preparations: chicken retina, to avoid any vascular interference; and cranial window exposing the cortical surface of anaesthetised rats. Spreading depression was produced by high-K medium, and AD by complete terminal ischaemia in rats. After dye loading, the preparation was illuminated at its excitation wavelength and fluorescence changes were recorded sequentially with a charge-coupled device camera. No light was recorded when the VS dye was omitted, ruling out the contribution of any endogenous fluorophore. With both preparations, the changes in VS dye fluorescence with SD were analogous to those of the DC (direct current) potential recorded with glass electrodes. Although some blood quenching of the emitted light was identified, the VS dye signatures of SD had a good signal-to-noise ratio and were reproducible. The changes in VS dye fluorescence associated with AD were more complex because of additional interferents, especially transient brain swelling with subsequent shrinkage. However, the kinetics of the AD-associated changes in VS dye fluorescence was also analogous to that of the DC potential. In conclusion, this method provides the imaging equivalent of electrical extracellular DC potential recording, with the SD and AD negative shifts translating directly to fluorescence increase.
Reduced Cerebral Fluoro-l-Dopamine Uptake in Adult Patients Suffering from Phenylketonuria
Authors: Landvogt Christian , Mengel Eugen , Bartenstein Peter , Buchholz Hans Georg , Schreckenberger Mathias , Siessmeier Thomas , Scheurich Armin , Feldmann Reinhold , Weglage Josef , Cumming Paul , Zepp Fred , Ullrich Kurt
Published: October 2007

Deficiency of phenylalanine hydroxylase activity in phenylketonuria (PKU) causes an excess of phenylalanine (Phe) throughout the body, predicting impaired synthesis of catecholamines in the brain. To test this hypothesis, we used positron emission tomography (PET) to measure the utilization of 6-[18F]fluoro-l-dopamine (FDOPA) in the brain of adult patients suffering from PKU and in healthy controls. Dynamic 2-h long FDOPA emission recordings were obtained in seven adult PKU patients (five females, two males; age: 21 to 27 years) with elevated serum Phe levels, but lacking neurologic deficits. Seven age-matched, healthy volunteers were imaged under identical conditions. The utilization of FDOPA in striatum was calculated by linear graphical analysis ( k3S, min−1), with cerebellum serving as a nonbinding reference region. The time to peak activity in all brain time—radioactivity curves was substantially delayed in the PKU patients relative to the control group. The mean magnitude of k3S in the striatum of the PKU patients (0.0052±0.0004 min−1) was significantly lower than in the control group (0.0088±0.0009 min−1) ( P<0.001). There was no significant correlation between individual serum Phe levels and k3S. The unidirectional clearance of FDOPA to brain was impaired in adult patients suffering from PKU, presumably reflecting the competitive inhibition of the large neutral amino acid carrier by Phe. Assuming this competition to be spatially uniform, the relationship between striatum and cerebellum time—activity curves additionally suggests inhibition of DOPA efflux, possibly also due to competition from Phe. The linear graphical analysis shows reduced k3S in striatum, indicating reduced DOPA decarboxylase activity.
Matrix Metalloproteinase Inhibition Facilitates Cell Death in Intracerebral Hemorrhage in Mouse
Authors: Grossetete Mark , Rosenberg Gary A
Published: October 2007

Intracerebral hemorrhage (ICH) initiates an inflammatory response with secondary growth of hemorrhage and cell death. Matrix metalloproteinase (MMP) gelatinolytic activity is increased in ICH, and synthetic inhibitors to MMPs reduce edema and hemorrhage size. Recently, we found that tissue inhibitor of metalloproteinase-3 (TIMP-3) is elevated after ischemia and colocalizes with TUNEL (terminal deoxynucleotidyl transferase-mediated 2′-deoxyuridine 5′-triphosphate-biotin nick end-labeled)-labeled cells. Tissue inhibitor of metalloproteinase-3 promotes neuronal apoptosis in vitro by blocking the shedding of the tumor necrosis factor (TNF) superfamily of death receptors/ligands by stromelysin-1 (MMP-3). However, the effect of TIMP-3 and synthetic MMP inhibitors on cell death in ICH is unclear. Therefore, we used the collagenase-induced intracerebral hemorrhage (CIH) model in Timp-3 knockout and C57Bl/6 wild-type mice to study MMP expression, hemorrhage volume, and cell death. Real-time PCR showed an increase in Mmp-3 mRNA in CIH, but similar Mmp-2 and -9 mRNA expression levels in CIH and saline-injected mice. Protein levels of pro and cleaved MMP-3 were increased in CIH, and zymographic gelatinolytic activity of MMP-9 was elevated after CIH at 72 h, suggesting an exogenous source. Apoptosis was shown by increased caspase-3 levels at 2 and 72 h, and active caspase-8 by 2 and 24 h. The Timp-3 null mouse and wild types had similar hemorrhage sizes and TUNEL-labeled cells. Unexpectedly, the broad-spectrum MMP inhibitor BB-94 increased hemorrhage size and TUNEL-labeled cells. Our results fail to implicate TIMP-3 in apoptosis in CIH, but show that BB-94 increased apoptosis in CIH, possibly by blocking shedding of TNF death receptors and/or their ligands.
Coupling of Angiogenesis and Neurogenesis in Cultured Endothelial Cells and Neural Progenitor Cells after Stroke
Authors: Teng Hua , Zhang Zheng Gang , Wang Lei , Zhang Rui Lan , Zhang Li , Morris Dan , Gregg Sara R , Wu Zhenhua , Jiang Angela , Lu Mei , Zlokovic Berislav V , Chopp Michael
Published: October 2007

Angiogenesis and neurogenesis are coupled processes. Using a coculture system, we tested the hypothesis that cerebral endothelial cells activated by ischemia enhance neural progenitor cell proliferation and differentiation, while neural progenitor cells isolated from the ischemic subventricular zone promote angiogenesis. Coculture of neural progenitor cells isolated from the subventricular zone of the adult normal rat with cerebral endothelial cells isolated from the stroke boundary substantially increased neural progenitor cell proliferation and neuronal differentiation and reduced astrocytic differentiation. Conditioned medium harvested from the stroke neural progenitor cells promoted capillary tube formation of normal cerebral endothelial cells. Blockage of vascular endothelial growth factor receptor 2 suppressed the effect of the endothelial cells activated by stroke on neurogenesis as well as the effect of the supernatant obtained from stroke neural progenitor cells on angiogenesis. These data suggest that angiogenesis couples to neurogenesis after stroke and vascular endothelial growth factor likely mediates this coupling.
Mitochondrial Ca2+ Uniporter Blockers Influence Activation-Induced CBF Response in the Rat Somatosensory Cortex
Authors: Kannurpatti Sridhar S , Biswal Bharat B
Published: October 2007

Effects of mitochondrial calcium signaling blockade on neural activation-induced CBF response were studied in urethane-anesthetized rats. Ruthenium red (RuR), a nonspecific inhibitor of the mitochondrial calcium uniporter (MCU), and Ru360, a highly specific inhibitor of the MCU, were delivered intravenously (i.v.) or intracerebroventricularly (i.c.v.). Baseline cerebral blood flow (CBF) and cerebral hyperemic response to whisker stimulation were measured through a thinned skull over the somatosensory cortex using laser Doppler imaging (LDI). Ruthenium red or Ru360 did not alter the baseline CBF at all doses used. However, the hyperemic response, defined as the activation area and amplitude of CBF increase in response to mechanical whisker stimulation, was significantly reduced in the presence of either RuR or Ru360 delivered i.c.v. The hyperemic response reduced significantly with a dose of 14.5 nmol RuR (i.c.v.), showing a further decrease with 29 nmol RuR (i.c.v.). A comparable decrease in the hyperemic response was observed during treatment with a relatively lower dose of 4.5 and 9 nmol Ru360 (i.c.v.). Delivered intravenously, Ru360 significantly diminished the cerebral hyperemic response at doses greater than 80 μg/kg i.v., up to a dose of 320 μg/kg i.v. However, RuR (i.v.) had an opposite effect with an enhancement in the cerebral hyperemic response at all doses studied. Ruthenium red or Ru360 had no significant effect on the cerebral reactivity to hypercapnia, indicating that altered cerebral hyperemic response to whisker stimulation was predominantly neural. We conclude that mitochondrial calcium signaling through the MCU mediates neural activation-induced CBF response in vivo.
Epitaxial growth of M-type Ba-hexaferrite films on MgO (111)‖SiC (0001) with low ferromagnetic resonance linewidths
Authors: Chen Zhaohui , Yang Aria , Gieler Antone , Harris V. G. , Vittoria C. , Ohodnicki P. R. , Goh K. Y. , McHenry M. E. , Cai Zhuhua , Goodrich Trevor L. , Ziemer Katherine S.
Published: October 2007

Barium hexaferrite (BaM) films were deposited on 10nm MgO (111) films on 6H silicon carbide (0001) substrates by pulsed laser deposition from a homogeneous BaFe12O19 target. The MgO layer, deposited by molecular beam epitaxy, alleviated lattice mismatch and interdiffusion between film and substrate. X-ray diffraction showed strong crystallographic alignment while pole figures exhibited reflections consistent with epitaxial growth. After optimized annealing, these BaM films have a perpendicular magnetic anisotropy field of 16900Oe, a magnetization (as 4πMs) of 4.4kG, and a ferromagnetic resonance peak-to-peak derivative linewidth at 53GHz of 96Oe, thus demonstrating sufficient properties for microwave device applications.
Influence of electrode configuration on dielectric properties of ferroelectric films with interdigital and parallel plate electrodes
Authors: Liu Hong , Zhu Jianguo , Xiao Dingquan , Gong Xiaogang , Liang Jin-e , Li Xuedong , Zhu Xiaohong
Published: October 2007

The interdigital electrodes (IDEs) and parallel plate electrodes (PPEs) were prepared by photolithographic techniques and dc sputtering on rf magnetron sputtered lanthanum-modified lead titanate (PLT) films, respectively. The PLT films with IDEs and PPEs exhibit almost the same permittivity at 1kHz, while the dielectric constant and loss of PLT films with IDE decrease faster than those of the films with PPE as increasing the frequency. The permittivity of the films with IDE can be calculated using a previously developed analytical model. The reasons for the impact of the IDE and PPE on dielectric properties of the films were discussed.
Nonalloyed Cr∕Au-based Ohmic contacts to n-GaN
Authors: Lee Ming-Lun , Sheu Jinn-Kong , Hu C. C.
Published: October 2007

Nonalloyed Cr∕Au-based metal contacts to n-GaN have been demonstrated. The deposited Au∕Cr∕n-GaN contacts exhibited a specific contact resistance (ρc) of approximately 5.6×10−5Ωcm2. Although the nonalloyed Ti∕Al-based contacts to n-GaN can also exhibit a comparable ρc value, their thermal stability is inferior to the Cr∕Au-based contacts. This could be attributed to the fact that Al tends to ball up during thermal annealing. Thus, the surface morphology of most of the annealed Ti∕Al-based contacts was quite rough, and the contacts became rectified when they were annealed at a temperature below 700°C. However, the annealed Cr∕Au-based contacts exhibited an Ohmic characteristic and had a smooth surface when annealing temperatures did not exceed 700°C. In addition, the thermal stability could be further improved by inserting a Pt layer between the Cr and Au layers. This scheme could prevent the diffusion of Au into the Cr layer, thus preventing Au from reaching the Cr∕GaN interface where it could form a possible Ga–Au phase, which would degrade the Ohmic contacts.
Substrate-emitting, distributed feedback quantum cascade lasers
Authors: Lyakh A. , Zory P. , D’Souza M. , Botez D. , Bour D.
Published: October 2007

By using a semiconductor/metal grating formed on the episide of a quantum-cascade structure, distributed feedback lasing has been achieved with beam emission through the substrate. Using short-pulse excitation (100ns, 16kHz), single-longitudinal-mode operation near 5.1μm is demonstrated over wide ranges in heatsink temperature and drive current. The beam divergence in the longitudinal direction at a distance 40cm away from the 2.5mm wide aperture is ∼0.5°.
Quantum dot solar cell tolerance to alpha-particle irradiation
Authors: Cress Cory D. , Hubbard Seth M. , Landi Brian J. , Raffaelle Ryne P. , Wilt David M.
Published: October 2007

The effects of alpha-particle irradiation on an InAs quantum dot (QD) array and GaAs-based InAs QD solar cells were investigated. Using photoluminescence (PL) mapping, the PL intensity at 872 and 1120nm, corresponding to bulk GaAs and InAs QD emissions, respectively, were measured for a five-layer InAs QD array which had a spatially varying total alpha-particle dose. The spectral response and normalized current-voltage parameters of the solar cells, measured as a function of alpha-particle fluence, were used to investigate the change in device performance between GaAs solar cells with and without InAs QDs.
Structural and electrical properties of Pb(Zr,Ti)O3 films grown by molecular beam epitaxy
Authors: Izyumskaya N. , Avrutin V. , Gu X. , Xiao B. , Chevtchenko S. , Yoon J.-G. , Morkoç H. , Zhou Lin , Smith David J.
Published: October 2007

Single-crystal, single-phase Pb(ZrxTi1−x)O3 films (x=0–0.4) were grown on (001) SrTiO3 and SrTiO3:Nb substrates by molecular beam epitaxy. Layer-by-layer growth of the Pb(Zr,Ti)O3 films was achieved by using PbTiO3 buffer layers between the SrTiO3 substrates and the Pb(Zr,Ti)O3 films. The layers with low Zr content showed high crystallinity with full width at half maximum of ω-rocking curves as low as 4arcmin, whereas increase in Zr concentration led to pronounced angular broadening. The PbZr0.07Ti0.93O3 films exhibited remanent polarization as high as 83μC∕cm2, but local areas suffered from nonuniform leakage current.
Electrically tunable extraordinary optical transmission gratings
Authors: Shaner E. A. , Cederberg J. G. , Wasserman D.
Published: October 2007

We report a semiconductor based mechanism for electrically controlling the frequency of light transmitted through extraordinary optical transmission gratings. In doing so, we demonstrate active control over the surface plasmon (SP) resonance at the metal/dielectric interface. The gratings, designed to operate in the midinfrared spectral range, are fabricated upon a doped GaAs epilayer. Tuning of over 25cm−1 is achieved, and the devices are modeled to investigate the physical origin of the tuning mechanism. Though our structures are designed for the midinfrared, the tuning mechanism demonstrated could be applied to other wavelength ranges, especially the visible and near infrared.
Built-in electric field enhancement/retardation on intermixing
Authors: Xu C. D. , Mei T. , Chin M. K. , Dong J. R. , Chua S. J.
Published: October 2007

The built-in electric field may impose a drift on charged point defects and may thus enhance or retard the intermixing during annealing. Electric field is built-in near the surface due to the pinning of surface Fermi level after argon plasma treatment on InP surfaces of InP∕InGaAs quantum well samples. Subsequent annealing leads to different intermixing results due to the different field directions on InP cap layers in different doping types. Experiments also showed different influences of the built-in field on the two sublattices largely due to different charge numbers of point defects on the respective sublattices.
In-plane excitation of thin silicon cantilevers using piezoelectric thin films
Authors: Leighton Glenn J. T. , Kirby Paul B. , Fox Colin H. J.
Published: October 2007

This paper deals with the actuation of in-plane and out-of-plane motions of silicon cantilevers, using a single thin film of lead zirconate titanate with a divided electrode configuration. In-plane actuation is demonstrated practically, and excellent agreement is obtained between theoretically predicted and experimentally measured resonant amplitudes, for the fundamental out-of-plane and in-plane modes of vibration of the fabricated test cantilevers.
Ordered, uniform-sized ZnO nanolaser arrays
Authors: Zhou Huijuan , Wissinger Markus , Fallert Johannes , Hauschild Robert , Stelzl Felix , Klingshirn Claus , Kalt Heinz
Published: October 2007

Ordered ZnO nanorod arrays with almost uniform rod size have been grown perpendicularly on GaN∕Al2O3 substrates by a controlled vapor phase transport growth method. The ZnO nanorods are [0001] oriented single crystals with diameter of 200nm and length of 4.7μm, with a rod-to-rod spacing of 500nm. Photoluminescence spectra of the rod arrays indicate that the rods are of high crystal quality: very strong, well-separated bound and free exciton emission in the ultraviolet (UV) region are resolved at low temperature. Time resolved microphotoluminescence measurements are performed on single nanorods standing on the substrate which demonstrates lasing behavior with multiple UV lasing modes. Under quasistationary excitation lasing is observed up to room temperature. The lasing emission peaks are sharp, with a linewidth about 0.1nm, and have a fast decay time of ∼8ps. These high crystal quality nanorod arrays may be promising candidates for UV nanolaser devices.
Efficiency droop behaviors of InGaN∕GaN multiple-quantum-well light-emitting diodes with varying quantum well thickness
Authors: Li Y.-L. , Huang Y.-R. , Lai Y.-H.
Published: October 2007

In Ga N ∕ Ga N multiple-quantum-well (MQW) light-emitting diodes with varied InGaN quantum well thicknesses are fabricated and characterized. The investigation of luminous efficiency versus current density reveals a variety of efficiency droop behaviors. It is found that the efficiency droop can be drastically reduced by increasing the quantum well thickness of the MQW structures. On the other hand, relative internal quantum efficiency (IQE) measurements indicate that a thinner well results to higher IQEs owing to the greater spatial overlap of electron and hole distribution functions.
Structural and electrical properties of Pb(Zr,Ti)O3 grown on (0001) GaN using a double PbTiO3∕PbO bridge layer
Authors: Xiao Bo , Gu Xing , Izyumskaya Natalia , Avrutin Vitaliy , Xie Jinqiao , Liu Huiyong , Morkoç Hadis
Published: October 2007

Pb ( Zr 0.52 Ti 0.48 ) O 3 films were deposited by rf magnetron sputtering on silicon-doped GaN(0001)∕c-sapphire with a PbTiO3∕PbO oxide bridge layer grown by molecular beam epitaxy. X-ray diffraction data showed the highly (111)-oriented perovskite phase in lead zirconate titanate (PZT) films with PbTiO3∕PbO bridge layers, compared to the pyrochlore phase grown directly on GaN. The in-plane epitaxial relationships were found from x-ray pole figures to be PZT[112¯]‖GaN[11¯00] and PZT[11¯0]‖GaN[112¯0]. The polarization-electric field measurements revealed the ferroelectric behavior with remanent polarization of 30–40μC∕cm2 and asymmetric hysteresis loops due to the depletion layer formed in GaN under reverse bias which resulted in a high negative coercive electric field (950kV∕cm).
Route to a correct description of the fundamental properties of cubic InN
Authors: Briki M. , Zaoui A. , Boutaiba F. , Ferhat M.
Published: October 2007

The main fundamental properties of the cubic InN are studied within the density functional theory. We used the full-potential augmented plane wave method with two different exchange-correlation potentials, the Perdew-Wang (PW) and the Engel-Vosko (EV) approximations, in both cases nonrelativistic and relativistic. We found that the PW and relativistic approximations give a metallic ground state. The use of the EV and nonrelativistic approximations gives, however, a semiconductor phase with a band-gap value of 0.57eV, which is in fairly good agreement with the recent measurement of 0.61eV.
Comparison of xylem sap mineral concentrations between kiwifruit shoot types using spittlebugs for non-destructive sampling of sap
Authors: Buxton Katrina N. , Clearwater Michael J. , Giles-Hansen K. , Hewett E. W. , Ferguson Ian B.
Published: October 2007

Excreta of the meadow spittlebug [Philaenus spumarius L. (Homoptera: Cercopidae)] feeding on leaves and pedicels of kiwifruit [Actinidia deliciosa (A. Chev.) C.F. Liang et A.R. Ferguson var. deliciosa ‘Hayward’] were collected from insects from two different positions in the vine: from long, non-terminating axillary shoots producing fruit that are high in Ca2+ and low in K+ and from short-terminating axillary shoots producing fruit that are low in Ca2+ and high in K+. The Ca2+, Mg2+, K+ and P concentrations in the excreta were determined, and found to be similar to those in the xylem sap. Daily and seasonal changes in xylem sap composition were compared in excreta collected from the two different shoot types. On average, Ca2+ and Mg2+ concentrations were higher and K+ and P concentrations were lower in xylem sap collected from pedicels on long, non-terminating axillary shoots than in sap collected from pedicels on short-terminating shoots. Differences in the mineral concentration between these two shoot types may therefore be due to differences in the xylem sap mineral concentration reaching the fruit. There was no measurable gradient in xylem sap composition within the parent shoots that could explain the differences between sap composition of the two axillary shoot types. Long, non-terminating shoots had higher leaf area, were more exposed, had higher stomatal conductance and rates of transpiration, and more negative leaf water potentials than short-terminating shoots. The higher xylem sap Ca2+ and Mg2+ concentrations of long shoots were therefore associated with higher rates of water transport to the long shoots. Xylem sap concentration differences between these two shoots types may have been because of differential loading or unloading of minerals between shoot types, associated with differences in transpiration rate or shoot growth rates. The higher transpiration rate of long shoots may cause phloem immobile minerals such as Ca2+ to accumulate to higher levels at cation exchange sites in the shoot apoplast, resulting in increased xylem sap concentrations arriving at the fruit.
Amino acid transporter expression and localisation studies in pea (Pisum sativum)
Authors: Tegeder Mechthild , Tan Qiumin , Grennan Aleel K. , Patrick John W.
Published: October 2007

Expression of the amino acid permeases PsAAP1 and PsAAP2 was analysed in developing pea (Pisum sativum L.) plants. Both transporters were expressed in seed coats and cotyledon epidermal transfer cells and storage parenchyma cells. AAP expression is developmentally regulated and coincides with the onset of storage protein synthesis. Nitrogen was shown to induce AAP expression and AAP transcript levels were upregulated during the photoperiod. Analysis of Arabidopsis thaliana AAP1 promoter activity in pea, using promoter-β-glucuronidase (promotor-GUS) studies, revealed targeting of GUS to seed coats and cotyledon epidermal transfer cells. Expression was found in the nutritious endosperm during the early stages of seed development, whereas GUS staining in embryos was detected from the heart stage onward. In addition, AAP1 expression was observed in the phloem throughout the plant. This finding equally applied to PsAAP1 expression as shown by in situ mRNA hybridisation, which also demonstrated that PsAAP1 expression was localised to companion cells. Overall, PsAAP1 expression patterns and cellular localisation point to a function of the transporter in phloem loading of amino acids for translocation to sinks and in seed loading for development and storage protein accumulation.
Reproduction of Heterodontus portusjacksoni in Victoria, Australia: evidence of two populations and reproductive parameters for the eastern population
Authors: Tovar-Ávila Javier , Walker Terence I. , Day Robert W.
Published: October 2007

Significant differences in the length–frequency composition of catch samples, mass–length relationships and length-at-maturity found between Heterodontus portusjacksoni from western and far-eastern Victoria, suggest the presence of at least two separate breeding populations off south-eastern Australia, with some mixing between these regions. In each region females attain a larger size than males, and collectively those sharks in western Victoria are smaller, present higher mass-at-length, and lower length-at-maturity than those in far-eastern Victoria. These regional differences might be a result of sampling bias, length-selective fishing mortality, environmental conditions, or genetic differences. However, tagging evidence from previous studies and the presence of two bio-geographic provinces in the region support the hypothesis of two separate breeding populations. The essential reproductive parameters for H. portusjacksoni population analysis in far-eastern Victoria were determined, using a novel method to estimate fecundity and the ovarian cycle of an egg-laying species. In this region, females have between 6 and 20 pre-ovulatory oocytes (average = 14, n = 29, standard deviation = 3.71) before the reproductive season. The species has an annual reproductive cycle correlated with water temperature, with ovulation starting during late winter to early spring and a ~6 month egg-laying period. The period from the onset of vitellogenesis to ovulation of oocytes is ~18 months.
Fish fauna of dry tropical and subtropical estuarine floodplain wetlands
Authors: Sheaves Marcus , Johnston Ross , Abrantes Kátya
Published: October 2007

Estuarine floodplain wetland pools occur adjacent to marine coasts and estuaries throughout the world. In Australia’s dry tropics and sub-tropics, low and irregular rainfall means estuarine wetland pools are isolated for much of the time, resulting in varied within-pool conditions, with chemistry ranging from fresh to hypersaline, depending on the balance between freshwater and marine inputs and the time between connections. Varied physical conditions and irregular connectivity provide the potential for substantial faunal difference among pools. The present study compares the compositions and structures of the fish fauna of a broad cross section of estuarine wetland pools adjacent to the estuary of the Fitzroy River, one of the largest rivers in Australia’s dry tropical/subtropical zone. Ten pools were sampled between February 2004 and May 2005. The total species richness was low, with the 6123 fish recorded over the study, comprising only 44 species. This low species richness was reflected at the individual pool level, with a maximum total richness of 25 species in a single pool. Different pools had faunas that differed as a function of the proportion of the community comprised of marine spawned, compared with freshwater spawned, species. This was a reflection of the extent of connectivity to freshwater and marine systems, which determined both the physical nature of pools and the sources of faunal supply. Despite faunal differences among pools, at a functional level pool fish faunas were dominated by detritivores, regardless of pool type, size, season or connectedness.
Simulation of the estimation of ageing bias inside an integrated assessment of canary rockfish using age estimates from a bomb radiocarbon study
Authors: Stewart Ian J. , Piner Kevin R.
Published: October 2007

The stock of canary rockfish off the west coast of the continental US is currently assessed using an integrated statistical catch-at-age model. The functional form of an ageing bias detected in production ageing (large numbers of ages read for use in stock assessment) from a bomb radiocarbon study with small sample size (n = 16) was estimated externally and used to adjust the age data in the most recent stock assessment. Using simulation methods, the present study evaluated whether integrating the estimation of the ageing bias inside the assessment model would (1) influence the uncertainty in assessment results and (2) improve our ability to differentiate between competing functional forms (linear, linear with intercept and jointed) for specifying the ageing bias. Internal estimation of the ageing bias relationship increased the approximate 95% confidence interval width about the spawning biomass estimate by 1–10% depending on the functional form assumed. The assessment model was not able to reliably distinguish between all competing functional forms of the ageing bias tested, even with increased radiocarbon sample sizes. However, significant under-ageing at the youngest ages was found to be inconsistent with other sources of data in the assessment model. The question of ageing bias form remains important because it had moderate effects on estimates of spawning biomass and assessment model uncertainty.
Validation of age and growth in a long-lived temperate reef fish using otolith structure, oxytetracycline and bomb radiocarbon methods
Authors: Ewing Graeme P. , Lyle Jeremy M. , Murphy Raymond J. , Kalish John M. , Ziegler Philippe E.
Published: October 2007

Generating age estimates for long-lived fish requires particular attention to validation because they are usually difficult to age owing to narrow increment structure. A robust validation of the accuracy and precision of banded morwong, Cheilodactylus spectabilis, sampled from Tasmanian waters, was undertaken. Age at the first enumerated increment was established from analysis of juvenile cohorts, and the timing and periodicity of increment formation was established using a quantitative model from oxytetracycline (OTC) mark-recaptures at liberty for periods of up to 8 years. The accuracy of age estimates was examined independently by comparing radiocarbon values in the otolith region corresponding to the first year of growth against the south-western Pacific calibration curve. C. spectabilis is very long-lived, with males and females living to over 90 years of age. Growth modelling revealed a fast initial growth phase, terminating in an abrupt plateau near the asymptotic length. This species displays substantial sexual dimorphism in growth, with males growing to larger sizes than females.
The effect of packaging of chlorophyll within phytoplankton and light scattering in a coupled physical - biological ocean model
Authors: Baird Mark E. , Timko Patrick G. , Wu Lujia
Published: October 2007

A coupled physical–biological model forced with spectrally resolved solar radiation is used to investigate the effect of packaging of pigment and light scattering on physical and biological properties in the open ocean. Simulations are undertaken with three alternate formulations of vertical attenuation, which consider: (1) chlorophyll as dissolved in the water column; (2) chlorophyll packaged into phytoplankton cells with no scattering; and (3) packaged chlorophyll with scattering. In the coupled model, depth-resolved solar heating depends on the vertical profile of phytoplankton concentration, creating a feedback mechanism between the physical and biological states.
The particular scenario investigated is a northerly wind off the coast of south-east Australia. The packaging of chlorophyll approximately halves the attenuation rate of 340–500 nm light and a phytoplankton maximum forms ~10 m deeper than in the dissolved chlorophyll case, with a corresponding adjustment of the dissolved inorganic nitrogen and zooplankton fields. Scattering approximately doubles the vertical attenuation of 340–600 nm light, lifting the phytoplankton maximum by ~10 m when compared with the packaged chlorophyll case. Additionally, strong horizontal gradients in chlorophyll distribution associated with filaments of upwelled water inshore of the East Australian Current, when modelled with alternate formulations of vertical light attenuation, result in circulation changes. The explicit representation of the packaging of pigment and light scattering is worth considering in coupled physical–biological modelling studies.
Observations of warming on the Western Australian continental shelf
Authors: Pearce Alan , Feng Ming
Published: October 2007

Global temperature datasets indicate a warming trend in the south-eastern Indian Ocean of ~0.02°C year–1. This is supported by in situ temperature measurements at a coastal monitoring station on the Western Australian continental shelf that have shown a mean temperature rise of 0.013°C year–1 since 1951, corresponding to ~0.6°C over the past 5 decades. Measurements from three other shallow stations between 1985 and 2004 indicated warming trends of 0.026–0.034°C year–1. It is suggested that enhanced air–sea heat flux into the south-eastern Indian Ocean may be a key factor in the rising temperature trend. There has also been a steady rise in salinity over the past half-century. At interannual scales, coherent temperature variability at the various stations indicates that larger-scale processes are influencing the shelf waters and are linked with El Niño/Southern Oscillation (ENSO)-related events in coastal sea level and hence the Leeuwin Current.
Occurrence and persistence of non-native Cichlasoma urophthalmus (family Cichlidae) in estuarine habitats of south-west Florida (USA): environmental controls and movement patterns
Authors: Adams Aaron J. , Wolfe R. Kirby
Published: October 2007

The geographic scope of species introductions has increased dramatically in the last 200 years. One of the greatest challenges to understanding the ecological consequences of non-native species is that it has been difficult to identify the attributes that allow them to become established outside their native range. This challenge is compounded by anthropogenic habitat alteration that often enhances the establishment and expansion of non-native species. Fishes in the family Cichlidae are notoriously adaptive, and contribute more non-native species to North America than any other fish family. This is especially true in Florida (USA), where 18 cichlid species have become established. The Mayan cichlid (Cichlasoma urophthalmus) was first documented in south Florida in 1983, and is present in many freshwater and estuarine habitats. This study reports a northward range expansion by C. urophthalmus, demonstrates the connectivity between altered freshwater habitats and tidal estuarine habitats, and suggests that the estuarine populations are ephemeral and dependent upon colonisation from populations in altered freshwater habitats.
BM88/CEND1 coordinates cell cycle exit and differentiation of neuronal precursors
Authors: Politis Panagiotis K. , Makri Georgia , Thomaidou Dimitra , Geissen Markus , Rohrer Hermann , Matsas Rebecca
Published: October 2007

During development, coordinate regulation of cell cycle exit and differentiation of neuronal precursors is essential for generation of appropriate number of neurons and proper wiring of neuronal circuits. BM88 is a neuronal protein associated
in vivo
with terminal neuron-generating divisions, marking the exit of proliferative cells from the cell cycle. Here, we provide functional evidence that BM88 is sufficient to initiate the differentiation of spinal cord neural precursors toward acquisition of generic neuronal and subtype-specific traits. Gain-of-function approaches show that BM88 negatively regulates proliferation of neuronal precursors, driving them to prematurely exit the cell cycle, down-regulate Notch1, and commit to a neuronal differentiation pathway. The combined effect on proliferation and differentiation results in precocious induction of neurogenesis and generation of postmitotic neurons within the ventricular zone. The dual action of BM88 is not recapitulated by the cell cycle inhibitor p27
Kip1
, suggesting that cell cycle exit does not induce differentiation by default. Mechanistically, induction of endogenous BM88 by forced expression of the proneural gene
Mash1
indicates that BM88 is part of the differentiation program activated by proneural genes. Furthermore, BM88 gene silencing conferred by small interfering RNA in spinal cord neural progenitor cells enhances cell cycle progression and impairs neuronal differentiation. Our results implicate BM88 in the synchronization of cell cycle exit and differentiation of neuronal precursors in the developing nervous system.
Single-molecule level analysis of the subunit composition of the T cell receptor on live T cells
Authors: James John R. , White Samuel S. , Clarke Richard W. , Johansen Adam M. , Dunne Paul D. , Sleep David L. , Fitzgerald William J. , Davis Simon J. , Klenerman David
Published: October 2007

The T cell receptor (TCR) expressed on most T cells is a protein complex consisting of TCRαβ heterodimers that bind antigen and cluster of differentiation (CD) 3εδ, εγ, and ζζ dimers that initiate signaling. A long-standing controversy concerns whether there is one, or more than one, αβ heterodimer per complex. We used a form of single-molecule spectroscopy to investigate this question on live T cell hybridomas. The method relies on detecting coincident fluorescence from single molecules labeled with two different fluorophores, as the molecules diffuse through a confocal volume. The fraction of events that are coincident above the statistical background is defined as the “association quotient,”
Q
. In control experiments,
Q
was significantly higher for cells incubated with wheat germ agglutinin dual-labeled with Alexa488 and Alexa647 than for cells incubated with singly labeled wheat germ agglutinin. Similarly, cells expressing the homodimer, CD28, gave larger values of
Q
than cells expressing the monomer, CD86, when incubated with mixtures of Alexa488- and Alexa647-labeled antibody Fab fragments. T cell hybridomas incubated with mixtures of anti-TCRβ Fab fragments labeled with each fluorophore gave a
Q
value indistinguishable from the
Q
value for CD86, indicating that the dominant form of the TCR comprises single αβ heterodimers. The values of
Q
obtained for CD86 and the TCR were low but nonzero, suggesting that there is transient or nonrandom confinement, or diffuse clustering of molecules at the T cell surface. This general method for analyzing the subunit composition of protein complexes could be extended to other cell surface or intracellular complexes, and other living cells.
Low genomic diversity in tropical oceanic N
2
-fixing cyanobacteria
Authors: Zehr Jonathan P. , Bench Shellie R. , Mondragon Elizabeth A. , McCarren Jay , DeLong Edward F.
Published: October 2007

High levels of genomic and allelic microvariation have been found in major marine planktonic microbial species, including the ubiquitous open ocean cyanobacterium,
Prochlorococcus marinus
.
Crocosphaera watsonii
is a unicellular cyanobacterium that has recently been shown to be important in oceanic N
2
fixation and has been reported from the Atlantic and Pacific oceans in both hemispheres, and the Arabian Sea. In direct contrast to the current observations of genomic variability in marine non-N
2
-fixing planktonic cyanobacteria, which can range up to >15% nucleotide sequence divergence, we discovered that the marine planktonic nitrogen-fixing cyanobacterial genus
Crocosphaera
has remarkably low genomic diversity, with <1% nucleotide sequence divergence in several genes among widely distributed populations and strains. The cultivated
C. watsonii
WH8501 genome sequence was virtually identical to DNA sequences of large metagenomic fragments cloned from the subtropical North Pacific Ocean with <1% sequence divergence even in intergenic regions. Thus, there appears to be multiple strategies for evolution, adaptation, and diversification in oceanic microbial populations. The
C. watsonii
genome contains multiple copies of several families of transposases that may be involved in maintaining genetic diversity through genome rearrangements. Although genomic diversity seems to be the rule in many, if not most, marine microbial lineages, different forces may control the evolution and diversification in low abundance microorganisms, such as the nitrogen-fixing cyanobacteria.
Estimation of the number of virus particles transmitted by an insect vector
Authors: Moury Benoît , Fabre Frédéric , Senoussi Rachid
Published: October 2007

Plant viruses are submitted to narrow population bottlenecks both during infection of their hosts and during horizontal transmission between host individuals. The size of bottlenecks exerted on virus populations during plant invasion has been estimated in a few pathosystems but is not addressed yet for horizontal transmission. Using competition for aphid transmission between two
Potato virus Y
variants, one of them being noninfectious but equally transmissible, we obtained estimates of the size of bottlenecks exerted on an insect-borne virus during its horizontal transmission. We found that an aphid transmitted on average 0.5–3.2 virus particles, which is extremely low compared with the census viral population into a plant. Such narrow bottlenecks emphasize the strength of stochastic events acting on virus populations, and we illustrate, in modeling virus emergence, why estimating this parameter is important.
Ablation of sarcolipin enhances sarcoplasmic reticulum calcium transport and atrial contractility
Authors: Babu Gopal J. , Bhupathy Poornima , Timofeyev Valeriy , Petrashevskaya Natalia N. , Reiser Peter J. , Chiamvimonvat Nipavan , Periasamy Muthu
Published: October 2007

Sarcolipin is a novel regulator of cardiac sarcoplasmic reticulum Ca
2+
ATPase 2a (SERCA2a) and is expressed abundantly in atria. In this study we investigated the physiological significance of sarcolipin in the heart by generating a mouse model deficient for sarcolipin. The sarcolipin-null mice do not show any developmental abnormalities or any cardiac pathology. The absence of sarcolipin does not modify the expression level of other Ca
2+
handling proteins, in particular phospholamban, and its phosphorylation status. Calcium uptake studies revealed that, in the atria, ablation of sarcolipin resulted in an increase in the affinity of the SERCA pump for Ca
2+
and the maximum velocity of Ca
2+
uptake rates. An important finding is that ablation of sarcolipin resulted in an increase in atrial Ca
2+
transient amplitudes, and this resulted in enhanced atrial contractility. Furthermore, atria from sarcolipin-null mice showed a blunted response to isoproterenol stimulation, implicating sarcolipin as a mediator of β-adrenergic responses in atria. Our study documented that sarcolipin is a key regulator of SERCA2a in atria. Importantly, our data demonstrate the existence of distinct modulators for the SERCA pump in the atria and ventricles.
High-resolution design of a protein loop
Authors: Hu Xiaozhen , Wang Huanchen , Ke Hengming , Kuhlman Brian
Published: October 2007

Despite having irregular structure, protein loops often adopt specific conformations that are critical to protein function. Most studies in
de novo
protein design have focused on creating proteins with regular elements of secondary structure connected by very short loops or turns. To design longer protein loops that adopt specific conformations, we have developed a protocol within the Rosetta molecular modeling program that iterates between optimizing the sequence and conformation of a loop in search of low-energy sequence–structure pairs. We have tested the procedure by designing 10-residue loops for the connection between the second and third strand in the β-sandwich protein tenascin. Three low-energy designs from 7,200 flexible backbone trajectories were selected for experimental characterization. All three designs, called LoopA, LoopB, and LoopC, adopt stable folded structures. High-resolution crystal structures of LoopA and LoopB have been solved. LoopB adopts a structure very similar to the design model (0.46 Å rmsd), and all but one of the side chains are modeled in the correct rotamers. LoopA crystallized at low pH in a structure that differs dramatically from our design model. It forms a strand-swapped dimer mediated by hydrogen bonds to protonated glutamic acids. Gel filtration indicates that the protein is not a dimer at neutral pH. These results suggest that the high-resolution design of protein loops is possible; however, they also highlight how small changes in protein energetics can dramatically perturb the low free energy structure of a protein.