bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanisms controlling crescentic bar amplitude
Authors: Garnier Roland , Dodd Nicholas , Falqués Albert , Calvete Daniel
Published: April 2010

The formation of crescentic bars from self‐organization of an initially straight shore‐parallel bar for shore‐normal incident waves is simulated with a two‐dimensional horizontal morphodynamical model. The aim is to investigate the mechanisms behind the saturation process defined as the transition between the linear regime (maximum and constant growth of the crescentic pattern) and the saturated state (negligible growth). The global properties of the morphodynamical patterns over the whole computational domain are studied (“global analysis”). In particular, consideration of the balance of the potential energy of the emerging bar gives its growth rate from the difference between a production term (related to the positive feedback leading to the instability) and a damping term (from the gravity‐driven downslope transport). The production is approximately proportional to the average over the domain of the cross‐shore flow velocity times the bed level perturbation. The damping is essential for the onset of the saturation, but it remains constant while the production decreases. Thus, it is notable that the saturation occurs because of a weakening of the instability mechanism rather than an increase of the damping. A reason for the saturation of the crescentic bar growth is the change in bar shape from its initial stage rather than the growth in amplitude itself. This change is mainly characterized by the narrowing of the rip channels, the onshore migration of the crests, and the change in the mean beach profile due to alongshore variability. These properties agree with observations of mature rip channel systems in nature.
Krueger, Schiff, and Valdés Revisited: Agricultural Price and Trade Policy Reform in Developing Countries since 1960
Authors: Anderson Kym
Published: April 2010

A study of distortions to agricultural incentives in 18 developing countries from 1960–84, by Krueger, Schiff, and Valdés (1988; 1991), found that policies in most of those developing countries were directly or indirectly harming their farmers. Since the mid‐1980s, there has been a substantial amount of policy reform and opening up of many developing countries. Indicators of that progress have been made available recently by a new study that has compiled estimates for a much larger sample of developing countries, and for as many years as possible since 1955. The new study also covers Europe's transition economies and comparable estimates for high‐income countries, thereby covering more than 90% of world agricultural output and employment. This article summarizes the methodology used in the new study, compares a synopsis of the indicators from Krueger, Schiff, and Valdés and the new study for the period to 1984, summarizes the changing extent of price distortions across countries and commodities globally since then, and concludes by evaluating the degree of distortion reduction over the years since 1984 compared with how much still remains, according to the results of a global economy wide model.
A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2
Authors: Lees William D. , Moss David S. , Shepherd Adrian J.
Published: April 2010

Motivation: Modelling antigenic shift in influenza A H3N2 can help to predict the efficiency of vaccines. The virus is known to exhibit sudden jumps in antigenic distance, and prediction of such novel strains from amino acid sequence differences remains a challenge.

Results: From analysis of 6624 amino acid sequences of wild-type H3, we propose updates to the frequently referenced list of 131 amino acids located at or near the five identified antibody binding regions in haemagglutinin (HA). We introduce a class of predictive models based on the analysis of amino acid changes in these binding regions, and extend the principle to changes in HA1 as a whole by dividing the molecule into regional bands.

Our results show that a range of simple models based on banded changes give better predictive performance than models based on the established five canonical regions and can identify a higher proportion of vaccine escape candidates among novel strains than a current state-of-the-art model.

Contact:  wlees01@mail.cryst.bbk.ac.uk

Supplementary information:  Supplementary Data is available at Bioinformatics online.
Prognostic value of chromogranin A in chronic heart failure: data from the GISSI‐Heart Failure trial
Authors: Røsjø Helge , Masson Serge , Latini Roberto , Flyvbjerg Allan , Milani Valentina , La Rovere Maria Teresa , Revera Miriam , Mezzani Alessandro , Tognoni Gianni , Tavazzi Luigi , Omland Torbjørn ,   on behalf of the GISSI‐HF Investigators
Published: April 2010

Aims

To assess the association between circulating levels of chromogranin A (CgA) and outcome in a large population of patients with chronic heart failure (HF).

Methods and results

Plasma CgA levels were measured at randomization and after 3 months in 1233 patients (median age 68 years, 80% male) with chronic, stable HF from the GISSI‐HF trial. Circulating CgA levels were associated with several established risk markers in HF, including increased age, diabetes, reduced renal function, and heart rate variability. During a median follow‐up of 3.9 years, 333 patients (27%) died. By univariable analysis, plasma CgA levels at baseline were strongly associated with all‐cause mortality during follow‐up; 2nd vs. 1st tertile: HR 1.58 (1.17–2.11), P = 0.002; and 3rd vs. 1st tertile: HR 2.35 (1.78–3.10), P < 0.0001. After adjustment for established risk factors of mortality, this association was attenuated and no longer significant. Randomized treatments with n‐3 polyunsaturated fatty acid or rosuvastatin did not significantly change plasma CgA concentration over 3 months.

Conclusion

Measurement of circulating CgA levels in patients with chronic, stable HF does not provide incremental prognostic information to that obtained from physical examination, routine biochemical analysis, and contemporary HF biomarkers.
Myocardial gene expression alterations in peripheral blood mononuclear cells of patients with idiopathic dilated cardiomyopathy
Authors: Kontaraki Joanna E. , Parthenakis Fragiskos I. , Nyktari Eva G. , Patrianakos Alexandros P. , Vardas Panos E.
Published: April 2010

Aims

To assess cardiac gene expression in peripheral blood cells of patients with idiopathic dilated cardiomyopathy (IDCM) and its relationship to echocardiographic left ventricular (LV) function.

Methods and results

A complete echocardiographic study and blood sampling were performed in 65 consecutive stable IDCM patients with LV ejection fraction (LVEF) 31.76 ± 10.07% and chronic mild to moderate heart failure (NYHA functional class II to III) for ≥9 months. Blood samples from 19 healthy individuals were included for comparison. Transcript levels of myocardin, GATA4, alpha‐ and beta‐myosin heavy chain (MHC), sarcoplasmic reticulum calcium ATPase 2 (SERCA2), and phospholamban were determined by quantitative real‐time reverse transcription‐polymerase chain reaction. Myocardin (24.88 ± 4.93 vs. 3.98 ± 1.12, P = 0.0048) and GATA4 (17.85 ± 4.85 vs. 0.45 ± 0.15, P = 0.0069 × 10−5) were upregulated in IDCM patients compared with controls, whereas SERCA2 (5.11 ± 0.42 vs. 8.93 ± 1.07, P = 0.001) was downregulated. In IDCM patients, myocardin (r = 0.279, P = 0.025), GATA4 (r = 0.314, P = 0.011), beta‐MHC (r = 0.444, P=0.0002), and alpha‐MHC (r = 0.272, P = 0.034) showed positive correlations, whereas SERCA2 (r = −0.264, P = 0.034) exhibited a negative correlation with LVEF. Patients with elevated LV filling pressures had lower myocardin (15.06 ± 3.10 vs. 43.12 ± 12.03, P = 0.048), GATA4 (8.96 ± 2.17 vs. 34.38 ± 12.60, P = 0.026), beta‐MHC (10.59 ± 4.05 vs. 16.43 ± 4.91, P = 0.013), and alpha‐MHC (0.27 ± 0.08 vs. 0.79 ± 0.20, P = 0.033) and higher SERCA2 (5.65 ± 0.54 vs. 3.90 ± 0.61, P = 0.037) levels. Patients with atrial fibrillation (AF) had higher SERCA2 levels compared with sinus rhythm patients (6.75 ± 0.84 vs. 4.54 ± 0.45, P = 0.017).

Conclusion

Our data indicate that cardiac gene expression alterations in peripheral blood cells of IDCM patients may reflect alterations in LV function, whereas the presence of AF may be associated with increased SERCA2 levels in these patients.
Contribution of the Chemokine (C-C Motif) Ligand 2 (CCL2) to Mechanical Hypersensitivity after Surgical Incision in Rats
Authors: Peters Christopher M. , Eisenach James C.
Published: April 2010

Background

Neural glial signaling in the spinal cord may underlie pain and sensitization after peripheral injury. The authors test the role of a glial activator, the chemokine (C-C motif) ligand 2 (CCL2), on mechanical hypersensitivity after plantar incision in a rat model of postoperative pain.

Methods

Twenty-four hours after hind paw incision, rats were intrathecally administered an anti-CCL2 neutralizing antibody (3 and 10 microg) or control immunoglobulin G (10 microg). Mechanical hypersensitivity was assessed acutely and for several days after administration of anti-CCL2 antibody using von Frey filaments. Immunohistochemical analysis was conducted on spinal cord sections to examine the effects of treatment on measures of microglial activation, including levels of ionized calcium-binding adaptor molecule 1 and phosphorylated p38 mitogen-activated protein kinase.

Results

Neutralization of spinal CCL2 acutely reversed mechanical hypersensitivity within 30 min in a dose-dependent manner. A single administration also produced a sustained decrease in mechanical hypersensitivity 48 and 72 h after incision. Anti-CCL2 antibody reduced microglial activation as measured by the levels of ionized calcium-binding adaptor molecule 1 immunoreactivity and the number of microglia containing phosphorylated p38 mitogen-activated protein kinase 48 h after incision but not within 30 min of administration.

Conclusions

These results provide evidence that CCL2 contributes to the maintenance of mechanical hypersensitivity after plantar incision and establish a role for neural glial signaling in postoperative pain. The long-term effects of anti-CCL2 treatment correlate with reduced microglial activation. Spinal blockade of CCL2 may serve as a useful therapy for the treatment of certain aspects of postoperative pain.
Dorsal Horn α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid Receptor Trafficking in Inflammatory Pain
Authors: Tao Yuan-Xiang , Warner David S.
Published: April 2010

Activation of synaptic N-methyl-D-aspartic acid receptor and its intracellular downstream signals in dorsal horn neurons of spinal cord contribute to central sensitization, a mechanism that underlies the development and maintenance of pain hypersensitivity in persistent pain. However, the molecular process of this event is not understood completely. Recently, new studies suggest that peripheral inflammatory insults drive changes in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit trafficking via N-methyl-D-aspartic acid receptor-triggered activation of protein kinases in dorsal horn and raise the possibility that such changes might contribute to central sensitization in persistent pain. This review presents current evidence regarding the changes that occur in the trafficking of dorsal horn alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunits GluR1 and GluR2 under persistent inflammatory pain conditions and discusses the potential mechanisms by which such changes participate in the development and maintenance of inflammatory pain.
SUMO-independent in vivo activity of a SUMO-targeted ubiquitin ligase toward a short-lived transcription factor
Authors: Xie Yang , Rubenstein Eric M. , Matt Tanja , Hochstrasser Mark
Published: April 2010

Many proteins are regulated by ubiquitin-dependent proteolysis. Substrate ubiquitylation can be stimulated by additional post-translational modifications, including small ubiquitin-like modifier (SUMO) conjugation. The recently discovered SUMO-targeted ubiquitin ligases (STUbLs) mediate the latter effect; however, no endogenous substrates of STUbLs that are degraded under normal conditions are known. From a targeted genomic screen, we now identify the yeast STUbL Slx5–Slx8, a heterodimeric RING protein complex, as a key ligase mediating degradation of the MATα2 (α2) repressor. The ubiquitin-conjugating enzyme Ubc4 was found in the same screen. Surprisingly, mutants with severe defects in SUMO–protein conjugation were not impaired for α2 turnover. Unmodified α2 also bound to and was ubiquitylated efficiently by Slx5–Slx8. Nevertheless, when we inactivated four SUMO-interacting motifs (SIMs) in Slx5 that together account for its noncovalent SUMO binding, both in vitro Slx5–Slx8-dependent ubiquitylation and in vivo degradation of α2 were inhibited. These data identify α2 as the first native substrate of the conserved STUbLs, and demonstrate that its STUbL-mediated ubiquitylation does not require SUMO. We suggest that α2, and presumably other proteins, have surface features that mimic SUMO, and therefore can directly recruit STUbLs without prior SUMO conjugation.
TRICHOME BIREFRINGENCEand Its HomologAT5G01360Encode Plant-Specific DUF231 Proteins Required for Cellulose Biosynthesis in Arabidopsis
Authors: Bischoff Volker , Nita Silvia , Neumetzler Lutz , Schindelasch Dana , Urbain Aurélie , Eshed Ravit , Persson Staffan , Delmer Deborah , Scheible Wolf-Rüdiger
Published: April 2010

The Arabidopsis (Arabidopsis thaliana) trichome birefringence (tbr) mutant has severely reduced crystalline cellulose in trichomes, but the molecular nature of TBR was unknown. We determined TBR to belong to the plant-specific DUF231 domain gene family comprising 46 members of unknown function in Arabidopsis. The genes harbor another plant-specific domain, called the TBL domain, which contains a conserved GDSL motif known from some esterases/lipases. TBR and TBR-like3 (TBL3) are transcriptionally coordinated with primary and secondary CELLULOSE SYNTHASE (CESA) genes, respectively. The tbr and tbl3 mutants hold lower levels of crystalline cellulose and have altered pectin composition in trichomes and stems, respectively, tissues generally thought to contain mainly secondary wall crystalline cellulose. In contrast, primary wall cellulose levels remain unchanged in both mutants as measured in etiolated tbr and tbl3 hypocotyls, while the amount of esterified pectins is reduced and pectin methylesterase activity is increased in this tissue. Furthermore, etiolated tbr hypocotyls have reduced length with swollen epidermal cells, a phenotype characteristic for primary cesa mutants or the wild type treated with cellulose synthesis inhibitors. Taken together, we show that two TBL genes contribute to the synthesis and deposition of secondary wall cellulose, presumably by influencing the esterification state of pectic polymers.
A Pollen-Specific RALF from Tomato That Regulates Pollen Tube Elongation
Authors: Covey Paul A. , Subbaiah Chalivendra C. , Parsons Ronald L. , Pearce Gregory , Lay Fung T. , Anderson Marilyn A. , Ryan Clarence A. , Bedinger Patricia A.
Published: April 2010

Rapid Alkalinization Factors (RALFs) are plant peptides that rapidly increase the pH of plant suspension cell culture medium and inhibit root growth. A pollen-specific tomato (Solanum lycopersicum) RALF (SlPRALF) has been identified. The SlPRALF gene encodes a preproprotein that appears to be processed and released from the pollen tube as an active peptide. A synthetic SlPRALF peptide based on the putative active peptide did not affect pollen hydration or viability but inhibited the elongation of normal pollen tubes in an in vitro growth system. Inhibitory effects of SlPRALF were detectable at concentrations as low as 10 nm, and complete inhibition was observed at 1 μ  m peptide. At least 10-fold higher levels of alkSlPRALF, which lacks disulfide bonds, were required to see similar effects. A greater effect of peptide was observed in low-pH-buffered medium. Inhibition of pollen tube elongation was reversible if peptide was removed within 15 min of exposure. Addition of 100 nm SlPRALF to actively growing pollen tubes inhibited further elongation until tubes were 40 to 60 μm in length, after which pollen tubes became resistant to the peptide. The onset of resistance correlated with the timing of the exit of the male germ unit from the pollen grain into the tube. Thus, exogenous SlPRALF acts as a negative regulator of pollen tube elongation within a specific developmental window.
Virus-Based MicroRNA Expression for Gene Functional Analysis in Plants
Authors: Tang Yang , Wang Fei , Zhao Jinping , Xie Ke , Hong Yiguo , Liu Yule
Published: April 2010

Traditional virus-induced gene silencing (VIGS) is a powerful virus-based short interfering RNA-mediated RNA silencing technique for plant functional genomics. Besides short interfering RNAs, microRNAs (miRNAs) have also been shown to regulate gene expression by RNA silencing in various organisms. However, plant virus-based miRNA silencing has not been reported. In addition, a number of plant miRNAs have been identified or predicted, while their functions are largely unknown. Thus, there is an urgent need for the development of new technologies to study miRNA function. Here, we report that a modified cabbage leaf-curl geminivirus vector can be used to express artificial and endogenous miRNAs in plants. Using this viral miRNA expression system, we demonstrate that VIGS using artificial miRNAs, dubbed as “MIR VIGS,” was effective to silence the expression of endogenous genes, including PDS, Su, CLA1, and SGT1, in Nicotiana benthamiana. Silencing of SGT1 led to the loss of N-mediated resistance to Tobacco mosaic virus. Furthermore, using this viral miRNA expression system, we found that viral ectopic expression of endogenous miR156 and miR165 but not their mutants in N. benthamiana resulted in earlier abnormal developmental phenotypes, and expression of miR165 induced abnormal chlorotic spots on leaves. These results demonstrate that the cabbage leaf-curl geminivirus-based miRNA expression system can be utilized not only to specifically silence genes involved in general metabolism and defense but also to investigate the function of endogenous miRNAs in plants.
Isothermal compressibility of macromolecular crystals and macromolecules derived from high-pressure X-ray crystallography
Authors: Ascone Isabella , Kahn Richard , Girard Eric , Prangé Thierry , Dhaussy Anne-Claire , Mezouar Mohamed , Ponikwicki Nikodem , Fourme Roger
Published: April 2010

The compressibility of several nucleic acid and globular protein crystals has been investigated by high-pressure macromolecular crystallography. Further, crystal structures at four different pressures allowed the determination of the intrinsic compressibilityversuspressure of d(GGTATACC)2and hen egg-white lysozyme. For lysozyme, the values for the intrinsic molecular compressibility at atmospheric pressure and the nonlinearity index were 0.070 GPa−1and 8.15, respectively. On the basis of two crystal structures at atmospheric and high pressure, similar, albeit less complete, information was derived for d(CGCGAATTCGCG)2and bovine erythrocyte Cu,Zn superoxide dismutase. Using these data and accurate calculations of the solvent-excluded volume, the apparent solvent compressibility in the crystalline state was determined as a function of pressure and compared with results from a simple model that assumes invariant unit-cell content, with the conclusion that solvent compressibility was abnormal for three out of the five crystals investigated. Experimental results suggest that macromolecular crystals submitted to high pressure may have a variable unit-cell mass due to solvent exchange with the surrounding pool, as already observed in other hydrated crystals such as zeolites.
Atomic structure analysis at the nanoscale using the pair distribution function: simulation studies of simple elemental nanoparticles
Authors: Mullen Katharine , Krayzman Victor , Levin Igor
Published: April 2010

The pair distribution function (PDF), as determined from total X-ray or neutron scattering, is a valuable probe of atomic arrangements in nanoparticles. Structural information in the experimental PDF is modified by the effects of particle shape, particle size, extended defects and internal substructure. This study uses synthetic PDF data, generated for simple elemental nanoparticles having different degrees of displacive atomic disorder in the particle surface compared with the interior, to explore the feasibility of reliably extracting key features (i.e.a lattice constant, particle diameter, atomic displacement parameters for the interior and the surface, and thickness of the surface layer) from experimental data in the absence of systematic errors using a statistical modeling approach. This approach determines a model PDFviasimulation of an ensemble of nanoparticles. Several methods for model optimization were tested and a differential evolution algorithm was selected as the most reliable and accurate. Fitting synthetic PDF data using this algorithm was demonstrated to estimate all features well with small standard uncertainties. Identification of larger displacive atomic disorder in the particle surface compared with the interior was shown to be possibleviamodel selection. Software for nanoparticle simulation and model optimization is provided in open-source form, to allow reproduction and extension of the results presented here.
The macromolecular neutron diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge: enhanced optics design, high-resolution neutron detectors and simulated diffraction
Authors: Coates L. , Stoica A. D. , Hoffmann C. , Richards J. , Cooper R.
Published: April 2010

The macromolecular neutron diffractometer MaNDi is currently under construction at the first target station of the Spallation Neutron Source at Oak Ridge National Laboratory. This instrument will collect neutron diffraction data from small single crystals (0.1–1 mm3) with lattice constants between 100 and 300 Å, as well as data from less well ordered systems such as fibers. A focusing neutron guide has been designed to filter the high-energy neutron component of the spectrum and to provide a narrow beam with a wide spectral window and angular divergence almost insensitive to neutron wavelength. The system includes a final interchangeable section of neutron guide and two slits, which enable tuning of the horizontal and vertical beam divergence between 0.12 and 0.80° (full width at half-maximum) at the sample position. This allows the trading of intensity for resolution, depending on the scientific requirements. Efforts to enhance and develop suitable high-resolution neutron detectors at an affordable price are also discussed. Finally, the parameters of the neutron guide and detectors were used to simulate diffraction from a large unit cell.
Enhancement of second harmonic generation, optical and dielectric properties inL-asparagine monohydrate single crystals due to an improvement in crystalline perfection by annealing
Authors: Shakir Mohd. , Kushawaha S. K. , Maurya K. K. , Kumar Sumeet , Wahab M. A. , Bhagavannarayana G.
Published: April 2010

Single crystals of the relatively new nonlinear optical material L-asparagine monohydrate have been successfully grown by the slow evaporation solution growth technique at room temperature in aqueous solution. The crystal system of the title material has been confirmed by powder X-ray diffraction. The crystalline perfection of the as-grown and annealed crystals has been evaluated by high-resolution X-ray diffraction. The as-grown single crystals (particularly when their size is large) were found to contain internal structural grain boundaries, and the crystalline perfection of these crystals was found to be improved substantially by annealing at low temperatures. The crystalline perfection and the measured physical properties were found to be correlated such that the second harmonic generation efficiency, optical transparency, fluorescence and dielectric properties are enhanced as the crystal quality improves.
Theory of geometrical broadening of diffraction peaks from twisted lamellar crystals for interpretation of X-ray microbeam and selected-area electron diffraction experiments
Authors: Luchnikov Valeriy A. , Ivanov Dimitri A.
Published: April 2010

A simple theory of angular broadening of diffraction peaks is presented for the X-ray and electron diffraction from twisted crystalline lamellae. The diffraction peak position, width and asymmetry are computed in the limit of a small natural reflection width. The peak broadening depends on the orientation of the corresponding reciprocal-space vector with respect to the helicoid axis and the normal to the lamellar basal plane. It is found that the equatorial peaks, which are close to the normal direction to the lamellar basal plane, are characterized by the highest azimuthal width. The theory also describes the azimuthal drift of the non-equatorial reflections on a flat two-dimensional detector as the incident beam scans along the main helicoid axis. The proposed approach can be useful for interpretation of microbeam diffractograms measured on banded polymer spherulites. It can be easily generalized to describe diffraction from crystals of any arbitrary shape obtained by deformation of a flat lamella, under the condition that upon the deformation all the in-plane angles and distances are preserved in the linear approximation.
Long-range ordering in anodic alumina films: a microradian X-ray diffraction study
Authors: Napolskii Kirill S. , Roslyakov Ilya V. , Eliseev Andrey A. , Petukhov Andrei V. , Byelov Dmytro V. , Grigoryeva Natalia A. , Bouwman Wim G. , Lukashin Alexey V. , Kvashnina Kristina O. , Chumakov Andrey P. , Grigoriev Sergey V.
Published: April 2010

A quantitative analysis of long-range order in the self-organized porous structure of anodic alumina films has been performed on the basis of a microradian X-ray diffraction study. The structure is shown to possess orientational order over macroscopic distances larger than 1 mm. At the same time, the interpore positional order is only short-range and does not extend over more than ∼10 interpore distances. These positional correlations are mostly lost gradually rather than at the domain boundaries, as suggested by the divergence of the peak width for the higher-order reflections. In the direction of the film growth the pores have a very long longitudinal self-correlation length of the order of tens of micrometres.
Extracting differential pair distribution functions usingMIXSCAT
Authors: Wurden Caroline , Page Katharine , Llobet Anna , White Claire E. , Proffen Thomas
Published: April 2010

Differently weighted experimental scattering data have been used to extract partial or differential structure factors or pair distribution functions in studying many materials. However, this is not done routinely partly because of the lack of user-friendly software. This paper presentsMIXSCAT, a new member of theDISCUSprogram package.MIXSCATallows one to combine neutron and X-ray pair distribution functions and extract their respective differential functions.
Effect of mechanical vibration on protein crystallization
Authors: Lu Qin-Qin , Yin Da-Chuan , Liu Yong-Ming , Wang Xi-Kai , Yang Peng-Fei , Liu Zheng-Tang , Shang Peng
Published: April 2010

Mechanical vibration often occurs during protein crystallization; however, it is seldom considered as one of the factors influencing the crystallization process. This paper reports an investigation of the crystallization of five proteins using various crystallization conditions in a temperature-controlled chamber on the table of a mechanical vibrator. The results show that mechanical vibration can reduce the number of crystals and improve their optical perfection. During screening of the crystallization conditions it was found that mechanical vibration could help to obtain crystals in a highly supersaturated solution in which amorphous precipitates often normally appear. It is concluded that mechanical vibration can serve as a tool for growing optically perfect crystals or for obtaining more crystallization conditions during crystallization screening.
Parentage testing of racing camels (Camelus dromedarius) using microsatellite DNA typing
Authors: Spencer P. B. S. , Wilson K. J. , Tinson A.
Published: April 2010

The camel racing industry would have added value in being able to assign parentage with high certainty. This study was aimed at assessing and applying microsatellite multiplexes to construct a parentage testing system for camels. An efficient system of 17 loci from 700 camel samples was used to construct a database of unrelated adults. Based on this, we estimated measures of polymorphism among the markers. In three multiplex reactions, we detected a total of 224 alleles, with 5–23 alleles/locus (mean = 13.18 ± 6.95 SD) and an average heterozygosity (HE) of 0.54 (range 0.032–0.905). The total parentage exclusion probability was 0.99999 for excluding a candidate parent from parentage of an arbitrary offspring, given only the genotype of the offspring, and 0.9999 for excluding a candidate parent from parentage of an arbitrary offspring, given the genotype of the offspring and the other parent. We used 15 juveniles for parentage testing, as well as 17 sires (bull camels) and 21 dams (cows). In the case of parentage assignment, the microsatellite panel assigned all 15 offspring parentage with high confidence. Overall, these findings offer a set of microsatellite markers that are easy, simple and highly informative for parentage testing in camels.
Genetic mapping of quantitative trait loci for milk production in sheep
Authors: Mateescu R. G. , Thonney M. L.
Published: April 2010

A backcross pedigree using dairy East Friesian rams and non‐dairy Dorset ewes was established specifically to map quantitative trait loci (QTL) affecting milk production in sheep. Ninety nine microsatellite markers of an initial set of 120 were successfully genotyped and informative on 188 animals of this backcross pedigree. Test‐day milk records on individual ewes were used to estimate several milk yield related traits, including peak milk yield and cumulative milk yield to 50 (MY50), 100 (MY100) and 250 days (MY250). These traits, as well as estimated breeding value of backcross ewes extracted from the genetic evaluation file of the entire flock, were used in interval mapping. Ovine chromosomes 2, 12, 18, 20 and 24 were identified to harbour putative QTL for different measures of milk production. The QTL on Ovis aries chromosomes (OAR) 2 and 20 mapped to locations where similar trait QTL have already been mapped in other studies, whereas QTL on OAR 12, 18 and 24 were unique to our backcross pedigree and have not been reported previously. In addition, all identified QTL regions were syntenic with bovine chromosomal segments revealed to harbour QTL affecting milk production traits, providing supporting evidence for the QTL identified here.
A genome‐wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle
Authors: Huang W. , Kirkpatrick B. W. , Rosa G. J. M. , Khatib H.
Published: April 2010

The decline in the reproductive efficiency of dairy cows, especially those with high producing potential, has become a challenging problem. In this study, a selective DNA pooling approach was applied to a cow population whose oocytes were fertilized and cultured to obtain phenotypic records of fertilization rate and blastocyst rate. Using a stringent 5% genome‐wide significance level, 22 and five single nucleotide polymorphisms (SNPs) were found to be associated with fertilization rate and blastocyst rate, respectively. SNPs that showed significant association in selective DNA pooling were further evaluated by individual genotyping. Interestingly, the majority of the SNP associations were confirmed by individual genotyping, testifying to the effectiveness of selective DNA pooling using a high‐density SNP genotyping array. This study is the first application of the selective DNA pooling approach using the BovineSNP50 array in cattle.
Effect of a major QTL affecting IPN resistance on production traits in Atlantic salmon
Authors: Gheyas A. A. , Haley C. S. , Guy D. R. , Hamilton A. , Tinch A. E. , Mota‐Velasco J. C. , Woolliams J. A.
Published: April 2010

This study investigated the effect of a major QTL for resistance to IPN in salmon on performance and production traits. The traits studied were related to growth, fillet and gutted yields, and fat content. Two different analyses were performed: (1) regression of the phenotypic data of the production traits on the predicted number of resistant IPN‐QTL alleles in individuals and (2) a variance component analysis using the (co)variance matrix calculated at the putative location of the QTL. No significant effect of the QTL was detected on any of the traits investigated by either method. The result has important practical implications in that it encourages the use of MAS to reduce the risks and impact of IPN mortality.
A haplotype ofCYP2C9associated with warfarin sensitivity in mechanical heart valve replacement patients
Authors: Lee Su‐Jun , Jang Yin Jin , Cha Eun‐Young , Kim Ho‐Sook , Lee Sang Seop , Shin Jae‐Gook
Published: April 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• CYP2C9single nucleotide polymorphisms (SNPs) are important in safe and effective oral anticoagulation with warfarin use.

• AlthoughCYP2C9*2and*3are important genetic factors for the warfarin dose, one of theCYP2C9SNPs, IVS‐65G>C, has been suggested to be associated with warfarin sensitivity. However, as of yet, there has been no explanation about the possible mechanism and linkage analysis.

WHAT THIS PAPER ADDS

• New information onCYP2C9SNPs and their occurrences in common haplotype structures in healthy unrelated Koreans and in individuals who require low warfarin dose after mechanical heart valve replacements (MHVRs) were studied.

• Additional evidence showed that an Asian dominant haplotype consisting of ‐1565C>T, ‐1188T>C, IVS3+197G>A, IVS3‐334C>T, IVS3‐65G>C, IVS4‐115A>G and IVS5‐73A>G could be associated with a low warfarin maintenance dose in mechanical heart valve replacement (MHVR) patients.

AIMS

The objectives of this study were to determine the distribution ofCYP2C9variants in Koreans and investigate their association with warfarin dose requirements in patients who received MHVRs.

METHODS

All nine exons, intron–exon junction, and promoter region ofCYP2C9were amplified and directly sequenced in 50 healthy normal Koreans. Additional direct DNA sequencing of theCYP2C9gene was conducted in 36 of the 267 MHVR patients who required low maintenance warfarin doses without carryingCYP2C9*3andVKORC1 1173Tmutations. The effects ofCYP2C9genetics on warfarin maintenance dose were assessed in 267 MHVR patients.

RESULTS

Thirty‐nine single nucleotide polymorphisms (SNPs) including seven previously unidentified SNPs were identified in 50 Koreans by direct DNA sequencing. One of theCYP2C9haplotypes exhibited an association with warfarin low dose requirement. The adjusted odds ratio for the haplotype between the low dose group and the normal subjects was 2.5 (95% confidence interval 1.05, 6.16). This haplotype consisting of ‐1565C>T, ‐1188T>C, IVS3+197G>A, IVS3‐334C>T, IVS3‐65G>C, IVS4‐115A>G, and IVS5‐73A>G was found in 15% of 36 MHVR patients who required low warfarin doses, while 4% of 50 normal healthy subjects exhibited this haplotype. One of the SNPs comprising this haplotype, ‐1565C>T, apparently changed a protein binding pattern as observed in electrophoretic mobility shift assay.

CONCLUSION

The haplotype including ‐1565C>T, ‐1188T>C, IVS3+197G>A, IVS3‐334C>T, IVS3‐65G>C, IVS4‐115A>G, and IVS5‐73A>G seems to be associated with low warfarin dose requirement and this haplotype could be considered in the development of a warfarin dose prediction model for Asian populations.
In vitro ovine articular chondrocyte proliferation: experiments and modelling
Authors: Mancuso L. , Liuzzo M. I. , Fadda S. , Pisu M. , Cincotti A. , Arras M. , La Nasa G. , Concas A. , Cao G.
Published: April 2010

This study focuses on analysis of in vitro cultures of chondrocytes from ovine articular cartilage. Isolated cells were seeded in Petri dishes, then expanded to confluence and phenotypically characterized by flow cytometry. The sigmoidal temporal profile of total counts was obtained by classic haemocytometry and corresponding cell size distributions were measured electronically using a Coulter Counter. A mathematical model recently proposed (1) was adopted for quantitative interpretation of these experimental data. The model is based on a 1‐D (that is, mass‐structured), single‐staged population balance approach capable of taking into account contact inhibition at confluence. The model’s parameters were determined by fitting measured total cell counts and size distributions. Model reliability was verified by predicting cell proliferation counts and corresponding size distributions at culture times longer than those used when tuning the model’s parameters. It was found that adoption of cell mass as the intrinsic characteristic of a growing chondrocyte population enables sigmoidal temporal profiles of total counts in the Petri dish, as well as cell size distributions at ‘balanced growth’, to be adequately predicted.
Terrestrial carbon stocks across a gradient of urbanization: a study of the Seattle, WA region
Authors: HUTYRA LUCY R. , YOON BYUNGMAN , ALBERTI MARINA
Published: April 2010

Most of our global population and its CO2emissions can be attributed to urban areas. The process of urbanization changes terrestrial carbon stocks and fluxes, which, in turn, impact ecosystem functions and atmospheric CO2concentrations. Using the Seattle, WA, region as a case study, this paper explores the relationships between aboveground carbon stocks and land cover within an urbanizing area. The major objectives were to estimate aboveground live and dead terrestrial carbon stocks across multiple land cover classes and quantify the relationships between urban cover and vegetation across a gradient of urbanization. We established 154 sample plots in the Seattle region to assess carbon stocks as a function of distance from the urban core and land cover [urban (heavy, medium, and low), mixed forest, and conifer forest land covers]. The mean (and 95% CI) aboveground live biomass for the region was 89±22 Mg C ha−1with an additional 11.8±4 Mg C ha−1of coarse woody debris biomass. The average live biomass stored within forested and urban land covers was 140±40 and 18±14 Mg C ha−1, respectively, with a 57% mean vegetated canopy cover regionally. Both the total carbon stocks and mean vegetated canopy cover were surprisingly high, even within the heavily urbanized areas, well exceeding observations within other urbanizing areas and the average US forested carbon stocks. As urban land covers and populations continue to rapidly increase across the globe, these results highlight the importance of considering vegetation in urbanizing areas within the terrestrial carbon cycle.
Does relative time of emergence affect stand composition and yield in a grass–legume mixture? Kura clover (Trifolium ambiguum)–meadow bromegrass (Bromus biebersteinii) and Kura clover–orchardgrass (Dactylis glomerata) mixtures
Authors: Walker J. A. , King J. R.
Published: April 2010

Establishing Kura clover (Trifolium ambiguum) in mixtures with grass species is challenging, because slow growth of clover seedlings results in low competitive ability. This study examined establishment success by altering time of seeding of the grass component to reduce competition with Kura clover seedlings. Two trials, one of Kura clover–meadow bromegrass (Bromus biebersteinii) and the other Kura clover–orchardgrass (Dactylis glomerata) mixtures were planted in Edmonton, Alberta. Grasses were seeded at the same time as the clover, or introduced when the clover reached one true leaf or three true leaves, in the autumn of the planting year or the following spring. Species composition varied significantly between treatments. When sown at the same time, Kura clover contributed 31 and 14% of yield in the establishment year when sown with meadow bromegrass and orchard grass, respectively. Delaying grass sowing until Kura clover had one or three leaves gave a higher percentage of Kura clover compared with planting at the same time. Autumn and spring grass sowing resulted in stands of 78 and 80% clover with meadow bromegrass, and 74 and 67% clover with orchardgrass. Altering the competitive advantage of the grass species to produce a more balanced mixture was successfully achieved by delaying seeding of the grass relative to Kura clover. A long interval before introducing the grass (autumn or following spring), was not successful as established Kura clover seedlings have an increased competitive ability.
Identification and characterization of Alix/AIP1 interacting proteins from the black tiger shrimp,Penaeus monodon
Authors: Sangsuriya P , Rojtinnakorn J , Senapin S , Flegel T W
Published: April 2010

Apoptosis is proposed to be a major cause of death in shrimp viral infections. From our previous study, an apoptosis‐related gene,Pm‐Alix, was identified from the black tiger shrimp. Its expression was high in defence‐related tissues including haemocytes and the lymphoid organ. To clarify its possible role in shrimp, we usedPm‐Alixas bait in a yeast two‐hybrid analysis to search for Alix interacting proteins in shrimp. Two cDNA sequences discovered had homology to a predicted ubiquitin C of the purple sea urchin,Strongylocentrotus purpuratus,and to a guanylyl cyclase of the red swamp crayfish,Procambarus clarkii.In vitropull‐down assays confirmed positive interaction between Pm‐Alix and both proteins. Tissue distribution analysis revealed thatPm‐Alixand the two binding partners were widely expressed in various tissues but more highly expressed in haemocytes. However, no significant positive or negative correlation was found in the expression of these genes as shrimp approached morbidity and death after challenge with white spot syndrome virus. Thus, the results suggested that Alix and its interacting partners did not play a direct role related to shrimp death.
MtsR is a dual regulator that controls virulence genes and metabolic functions in addition to metal homeostasis in the group A streptococcus
Authors: Toukoki Chadia , Gold Kathryn M. , McIver Kevin S. , Eichenbaum Zehava
Published: April 2010

MtsR is a metal‐dependent regulator in the group A streptococcus (GAS) that directly represses the transcription of genes involved in haem and metal uptake. While MtsR has been implicated in GAS virulence, the DNA recognition and full regulatory scope exerted by the protein are unknown. In this study we identified the shr promoter (Pshr) and mapped MtsR binding to a 69 bp segment in Pshr that overlaps the core promoter elements. A global transcriptional analysis demonstrated that MtsR modulates the expression of 64 genes in GAS, 44 of which were upregulated and 20 were downregulated in the mtsR mutant. MtsR controls genes with diverse functions including metal homeostasis, nucleic acid and amino acid metabolism, and protein fate. Importantly, the MtsR regulon includes mga, emm49 and ska, which are central for GAS pathogenesis. MtsR binding to the promoter region of both negatively and positively regulated genes demonstrates that it functions as a dual regulator. MtsR footprints are large (47–130 bp) and vary between target promoters. A 16 bp motif that consists of an interrupted palindrome is implicated in the DNA recognition by the metalloregulator. In conclusion, we report here that MtsR is a global regulator in GAS that shapes the expression of vital virulence factors and genes involved in metabolic functions and metal transport, and we discuss the implications for the GAS disease process.
Farnesol misplaces tip‐localized Rho proteins and inhibits cell wall integrity signalling in Aspergillus fumigatus
Authors: Dichtl Karl , Ebel Frank , Dirr Franziska , Routier Françoise H. , Heesemann Jürgen , Wagener Johannes
Published: April 2010

Farnesol is known for inducing apoptosis in some fungi and mammalian cells. To evaluate its potential role as an antifungal agent, we studied its impact on the human pathogen Aspergillus fumigatus. We found that growth of A. fumigatus wild type is inhibited, but two cell wall mutants, Δmnt1 andΔglfA, are much more susceptible to farnesol. This susceptibility is partially rescued by osmotic stabilization, suggesting that farnesol is a cell wall perturbing agent. However, farnesol does not activate but inhibit the cell wall integrity (CWI) pathway. Remarkably, mutants lacking AfMkk2 or AfMpkA, two kinases essential for CWI signalling, are also highly susceptible to farnesol, suggesting that its mode of action goes beyond inhibition of CWI signalling. Farnesyl derivatives are known for interfering with the function of prenylated proteins. We analysed the subcellular localization of two prenylated Rho family GTPases, AfRho1 and AfRho3, which are implicated in controlling CWI and the cytoskeleton. We found that under normal growth conditions AfRho1 and AfRho3 predominantly localize to the hyphal tip. After farnesol treatment this localization is rapidly lost, which is accompanied by swelling of the hyphal tips. Parallel displacement of tropomyosin from the tips suggests a concomitant disorganization of the apical actin cytoskeleton.
Translocation of Borrelia burgdorferi surface lipoprotein OspA through the outer membrane requires an unfolded conformation and can initiate at the C‐terminus
Authors: Schulze Ryan J. , Chen Shiyong , Kumru Ozan S. , Zückert Wolfram R.
Published: April 2010

Borrelia burgdorferi surface lipoproteins are essential to the pathogenesis of Lyme borreliosis, but the mechanisms responsible for their localization are only beginning to emerge. We have previously demonstrated the critical nature of the amino‐terminal ‘tether’ domain of the mature lipoprotein for sorting a fluorescent reporter to the Borrelia cell surface. Here, we show that individual deletion of four contiguous residues within the tether of major surface lipoprotein OspA results in its inefficient translocation across the Borrelia outer membrane. Intriguingly, C‐terminal epitope tags of these N‐terminal deletion mutants were selectively surface‐exposed. Fold‐destabilizing C‐terminal point mutations and deletions did not block OspA secretion, but rather restored one of the otherwise periplasmic tether mutants to the bacterial surface. Together, these data indicate that disturbance of a confined tether feature leads to premature folding of OspA in the periplasm and thereby prevents secretion through the outer membrane. Furthermore, they suggest that OspA emerges tail‐first on the bacterial surface, yet independent of a specific C‐terminal targeting peptide sequence.