bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and characterization of a lectin with potentially exploitable activities from caper (Capparis spinosa) seeds
Authors: Lam Sze Kwan , Han Qi Feng , Ng Tzi Bun
Published: October 2008

A dimeric 62-kDa lectin exhibiting a novel N-terminal amino acid sequence was purified from caper (Capparis spinosa) seeds. The purification protocol involved anion-exchange chromatography, cation-exchange chromatography and, finally, gel filtration by FPLC on Superdex 75. Approx. 100-fold purification was achieved. The haemagglutinating activity of the lectin, which was stable in the pH range 1–12 and up to 40°C, could be inhibited by D(+) galactose, α-lactose, raffinose and rhamnose at 1 mM concentration, by 25 mM L(+)-arabinose and by 100 mM D(+)GlcN (glucosamine). The lectin potently inhibited HIV-1 reverse transcriptase with an IC50 of 0.28 μM and proliferation of both hepatoma HepG2 and breast cancer MCF-7 cells with an IC50 of approx. 2 μM. It induced apoptosis in HepG2 and MCF-7 cells. It manifested a weaker mitogenic activity on mouse splenocytes than ConA (concanavalin A). It inhibited mycelial growth in Valsa mali with an IC50 of 18 μM.
Total leucocyte count, but not C-reactive protein, predicts 1-year mortality in patients with acute coronary syndromes treated with percutaneous coronary intervention
Authors: Ndrepepa Gjin , Braun Siegmund , Iijima Raisuke , Keta Dritan , Byrne Robert A. , Schulz Stefanie , Mehilli Julinda , Schömig Albert , Kastrati Adnan
Published: October 2008

Although an association between elevated leucocyte count and mortality in patients with ACS (acute coronary syndromes) has been established, the independence of this association from coronary risk factors and C-reactive protein has been inadequately studied. In the present study, this prospective registry included 4329 patients with ACS treated with PCI (percutaneous coronary intervention): 1059 patients with STEMI [ST-segment elevation MI (myocardial infarction)], 1753 patients with NSTEMI (non-STEMI) and 1517 patients with unstable angina. Blood samples were obtained before angiography for leucocyte count and C-reactive protein measurements. The primary outcome of this analysis was 1-year mortality. At 1 year, 345 patients (8%) had died: 45 patients in the 1st tertile, 93 patients in the 2nd tertile and 207 patients in the 3rd tertile of leucocyte count [Kaplan–Meier estimates of mortality, 3.2%, 6.4% and 14.1% with an OR (odds ratio)=2.42, 95% CI (confidence interval)1.78–3.12; P<0.001 for tertile 3 compared with tertile 2 and an OR=1.99, 95% CI 1.77–2.25; P<0.001 for tertile 2 compared with tertile 1]. The Cox proportional hazards model adjusting for coronary risk factors, ACS presentation, extent of coronary artery disease, C-reactive protein and other covariates identified leucocyte count with a HR (hazard ratio)=1.05 (95% CI 1.02–1.07; P<0.001 for 1000 cells/mm3 increase in the leucocyte count), but not C-reactive protein (HR=1.13, 95% CI 0.95–1.34; P=0.15 for a 1 tertile increase in the C-reactive protein concentration) as an independent correlate of 1-year mortality. We conclude that elevated leucocyte count, but not C-reactive protein, predicts 1-year mortality independent of cardiovascular risk factors across the entire spectrum of patients with ACS treated with PCI.
Measurement of absolute transition dipole moment functions of the 3 Π1→1(X)Σ1+ and 3 Π1→2(A)Σ1+ transitions in NaK using Autler–Townes spectroscopy and calibrated fluorescence
Authors: Sweeney S. J. , Ahmed E. H. , Qi P. , Kirova T. , Lyyra A. M. , Huennekens J.
Published: October 2008

We describe a two-laser experiment using optical-optical double resonance fluorescence and Autler–Townes (AT) splittings to determine the NaK 3 Π1→1(X)Σ1+, 2(A)Σ1+ absolute transition dipole moment functions. Resolved 3 Π1→A Σ1+ and 3 Π1→X Σ1+ fluorescence was recorded with the frequencies of a titanium-sapphire laser (L1) and a ring dye laser (L2) fixed to excite particular 3 Π1(υ=19,J=11,f)←A Σ1+(υ′,J′=J=11,e)←X Σ1+(υ″,J″=J′±1,e) double resonance transitions. The coefficients of a trial transition dipole moment function μe(R)=a0+a1(Req/R)2+a2(Req/R)4+… were adjusted to match the relative intensities of resolved spectral lines terminating on the lower A Σ1+(υ′,11,e) and X Σ1+(υ″,11,e) levels. These data provide a relative measure of the functions μe(R) over a broad range of R. Next, L2 was tuned to either the 3 Π1(19,11,f)←A Σ1+(10,11,e) or 3 Π1(19,11,f)←A Σ1+(9,11,e) transition and focused to an intensity large enough to split the levels via the AT effect. L1 was scanned over the A Σ1+(10,11,e)←X Σ1+(1,10,e) or A Σ1+(9,11,e)←X Σ1+(0,12,e) transition to probe the AT line shape, which was fit using density matrix equations to yield an absolute value for μik=∫ψvibi(R)μe(R)ψvibk(R)dR, where i and k represent the upper and lower levels, respectively, of the coupling laser (L2) transition. Finally, the values of μik were used to place the relative μe(R) functions obtained with resolved fluorescence onto an absolute scale. We compare our experimental transition dipole moment functions to the theoretical work of Magnier et al. [J. Mol. Spectrosc. 200, 96 (2000)].
On the growth mechanism of plasma deposited amorphous silicon thin films
Authors: Pandey Sumeet C. , Singh Tejinder , Maroudas Dimitrios
Published: October 2008

We propose a comprehensive mechanism of amorphous silicon thin film growth by plasma deposition based on results of kinetic Monte Carlo simulations according to a database constructed by first-principles density functional theory calculations. The growth mechanism consists of various surface kinetic events including radical-surface and adsorbed radical-radical interactions, radical-surface diffusion, and surface hydride dissociation reactions. Of particular importance is the radical dissociative adsorption mediated by Si over-coordination defects along the reaction pathway. The proposed mechanism explains fully the experimentally measured surface composition of plasma deposited films under conditions that make the silyl radical the dominant deposition precursor.
A magic-angle-spinning NMR method for H1–H1 distance measurement using coherent polarization transfer in C13-labeled organic solids
Authors: Takahashi Hiroki , Akutsu Hideo , Fujiwara Toshimichi
Published: October 2008

We have developed a theory for H1–H1 distance measurements from the direct polarization transfer in C13-labeled solids under magic-angle spinning. The polarization transfer caused by the H1–H1 dipolar interactions was analyzed with zeroth-order average Hamiltonian for a H1–C13–C13–H1 spin system in the frame modulated by C13–H1 dipolar interactions and chemical shifts. Strong C13–H1 dipolar couplings primarily determine the recovery of the H1–H1 coupling as a function of sample spinning frequency. The effect of additional H1 spins on the polarization transfer was also taken into account. We have applied this method to the distance measurements for uniformly C13-, N15-labeled L-valine and adenosine. Experimental H1 polarization transfer was monitored through high-resolution C13-NMR. The theoretical analysis provided the distances up to about 3 Å with an accuracy of about 0.2 Å and those of about 4 Å with 1 Å even from the transfer amplitudes at a few mixing times. The longer distances are partly affected by the relayed polarization transfer which makes apparent H1–H1 distances shorter. Our theory based on the coherent polarization transfer in the initial build-up regime was compared to the description by the rate equations with spin diffusion time constants.
Oscillations and multiscale dynamics in a closed chemical reaction system: Second law of thermodynamics and temporal complexity
Authors: Li Yongfeng , Qian Hong , Yi Yingfei
Published: October 2008

We investigate the oscillatory reaction dynamics in a closed isothermal chemical system: the reversible Lotka–Volterra model. The second law of thermodynamics dictates that the system ultimately reaches an equilibrium. Quasistationary oscillations are analyzed while the free energy of the system serves as a global Lyapunov function of the dissipative dynamics. A natural distinction between regions near and far from equilibrium in terms of the free energy can be established. The dynamics is analogous to a nonlinear mechanical system with time-dependent increasing damping. Near equilibrium, no oscillation is possible as dictated by Onsager’s reciprocal symmetry relation. We observe that while the free energy decreases in the closed system’s dynamics, it does not follow the steepest descending path.
The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier
Authors: Lei Hongxing , Deng Xiaojian , Wang Zhixiang , Duan Yong
Published: October 2008

The LYS24/29NLE double mutant of villin headpiece subdomain (HP35) is the fastest folding protein known so far with a folding time constant of 0.6μs. In this work, the folding mechanism of the mutant has been investigated by both conventional and replica exchange molecular dynamics (CMD and REMD) simulations with AMBER FF03 force field and a generalized-Born solvation model. Direct comparison to the ab initio folding of the wild type HP35 enabled a close examination on the mutational effect on the folding process. The mutant folded to the native state, as demonstrated by the 0.50Å Cα-root mean square deviation (RMSD) sampled in both CMD and REMD simulations and the high population of the folded conformation compared with the denatured conformations. Consistent with experiments, the significantly reduced primary folding free energy barrier makes the mutant closer to a downhill folder than the wild type HP35 that directly leads to the faster transition and higher melting temperature. However, unlike the proposed downhill folding which envisages a smooth shift between unfolded and folded states without transition barrier, we observed a well-defined folding transition that was consistent with experiments. Further examination of the secondary structures revealed that the two mutated residues have higher intrinsic helical preference that facilitated the formation of both helix III and the intermediate state which contains the folded segment helix II∕III. Other factors contributing to the faster folding include the more favorable electrostatic interactions in the transition state with the removal of the charged NH3+ groups from LYS. In addition, both transition state ensemble and denatured state ensemble are shifted in the mutant.
Measurement of the transport spin polarization of doped strontium ruthenates using point contact Andreev reflection
Authors: Woods G. T. , Sanders J. , Kolesnik S. , Maxwell T. , Srikanth H. , Dabrowski B. , Osofsky M. S. , Soulen R. J.
Published: October 2008

Electrical conductivity, magnetic susceptibility, and point contact Andreev reflection (PCAR) studies were done on bulk, polycrystalline SrRu1−x(TM)xO3 (TM=Cr, Mn, Ti) and SrRu0.92O3 with a high degree of disorder. Fits of the temperature dependence of the latter using the Curie–Weiss law yielded values for the Curie–Weiss temperature, Θ. Furthermore, the values of the Curie temperature, TC were identified by determining the maximum susceptibility as a function of temperature. PCAR measurements were done to determine the transport spin polarization, Pt (0⩽Pt⩽1.0). Pure SrRuO3 undergoes ferromagnetic ordering at a Curie temperature of TC∼160K and has a relatively high spin polarization (∼0.6). Our results indicate that when the lattice is disordered from either the presence of Ru lattice site defects or the substitution of a transition metal for the Ru, TC changes by a factor of 2, and Θ by a factor of 1.7. By contrast, the spin polarization is unchanged for both SrRu0.94Ti0.06O3 and SrRu0.9Mn0.1O3, while it is barely changed (P=0.5) for SrRu0.9Cr0.1O3.
Refractive-index nonlinearities of intersubband transitions in GaN/AlN quantum-well waveguides
Authors: Li Yan , Bhattacharyya Anirban , Thomidis Christos , Liao Yitao , Moustakas Theodore D. , Paiella Roberto
Published: October 2008

The refractive-index nonlinearities of intersubband transitions in GaN/AlN quantum-well waveguides are investigated. A large spectral broadening of TM-polarized near-infrared pulses is observed after propagation through these devices due to intersubband self-phase modulation. From the measured data, a nonlinear refractive index n2 of 1.8×10−12 cm2/W is estimated at the operating wavelength of 1550 nm. A detailed theoretical model of the intersubband refractive index as a function of wavelength and optical intensity is then presented. This model assumes an inhomogeneously broadened transition line and is based on experimentally determined material and device parameters. The results of this study are finally used to discuss the prospects of nitride quantum wells for all-optical switching via cross-phase modulation.
The time reversed elastic nonlinearity diagnostic applied to evaluation of diffusion bonds
Authors: Ulrich T. J. , Sutin Alexander M. , Claytor Thomas , Papin Pallas , Le Bas Pierre-Yves , TenCate James A.
Published: October 2008

With the recent application of time reversed acoustics and nonlinear elasticity to imaging mechanical damage, the development of time reversal based nondestructive evaluation techniques has begun. Here, diffusion bonded metal disks containing intentionally disbonded regions are analyzed using the time reversed elastic nonlinearity diagnostic. The nonlinear results are compared with linear ultrasonic imaging (C scan). Scanning electron microscopy is shown to illustrate the differences between the features seen by the linear and nonlinear methods.
Geometry-controlled droplet generation in head-on microfluidic devices
Authors: Shui Lingling , Mugele Frieder , van den Berg Albert , Eijkel Jan C. T.
Published: October 2008

We investigated the generation of droplets in a head-on microfluidic device operated with the two identical channels as inlets and the “long leg” as a constriction channel leading to a wider outlet section. For capillary numbers (Ca) of approximately 10−5 or less, we find a Ca-independent droplet volume equal to the volume of the constriction channel, which decreases at higher Ca when shear forces become relevant. The droplet generation mechanism is explained in terms of a global capillary instability involving surprisingly stable intermediate surface configurations.
Experimental manifestation of the breakpoint region in the current-voltage characteristics of intrinsic Josephson junctions
Authors: Irie A. , Shukrinov Yu. M. , Oya G.
Published: October 2008

The experimental evidence of the breakpoint on the current-voltage characteristics (IVCs) of the stacks of intrinsic Josephson junctions (IJJs) is presented. The influence of the capacitive coupling on the IVCs of Bi2Sr2CaCu2Oy IJJs has been investigated. At 4.2K, clear breakpoint region is observed on the branches in the IVCs. It is found that due to the coupling between junctions, the hysteresis observed on the IVC is small compared to that expected from the McCumber parameter. Measurements agree well with the results predicted by the capacitively coupled Josephson junction model including the diffusion current.
Learning Building Layouts with Non-Geometric Visual Information: The Effects of Visual Impairment and Age
Authors: Kalia Amy A , Legge Gordon E , Giudice Nicholas A
Published: October 2008

Previous studies suggest that humans rely on geometric visual information (hallway structure) rather than non-geometric visual information (eg doors, signs, and lighting) for acquiring cognitive maps of novel indoor layouts. In this study we asked whether visual impairment and age affect reliance on non-geometric visual information for layout learning. We tested three groups of participants—younger (<50 years of age) normally sighted; older (50–70 years of age) normally sighted; and low-vision (people with heterogeneous forms of visual impairment ranging in age from 18 to 67 years). Participants learned target locations in building layouts using four presentation modes: a desktop virtual environment (VE) displaying only geometric cues (sparse VE); a VE displaying both geometric and non-geometric cues (photorealistic VE); a map; and a real building. Layout knowledge was assessed by map drawing and by asking participants to walk to specified targets in the real space. Results indicate that low-vision and older normally sighted participants relied on additional non-geometric information to accurately learn layouts. In conclusion, visual impairment and age may result in reduced perceptual and/or memory processing that makes it difficult to learn layouts without non-geometric visual information.
Demographic and design effects on beef sensory scores given by Korean and Australian consumers
Authors: Hwang I. H. , Polkinghorne R. , Lee J. M. , Thompson J. M.
Published: October 2008

Data from 648 beef samples, which had been sensory tested by 720 Korean and 540 Australian consumers were used to quantify design and demographic effects on beef sensory scores. The samples were from 36 carcasses, where sides had been either hung by the Achilles tendon or hip suspended. At boning, samples from three muscles (M. triceps brachii, M. longissimus dorsi and M. semimembranosus) were prepared and cooked by either grill (25-mm-thick steaks) or Korean barbeque (BBQ, 4-mm-thick samples) methods. A Latin square design was used to allocate samples to different presentation orders to be tasted in association with different samples. For both cooking techniques each consumer tested a starter sample followed by six experimental samples, with each sample being tasted by 10 different consumers.
Design (taste panel, session, order, carry-over, sample and consumer) and demographic (age class, gender, occupation, frequency of eating meat, number of adults and children living in the house, their appreciation of meat and degree of doneness and income) effects were examined separately for tenderness, juiciness, like flavour, overall liking and a composite palatability score, within the four consumer group/cooking method subclasses. For grill samples, order of presentation was significant for most sensory variables. For BBQ samples, order of presentation failed to achieve significance for Australian consumers, but was significant (P < 0.05) for Korean consumers. Carry-over effects tended to be more important for juiciness and like flavour scores than other sensory scores. Demographic effects were generally not significant (P > 0.05) for all consumer group/cooking methods. Correlations between raw scores and those adjusted for design and demographic effects ranged from 0.93 to 0.99, indicating that if the design was balanced, or nearly balanced for design effects, then further adjustment of sensory scores was not necessary. Clipping 40% of outlying consumer scores reduced the variance of the sample mean by ~30%.
Effect of repeated implants of oestradiol-17β on beef palatability in Brahman and Braham cross steers finished to different market end points
Authors: Thompson J. M. , Polkinghorne R. , Porter M. , Burrow H. M. , Hunter R. A. , McCrabb G. J. , Watson R.
Published: October 2008

The effect of repeated implantation with 20 mg oestradiol-17β (Compudose 100) on carcass and meat quality traits was investigated using 478 Bos indicus and B. indicus × Bos taurus cross steers finished on either pasture or grain to achieve carcass weight for one of three market end points (domestic, 220 kg; Korean, 280 kg; or Japanese, 340 kg). In the oestradiol-17β treatment group, animals were administered implants at ~100-day intervals, with the number of implants administered to any steer ranging from one to eight. Cattle were slaughtered and at boning the anterior portion of the M. longissimus lumborum was removed and frozen after aging for 1 day for later objective meat quality measurements (shear force, compression and cook loss %). The adjoining portion was aged for 14 days before consumer sensory testing using the Meat Standards Australia protocols. Each sample was scored for tenderness, juiciness, like flavour and overall liking by 10 untrained consumers. Implanting increased carcass weights and ossification scores (P < 0.05) and reduced marbling scores in comparison to non-implanted carcasses. For tenderness, like flavour, overall liking and MQ4 scores there was a significant (P < 0.05) interaction between B. indicus content and oestradiol-17β treatment, whereby high B. indicus content cattle that were implanted with oestradiol-17β had the lowest sensory scores. The number of implants administered did not affect carcass weights or marbling scores, whereas ossification scores increased in carcasses as the number of implants increased. The number of implants administered had no effect (P > 0.05) on sensory scores, or objective meat tenderness.
Temporal dynamics of neuronal modulation during exogenous and endogenous shifts of visual attention in macaque area MT
Authors: Busse Laura , Katzner Steffen , Treue Stefan
Published: October 2008

Dynamically shifting attention between behaviorally relevant stimuli in the environment is a key condition for successful adaptive behavior. Here, we investigated how exogenous (reflexive) and endogenous (voluntary) shifts of visual spatial attention interact to modulate activity of single neurons in extrastriate area MT. We used a double-cueing paradigm, in which the first cue instructed two macaque monkeys to covertly attend to one of three moving random dot patterns until a second cue, whose unpredictable onset exogenously captured attention, either signaled to shift or maintain the current focus of attention. The neuronal activity revealed correlates of both exogenous and endogenous attention, which could be well distinguished by their characteristic temporal dynamics. The earliest effect was a transient interruption of the focus of endogenous attention by the onset of the second cue. The neuronal signature of this exogenous capture of attention was a short-latency decrease of responses to the stimulus attended so far. About 70 ms later, the influence of exogenous attention leveled off, which was reflected in two concurrent processes: responses to the newly cued stimulus continuously increased because of allocation of endogenous attention, while, surprisingly, there was also a gradual rebound of attentional enhancement of the previously relevant stimulus. Only after an additional 110 ms did endogenous disengagement of attention from this previously relevant stimulus become evident. These patterns of attentional modulation can be most parsimoniously explained by assuming two distinct attentional mechanisms drawing on the same capacity-limited system, with exogenous attention having a much faster time course than endogenous attention.
Molecular phylogeny of choanoflagellates, the sister group to Metazoa
Authors: Carr M. , Leadbeater B. S. C. , Hassan R. , Nelson M. , Baldauf S. L.
Published: October 2008

Choanoflagellates are single-celled aquatic flagellates with a unique morphology consisting of a cell with a single flagellum surrounded by a “collar” of microvilli. They have long interested evolutionary biologists because of their striking resemblance to the collared cells (choanocytes) of sponges. Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. However, molecular phylogenetic studies within choanoflagellates are still extremely limited. Thus, little is known about choanoflagellate evolution or the exact nature of the relationship between choanoflagellates and Metazoa. We have sequenced four genes from a broad sampling of the morphological diversity of choanoflagellates including most species currently available in culture. Phylogenetic analyses of these sequences, alone and in combination, reject much of the traditional taxonomy of the group. The molecular data also strongly support choanoflagellate monophyly rejecting proposals that Metazoa were derived from a true choanoflagellate ancestor. Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor.
Dynamics of shear-induced ATP release from red blood cells
Authors: Wan Jiandi , Ristenpart William D. , Stone Howard A.
Published: October 2008

Adenosine triphosphate (ATP) is a regulatory molecule for many cell functions, both for intracellular and, perhaps less well known, extracellular functions. An important example of the latter involves red blood cells (RBCs), which help regulate blood pressure by releasing ATP as a vasodilatory signaling molecule in response to the increased shear stress inside arterial constrictions. Although shear-induced ATP release has been observed widely and is believed to be triggered by deformation of the cell membrane, the underlying mechanosensing mechanism inside RBCs is still controversial. Here, we use anin vitromicrofluidic approach to investigate the dynamics of shear-induced ATP release from human RBCs with millisecond resolution. We demonstrate that there is a sizable delay time between the onset of increased shear stress and the release of ATP. This response time decreases with shear stress, but surprisingly does not depend significantly on membrane rigidity. Furthermore, we show that even though the RBCs deform significantly in short constrictions (duration of increased stress <3 ms), no measurable ATP is released. This critical timescale is commensurate with a characteristic membrane relaxation time determined from observations of the cell deformation by using high-speed video. Taken together our results suggest a model wherein the retraction of the spectrin-actin cytoskeleton network triggers the mechanosensitive ATP release and a shear-dependent membrane viscosity controls the rate of release.
Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore
Authors: Luecke Hartmut , Schobert Brigitte , Stagno Jason , Imasheva Eleonora S. , Wang Jennifer M. , Balashov Sergei P. , Lanyi Janos K.
Published: October 2008

Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein–carotenoid complex by X-ray diffraction, to 1.9-Å resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine–aspartate complex for regulating the pK
a
of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as ≈45%, and the 46° angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.
Striatal progenitors derived from human ES cells mature into DARPP32 neuronsin vitroand in quinolinic acid-lesioned rats
Authors: Aubry Laetitia , Bugi Aurore , Lefort Nathalie , Rousseau France , Peschanski Marc , Perrier Anselme L.
Published: October 2008

Substitutive cell therapy using fetal striatal grafts has demonstrated preliminary clinical success in patients with Huntington's disease, but the logistics required for accessing fetal cells preclude its extension to the relevant population of patients. Human embryonic stem (hES) cells theoretically meet this challenge, because they can be expanded indefinitely and differentiated into any cell type. We have designed anin vitroprotocol combining substrates, media, and cytokines to push hES cells along the neural lineage, up to postmitotic neurons expressing striatal markers. The therapeutic potential of such hES-derived cells was further substantiated by theirin vivodifferentiation into striatal neurons following xenotransplantation into adult rats. Our results open the way toward hES cell therapy for Huntington's disease. Long-term proliferation of human neural progenitors leads, however, to xenograft overgrowth in the rat brain, suggesting that the path to the clinic requires a way to switch them off after grafting.
Mesothelium contributes to vascular smooth muscle and mesenchyme during lung development
Authors: Que Jianwen , Wilm Bettina , Hasegawa Hiroshi , Wang Fan , Bader David , Hogan Brigid L. M.
Published: October 2008

During mouse development, the sophisticated vascular network of the lung is established from embryonic day (E)≈10.5 and continues to develop postnatally. This network is composed of endothelial cells enclosed by vascular smooth muscle, pericytes, and other mesenchymal cells. Recent
in vivo
lineage labeling studies in the developing heart and intestine suggest that some of the vascular smooth muscle cells arise from the surface mesothelium. In the developing lung, the Wilm's tumor 1 gene (
Wt1
) is expressed only in the mesothelial cells. Therefore, we lineage-labeled the mesothelium
in vivo
by using a
Wt1-Cre
transgene in combination with either
Rosa26R

lacZ

,
Rosa26R

CAG-hPLAP

, or
Rosa26R

EYFP

reporter alleles. In all three cases, cells derived from lineage-labeled mesothelium are found inside the lung and as smooth muscle actin (SMA) and PDGF receptor-beta positive cells in the walls of pulmonary blood vessels. To corroborate this finding, we used 5-(and-6)-carboxy-2′,7′-dichlorofluorescein diacetate, succinimidyl ester “mixed isomers” (CCFSE) dye to label mesothelial cells on the surface of the embryonic lung. Over the course of 72-h culture, dye-labeled cells also appear within the lung mesenchyme. Together, our data provide evidence that mesothelial cells serve as a source of vascular smooth muscle cells in the developing lung and suggest that a conserved mechanism applies to the development of blood vessels in all coelomic organs.
Matrix Metalloproteinase 2-Integrin αvβ3 Binding Is Required for Mesenchymal Cell Invasive Activity but Not Epithelial Locomotion: A Computational Time-Lapse Study
Authors: Rupp Paul A. , Visconti Richard P. , Czirók András , Cheresh David A. , Little Charles D.
Published: October 2008

Cellular invasive behavior through three-dimensional collagen gels was analyzed using computational time-lapse imaging. A subpopulation of endocardial cells, derived from explanted quail cardiac cushions, undergoes an epithelial-to-mesenchymal transition and invades the substance of the collagen gels when placed in culture. In contrast, other endocardial cells remain epithelial and move over the gel surface. Here, we show that integrin αvβ3 and matrix metalloproteinase (MMP)2 are present and active in cushion mesenchymal tissue. More importantly, functional assays show that mesenchymal invasive behavior is dependent on MMP2 activity and integrin αvβ3 binding. Inhibitors of MMP enzymatic activity and molecules that prevent integrin αvβ3 binding to MMP2, via its hemopexin domain, result in significantly reduced cellular protrusive activity and invasive behavior. Computational analyses show diminished intensity and persistence time of motility in treated invasive mesenchymal cells, but no reduction in motility of the epithelial-like cells moving over the gel surface. Thus, quantitative time-lapse data show that mesenchymal cell invasive behavior, but not epithelial cell locomotion over the gel surface, is partially regulated by the MMP2–integrin interactions.
Regulation of Kinetochore Recruitment of Two Essential Mitotic Spindle Checkpoint Proteins by Mps1 Phosphorylation
Authors: Xu Quanbin , Zhu Songcheng , Wang Wei , Zhang Xiaojuan , Old William , Ahn Natalie , Liu Xuedong
Published: October 2008

Mps1 is a protein kinase that plays essential roles in spindle checkpoint signaling. Unattached kinetochores or lack of tension triggers recruitment of several key spindle checkpoint proteins to the kinetochore, which delays anaphase onset until proper attachment or tension is reestablished. Mps1 acts upstream in the spindle checkpoint signaling cascade, and kinetochore targeting of Mps1 is required for subsequent recruitment of Mad1 and Mad2 to the kinetochore. The mechanisms that govern recruitment of Mps1 or other checkpoint proteins to the kinetochore upon spindle checkpoint activation are incompletely understood. Here, we demonstrate that phosphorylation of Mps1 at T12 and S15 is required for Mps1 recruitment to the kinetochore. Mps1 kinetochore recruitment requires its kinase activity and autophosphorylation at T12 and S15. Mutation of T12 and S15 severely impairs its kinetochore association and markedly reduces recruitment of Mad2 to the kinetochore. Our studies underscore the importance of Mps1 autophosphorylation in kinetochore targeting and spindle checkpoint signaling.
Lysosome Biogenesis Mediated byvps-18Affects Apoptotic Cell Degradation inCaenorhabditis elegans
Authors: Xiao Hui , Chen Didi , Fang Zhou , Xu Jing , Sun Xiaojuan , Song Song , Liu Jiajia , Yang Chonglin
Published: October 2008

Appropriate clearance of apoptotic cells (cell corpses) is an important step of programmed cell death. Although genetic and biochemical studies have identified several genes that regulate the engulfment of cell corpses, how these are degraded after being internalized in engulfing cell remains elusive. Here, we show that VPS-18, the Caenorhabditis elegans homologue of yeast Vps18p, is critical to cell corpse degradation. VPS-18 is expressed and functions in engulfing cells. Deletion of vps-18 leads to significant accumulation of cell corpses that are not degraded properly. Furthermore, vps-18 mutation causes strong defects in the biogenesis of endosomes and lysosomes, thus affecting endosomal/lysosomal protein degradation. Importantly, we demonstrate that phagosomes containing internalized cell corpses are unable to fuse with lysosomes in vps-18 mutants. Our findings thus provide direct evidence for the important role of endosomal/lysosomal degradation in proper clearance of apoptotic cells during programmed cell death.
BioCaster: detecting public health rumors with a Web-based text mining system
Authors: Collier Nigel , Doan Son , Kawazoe Ai , Goodwin Reiko Matsuda , Conway Mike , Tateno Yoshio , Ngo Quoc-Hung , Dien Dinh , Kawtrakul Asanee , Takeuchi Koichi , Shigematsu Mika , Taniguchi Kiyosu
Published: October 2008

Summary: BioCaster is an ontology-based text mining system for detecting and tracking the distribution of infectious disease outbreaks from linguistic signals on the Web. The system continuously analyzes documents reported from over 1700 RSS feeds, classifies them for topical relevance and plots them onto a Google map using geocoded information. The background knowledge for bridging the gap between Layman's terms and formal-coding systems is contained in the freely available BioCaster ontology which includes information in eight languages focused on the epidemiological role of pathogens as well as geographical locations with their latitudes/longitudes. The system consists of four main stages: topic classification, named entity recognition (NER), disease/location detection and event recognition. Higher order event analysis is used to detect more precisely specified warning signals that can then be notified to registered users via email alerts. Evaluation of the system for topic recognition and entity identification is conducted on a gold standard corpus of annotated news articles.

Availability: The BioCaster map and ontology are freely available via a web portal at http://www.biocaster.org.

Contact:  collier@nii.ac.jp
Osiris: an integrated promoter database for Oryza sativa L.
Authors: Morris Robert T. , O'Connor Timothy R. , Wyrick John J.
Published: October 2008

Summary: Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database containing promoter sequences, predicted transcription factor (TF) binding sites, gene ontology annotation and microarray expression data for 24 209 genes in the rice genome. These tools are seamlessly integrated in the Osiris web site, allowing the user to visualize TF binding sites in multiple promoters; analyze the statistical significance of enriched TF binding sites; query for genes containing similar promoter regulatory logic or gene function and visualize the microarray expression patterns of queried or selected gene sets.

Availability:  http://www.bioinformatics2.wsu.edu/Osiris

Contact:  jwyrick@wsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Distribution of emm type and antibiotic susceptibility of group A streptococci causing invasive and noninvasive disease
Authors: Wajima Takeaki , Murayama Somay Y. , Sunaoshi Katsuhiko , Nakayama Eiichi , Sunakawa Keisuke , Ubukata Kimiko
Published: October 2008

To determine the prevalence of macrolide antibiotic and levofloxacin resistance in infections with Streptococcus pyogenes (group A streptococcus or GAS), strains were collected from 45 medical institutions in various parts of Japan between October 2003 and September 2006. Four hundred and eighty-two strains from patients with GAS infections were characterized genetically. Strains were classified into four groups according to the type of infection: invasive infections (n=74) including sepsis, cellulitis and toxic-shock-like syndrome; acute otitis media (AOM; n=23); abscess (n=53); and pharyngotonsillitis (n=332). Among all strains, 32 emm types were identified; emm1 was significantly more common in invasive infections (39.2 %) and AOM (43.5 %) than in abscesses (3.8 %) or pharyngotonsillitis (10.2 %). emm12 and emm4 each accounted for 23.5 % of pharyngotonsillitis cases. Susceptibility of GAS strains to eight β-lactam agents was excellent, with MICs of 0.0005–0.063 μg ml−1. Macrolide-resistant strains accounted for 16.2 % of all strains, while the percentages of strains possessing the resistance genes erm(A), erm(B) and mef(A) were 2.5 %, 6.2 % and 7.5 %, respectively. Although no strains with high resistance to levofloxacin were found, strains with an MIC of 2–4 μg ml−1 (17.4 %) had amino acid substitutions at either Ser-79 or Asp-83 in ParC. These levofloxacin-intermediately resistant strains included 16 emm types, but macrolide-resistant strains were more likely than others to represent certain emm types.
Pulmonary Coccidioides nodule in a Swiss patient with chronic lymphatic leukaemia
Authors: Hombach Michael , Stulz Peter , Arnold Walter , Pfyffer Gaby E.
Published: October 2008

The dimorphic fungus Coccidioides immitis, causative agent of coccidioidomycosis, is endemic in semi-arid regions of the Americas. The disease is rarely encountered in Europe. We describe the case of a 61-year-old Swiss patient with chronic lymphatic leukaemia who was eventually diagnosed with an initially unnoticed pulmonary coccidioidomycosis.
The potential pathogenicity of chlorhexidine-sensitive Acanthamoeba strains isolated from contact lens cases from asymptomatic individuals in Tenerife, Canary Islands, Spain
Authors: Martín-Navarro Carmen M. , Lorenzo-Morales Jacob , Cabrera-Serra M. Gabriela , Rancel Fernando , Coronado-Álvarez Nieves M. , Piñero José E. , Valladares Basilio
Published: October 2008

Pathogenic strains of the genus Acanthamoeba are causative agents of a serious sight-threatening infection of the eye known as Acanthamoeba keratitis. The prevalence of this infection has risen in the past 20 years, mainly due to the increase in number of contact lens wearers. In this study, the prevalence of Acanthamoeba in a risk group constituted by asymptomatic contact lens wearers from Tenerife, Canary Islands, Spain, was evaluated. Contact lenses and contact lens cases were analysed for the presence of Acanthamoeba isolates. The isolates' genotypes were also determined after rDNA sequencing. The pathogenic potential of the isolated strains was subsequently established using previously described molecular and biochemical assays, which allowed the selection of three strains with high pathogenic potential. Furthermore, the sensitivity of these isolates against two standard drugs, ciprofloxacin and chlorhexidine, was analysed. As the three selected strains were sensitive to chlorhexidine, its activity and IC50 were evaluated. Chlorhexidine was found to be active against these strains and the obtained IC50 values were compared to the concentrations of this drug present in contact lens maintenance solutions. It was observed that the measured IC50 was higher than the concentration found in these maintenance solutions. Therefore, the ineffectiveness of chlorhexidine-containing contact lens maintenance solutions against potentially pathogenic strains of Acanthamoeba is demonstrated in this study.
Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping
Authors: Indra A. , Huhulescu S. , Schneeweis M. , Hasenberger P. , Kernbichler S. , Fiedler A. , Wewalka G. , Allerberger F. , Kuijper E. J.
Published: October 2008

We have developed a Clostridium difficile PCR ribotyping method based on capillary gel electrophoresis and have compared it with conventional PCR ribotyping. A total of 146 C. difficile isolates were studied: five isolates were reference strains (PCR ribotypes 001, 014, 017, 027 and 053); 141 were clinical isolates comprising 39 Austrian PCR ribotypes collected in the period 2006–2007 at 25 Austrian healthcare facilities. Capillary gel electrophoresis yielded up to 11 fragments per isolate and 47 ribotype patterns. All but one of the five PCR ribotypes of reference strains were clearly reflected in the chromatograms of capillary-based typing. Capillary gel electrophoresis divided 24 isolates belonging to PCR ribotype type 014 into seven subgroups, whereas subtyping the same isolates using multiple-locus variable-number tandem-repeat analysis yielded three unrelated subgroups, without obvious correlation to sr subgroups. Using a web-based software program (http://webribo.ages.at), we were able to correctly identify these 014 isolates by simply allocating the seven subgroup patterns to one ribotype, i.e. to PCR ribotype 014. We consider capillary gel electrophoresis-based PCR ribotyping to be a way of overcoming the problems associated with inter-laboratory comparisons of typing results, while at the same time substantially diminishing the hands-on time for PCR ribotyping.
Phylogenetic relationships among Streptococcus agalactiae isolated from piscine, dolphin, bovine and human sources: a dolphin and piscine lineage associated with a fish epidemic in Kuwait is also associated with human neonatal infections in Japan
Authors: Evans Joyce J. , Bohnsack John F. , Klesius Phillip H. , Whiting April A. , Garcia Julio C. , Shoemaker Craig A. , Takahashi Shinji
Published: October 2008

Streptococcus agalactiae, commonly known as group B streptococcus (GBS), is a cause of infectious disease in numerous animal species. This study examined the genetic relatedness of piscine, dolphin and human GBS isolates and bovine GBS reference strains from different geographical regions using serological and molecular serotyping and multilocus sequence typing (MLST) techniques. Piscine isolates originating from Kuwait, Brazil, Israel and the USA were capsular serotype Ia, a serotype previously unreported in GBS isolated from fish. Sequence typing of piscine isolates produced six sequence types (ST-7, ST-257, ST-258, ST-259, ST-260 and ST-261), the latter five representing allelic designations and allelic combinations not previously reported in theS. agalactiaeMLST database. Genomic diversity existed between dolphin and piscine GBS isolates from Kuwait and other geographical areas. Piscine GBS isolates from Brazil, Israel, Honduras and the USA appeared to represent a distinct genetic population of strains that were largely unrelated to human and bovine GBS. The Kuwait dolphin and piscine lineage (ST-7, Ia) was also associated with human neonatal infections in Japan. Comparative genomics of piscine, human and bovine GBS could help clarify those genes important for host tropism, the emergence of unique pathogenic clones and whether these hosts act as reservoirs of one another's pathogenic lineages.
Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation
Authors: Day Robert C. , Herridge Rowan P. , Ambrose Barbara A. , Macknight Richard C.
Published: October 2008

During the early stages of seed development, Arabidopsis (Arabidopsis thaliana) endosperm is syncytial and proliferates rapidly through repeated rounds of mitosis without cytokinesis. This stage of endosperm development is important in determining final seed size and is a model for studying aspects of cellular and molecular biology, such as the cell cycle and genomic imprinting. However, the small size of the Arabidopsis seed makes high-throughput molecular analysis of the early endosperm technically difficult. Laser capture microdissection enabled high-resolution transcript analysis of the syncytial stage of Arabidopsis endosperm development at 4 d after pollination. Analysis of Gene Ontology representation revealed a developmental program dominated by the expression of genes associated with cell cycle, DNA processing, chromatin assembly, protein synthesis, cytoskeleton- and microtubule-related processes, and cell/organelle biogenesis and organization. Analysis of core cell cycle genes implicates particular gene family members as playing important roles in controlling syncytial cell division. Hormone marker analysis indicates predominance for cytokinin signaling during early endosperm development. Comparisons with publicly available microarray data revealed that approximately 800 putative early seed-specific genes were preferentially expressed in the endosperm. Early seed expression was confirmed for 71 genes using quantitative reverse transcription-polymerase chain reaction, with 27 transcription factors being confirmed as early seed specific. Promoter-reporter lines confirmed endosperm-preferred expression at 4 d after pollination for five transcription factors, which validates the approach and suggests important roles for these genes during early endosperm development. In summary, the data generated provide a useful resource providing novel insight into early seed development and identify new target genes for further characterization.