bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxygenase Coordination Is Required for Morphological Transition and the Host–Fungus Interaction ofAspergillus flavus
Authors: Brown Sigal Horowitz , Scott James B. , Bhaheetharan Jeyanthi , Sharpee William C. , Milde Lane , Wilson Richard A. , Keller Nancy P.
Published: June 2009

Oxylipins, a class of oxygenase-derived unsaturated fatty acids, are important signal molecules in many biological systems. Recent characterization of an Aspergillus flavus lipoxygenase gene, lox, revealed its importance in maintaining a density-dependent morphology switch from sclerotia to conidia as population density increased. Here, we present evidence for the involvement of four more oxylipin-generating dioxygenases (PpoA, PpoB, PpoC, and PpoD) in A. flavus density-dependent phenomena and the effects of loss of these genes on aflatoxin production and seed colonization. Although several single mutants showed alterations in the sclerotia-to-conidia switch, the major effect was observed in a strain downregulated for all five oxygenases (invert repeat transgene [IRT] strain IRT4 = ppoA, ppoB, ppoC, ppoD, and lox). In strain IRT4, sclerotia production was increased up to 500-fold whereas conidiation was decreased down to 100-fold and the strain was unable to switch into conidial production. Aflatoxin (AF) production for all mutant strains and the wild type was greatest at low population densities and absent in high populations except for strain IRT4, which consistently produced high levels of the mycotoxin. Growth on host seed by both IRT4 and IRT2 (downregulated in ppoA, ppoB, and ppoD) was marked by decreased conidial but increased AF production. We propose that A. flavus oxygenases and the oxylipins they produce act in a highly interdependent network with some redundancy of biological function. These studies provide substantial evidence for oxylipin-based mechanisms in governing fungus–seed interactions and in regulating a coordinated quorum-sensing mechanism in A. flavus.
Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum
Authors: Grünwald Niklaus J. , Goss Erica M. , Ivors Kelly , Garbelotto Matteo , Martin Frank N. , Prospero Simone , Hansen Everett , Bonants Peter J. M. , Hamelin Richard C. , Chastagner Gary , Werres Sabine , Rizzo David M. , Abad Gloria , Beales Paul , Bilodeau Guillaume J. , Blomquist Cheryl L. , Brasier Clive , Brière Stephan C. , Chandelier Anne , Davidson Jennifer M. , Denman Sandra , Elliott Marianne , Frankel Susan J. , Goheen Ellen M. , de Gruyter Hans , Heungens Kurt , James Delano , Kanaskie Alan , McWilliams Michael G. , Man in ‘t Veld Willem , Moralejo Eduardo , Osterbauer Nancy K. , Palm Mary E. , Parke Jennifer L. , Sierra Ana Maria Perez , Shamoun Simon F. , Shishkoff Nina , Tooley Paul W. , Vettraino Anna Maria , Webber Joan , Widmer Timothy L.
Published: June 2009

Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based on a consensus established by the P. ramorum research community. Clonal lineages are named with a two letter identifier for the continent on which they were first found (e.g., NA = North America; EU = Europe) followed by a number indicating order of appearance. Clonal lineages known to date are designated NA1 (mating type: A2; distribution: North America; environment: forest and nurseries), NA2 (A2; North America; nurseries), and EU1 (predominantly A1, rarely A2; Europe and North America; nurseries and gardens). It is expected that novel lineages or new variants within the existing three clonal lineages could in time emerge.
Fluctuations in Number of Cercospora beticola Conidia in Relationship to Environment and Disease Severity in Sugar Beet
Authors: Khan J. , Qi A. , Khan M. F. R.
Published: June 2009

Cercospora leaf spot, caused by Cercospora beticola, is the most damaging foliar disease of sugar beet in Minnesota (MN) and North Dakota (ND). Research was conducted to characterize the temporal progression of aerial concentration of C. beticola conidia in association with the environment and disease severity in sugar beet. In 2003 and 2004, volumetric spore traps were placed within inoculated sugar beet plots to determine daily dispersal of conidia at Breckenridge, MN, and St. Thomas, ND. Plots were rated weekly for disease severity. At both locations, conidia were first collected in early July 2003 and late June in 2004. Peaks of conidia per cubic meter of air were observed with maxima in late August 2003 and in early September 2004 at both locations. Peaks of airborne conidium concentration were significantly correlated with the average temperature of daily hours when relative humidity was greater than 87%. Weekly mean hourly conidia per cubic meter of air was significantly (P < 0.01) associated with disease severity during both years and across locations. This study showed that C. beticola conidial numbers may be used to estimate potential disease severity that, with further research, could be incorporated in a disease forecasting model to rationalize Cercospora leaf spot management.
Internal Resistance in Winter Oilseed Rape Inhibits Systemic Spread of the Vascular Pathogen Verticillium longisporum
Authors: Eynck C. , Koopmann B. , Karlovsky P. , von Tiedemann A.
Published: June 2009

Verticillium longisporum is a vascular fungal pathogen presently threatening oilseed rape production in Europe. Systemic spread and vascular responses were studied in a susceptible (‘Falcon’) and a resistant genotype (SEM 05-500256) of Brassica napus. Colonization of both genotypes after dip-inoculation of the roots followed by quantitative polymerase chain reaction revealed similarities only in the initial stages of root penetration and colonization of the hypocotyl, while a substantial invasion of the shoot was only recorded in ‘Falcon’. It is concluded that the type of resistance represented in SEM 05-500256 does not prevent the plant base from being invaded as it is internally expressed well after root penetration and colonization of the plant base. The morphological and biochemical nature of barriers induced in the hypocotyl tissue upon infection was studied with histochemical methods accompanied by biochemical analyses. Histochemical studies revealed the build-up of vascular occlusions and the reinforcement of tracheary elements through the deposition of cell wall-bound phenolics and lignin. Furthermore, the accumulation of soluble phenolics was observed. Although these responses were found in vascular tissues of both genotypes, they occurred with a significantly higher intensity in the resistant genotype and corresponded with the disease phenotype. In the resistant genotype phenols were differentially expressed in a time-dependent manner with preformed soluble and cell wall-bound phenolics at earlier time points and de novo formation of lignin and lignin-like polymers at later stages of infection. This is the first study identifying a crucial role of phenol metabolism in internal defense of B. napus against V. longisporum and locating the crucial defense responses in the plant hypocotyl.
Unusual Events Involved in Banana bunchy top virus Strain Evolution
Authors: Fu Hui-Chuan , Hu Jer-Ming , Hung Ting-Hsuan , Su Hong-Ji , Yeh Hsin-Hung
Published: June 2009

Banana bunchy top virus (BBTV) can be transmitted by aphids and consists of at least six integral components (DNA-R, -U3, -S, -M, -C, and -N). Several additional replication-competent components (additional Reps) are associated with some BBTV isolates. A collected BBTV strain (TW3) that causes mild symptoms was selected to study the processes in BBTV evolution. Southern blot hybridization, polymerase chain reaction (PCR), and real-time PCR did not detect DNA-N in TW3. Real-time PCR quantification of BBTV components revealed that, except for the copy number of TW3 DNA-U3, each detected integral component of BBTV TW3 was at least two orders lower than that of the severe strains. No infection was observed in plants inoculated with aphids, which were first given acquisition access to the TW3-infected banana leaves. Recombination analysis revealed recombination between the integral component TW3 DNA-U3 and the additional Rep DNA-Y. All BBTV integral components contain a replication initiation region (stem-loop common region) that share high sequence identity. Sequence alignment revealed that TW3 DNA-R, -S, -M, and -C all have a stem-loop common region containing a characteristic 9-nucleotide deletion found only in all reported DNA-N. Our data suggest that the additional Rep DNAs can serve as sources of additional genetic diversity for integral BBTV components.
Cascade: An Epidemiological Model to Simulate Disease Spread and Aggregation Across Multiple Scales in a Spatial Hierarchy
Authors: Gosme M. , Lucas P.
Published: June 2009

Disease spread occurs at several spatial scales, e.g., from field to field, plant to plant, and leaf to leaf. So far, epidemiological models have largely overlooked the multiscale nature of epidemics. Here, we propose a model that simulates disease spread across multiple scales in a nested hierarchy. The model is based on the central ideas of hierarchy theory, i.e., (i) the system is decomposed vertically into levels and horizontally into holons (elements at one level, which are complete systems when seen from the lower level), and (ii) higher levels are characterized by slower processes than lower levels. The model is individual-based, the individuals being the holons, which are either susceptible or infected. At each level, infections within one holon (i.e., infections between holons of the level below) occur independently from the other holons: infections between holons happen at the higher level. The self-similarity of the model structure and processes across all levels allows implementing the model with a simple recursive algorithm. The behavior of the model was studied using methods commonly applied to field data. Aggregation of the disease was characterized through the incidence-incidence relationship and the binomial power law, in order to study the effect of infectiousness at each level on disease aggregation. Sensitivity analyses showed that disease incidences at all levels were influenced by the infectiousness at any level, but infectiousness at higher levels had more effect than infectiousness at lower levels. It was also shown that increasing the probability of infection at a given level increased aggregation at higher level(s) and decreased aggregation at lower level(s). The results were consistent between incidence-incidence relationship and power law analysis, but the incidence-incidence relationship was more sensitive in detecting the differences in aggregation between treatments.
Disease Spread Across Multiple Scales in a Spatial Hierarchy: Effect of Host Spatial Structure and of Inoculum Quantity and Distribution
Authors: Gosme Marie , Lucas Philippe
Published: June 2009

Spatial patterns of both the host and the disease influence disease spread and crop losses. Therefore, the manipulation of these patterns might help improve control strategies. Considering disease spread across multiple scales in a spatial hierarchy allows one to capture important features of epidemics developing in space without using explicitly spatialized variables. Thus, if the system under study is composed of roots, plants, and planting hills, the effect of host spatial pattern can be studied by varying the number of plants per planting hill. A simulation model based on hierarchy theory was used to simulate the effects of large versus small planting hills, low versus high level of initial infections, and aggregated versus uniform distribution of initial infections. The results showed that aggregating the initially infected plants always resulted in slower epidemics than spreading out the initial infections uniformly. Simulation results also showed that, in most cases, disease epidemics were slower in the case of large host aggregates (100 plants/hill) than with smaller aggregates (25 plants/hill), except when the initially infected plants were both numerous and spread out uniformly. The optimal strategy for disease control depends on several factors, including initial conditions. More importantly, the model offers a framework to account for the interplay between the spatial characteristics of the system, rates of infection, and aggregation of the disease.
Population Genetic Analysis of an Eastern U.S. Wheat Powdery Mildew Population Reveals Geographic Subdivision and Recent Common Ancestry with U.K. and Israeli Populations
Authors: Parks Ryan , Carbone Ignazio , Murphy J. Paul , Cowger Christina
Published: June 2009

The structure of the U.S. wheat powdery mildew population (Blumeria graminis f. sp. tritici) has not been previously investigated, and the global evolutionary history of B. graminis f. sp. tritici is largely unknown. After gathering 141 single-ascosporic B. graminis f. sp. tritici isolates from 10 eastern U.S. locations, 34 isolates from the United Kingdom, and 28 isolates from Israel, we analyzed pathogen population structure using presumptively neutral markers. DNA was extracted from conidia, primers for 12 “housekeeping” genes were designed, and amplicons were examined for polymorphism. Four genes were found to contain a total of 12 single-nucleotide polymorphisms in the U.S. population and were also analyzed in the U.K. and Israeli populations. In total, 25 haplotypes were inferred from the four concatenated genes, with 2 haplotypes comprising over 70% of the U.S. population. Using Hudson's tests and analysis of molecular variance, we found the wheat mildew isolates subdivided into four groups corresponding to distinct regions: the mid-Atlantic United States, the southern United States, the United Kingdom, and Israel. Genotypic diversity was greatest in samples from the United Kingdom, Israel, Virginia, and Kinston, NC. Using rarefaction, a procedure that compensates for differing sample sizes when estimating population richness and diversity, we found that cooler locations with greater conduciveness to regular powdery mildew epidemics had the greatest haplotype richness. Our results suggest that the eastern U.S. B. graminis f. sp. tritici population is young, descended recently from Old World populations with isolation and genetic drift, and is currently subdivided into northern and southern subpopulations.
Epidemiological Analysis of Take-All Decline in Winter Wheat
Authors: Bailey D. J. , Paveley N. , Spink J. , Lucas P. , Gilligan C. A.
Published: June 2009

Take-all dynamics within crops differing in cropping history (the number of previous consecutive wheat crops) were analyzed using an epidemiological model to determine the processes affected during take-all decline. The model includes terms for primary infection, secondary infection, inoculum decay, and root growth. The average rates of root production did not vary with cropping history. The force of primary infection increased from a low level in 1st wheat crops, to a maximum in 2nd to 4th wheat crops, and then to intermediate levels thereafter. The force of secondary infection was low but increased steadily during the season in first wheat crops, was delayed but rose and fell sharply in 2nd to 4th wheat crops, and for 5th and 7th wheat crops returned to similar dynamics as that for 1st wheat crops. Chemical seed treatment with silthiofam had no consistent effect on the take-all decline process. We conjecture that these results are consistent with (i) low levels of particulate inoculum prior to the first wheat crop leading to low levels of primary infection, low levels of secondary infection, and little disease suppression; (ii) net amplification of inoculum during the first wheat crop and intercrop period; (iii) increased levels of primary and secondary infection in subsequent crops, but higher levels of disease suppression; and (iv) an equilibrium between the pathogen and antagonist populations by the 5th wheat, reflected by lower overall rates of primary infection, secondary infection, disease suppression and hence, disease severity.
Aggressiveness Components and Adaptation to a Host Cultivar in Wheat Leaf Rust
Authors: Pariaud Bénédicte , Robert Corinne , Goyeau Henriette , Lannou Christian
Published: June 2009

Experimental evidence on the capacity of pathogen populations to quantitatively adapt to their hosts and on the life traits that are involved is lacking at this time. In this article, we identified a situation in which a leaf rust pathotype (P1) was found at a high frequency on a widely grown cultivar (Soissons) and we tested the hypothesis that P1 was more aggressive on Soissons than other virulent pathotypes (P2 and P3). Several components of the pathogen life cycle were measured on adult wheat plants in two different experiments under greenhouse conditions: latent period, spore production per lesion and per unit of sporulating tissue, uredinium size, and lesion life span. Regardless of the component, pathotype P1 was repeatedly found to be more aggressive than at least one of the other two pathotypes, with differences of 5 to 51%. Breaking down spore production per lesion into uredinium size and spore production per square millimeter of sporulating tissue showed that the three pathotypes presented different aggressiveness profiles, suggesting different development constraints for the pathogen, either for its growth capacity into host tissues or its ability to exploit the host resources for spore production. Although leaf rust pathotypes present a clonal structure, quantitative differences were found for aggressiveness traits within a pathotype.
Scenario Approach for Assessing the Utility of Dispersal Information in Decision Support for Aerially Spread Plant Pathogens, Applied to Phytophthora infestans
Authors: Skelsey P. , Rossing W. A. H. , Kessel G. J. T. , van der Werf W.
Published: June 2009

Opportunities exist to improve decision support systems through the use of dispersal information gained from epidemiological research. However, dispersal and demographic information is often fragmentary in plant pathology, and this uncertainty creates a risk of inappropriate action whenever such information is used as a basis for decision making. In this article, a scenario-based simulation approach is used to evaluate crop and economic risks and benefits in the use of dispersal information for decision making using the potato late blight pathosystem (Phytophthora infestans–Solanum tuberosum) as a case study. A recently validated spatiotemporal potato late blight model was coupled to submodels for crop growth, tuber dry matter production, and fungicide efficacy. The yield response of a range of management scenarios to a single influx of primary inoculum (the initial spore load) was calculated. Damage curves (relative yield loss versus initial spore load) from a range of combinations of varietal susceptibility and fungicide treatments were used to classify the various management scenarios as either sensitive to initial spore load or tolerant to initial spore load, thus identifying where a high degree of accuracy would be required in dispersal information for appropriate decision making, and where a greater degree of uncertainty could be tolerated. General epidemics, resulting from spatially homogeneous initial spore loads, responded more strongly to the size of the initial spore load than focal epidemics, resulting from an initial spot infection. Susceptible cultivars responded with sizeable yield losses even at low levels of initial spore load, regardless of the fungicide management regime used. These results indicated that, for susceptible cultivars (late cultivars in particular), the degree of accuracy that would be required in dispersal information for appropriate decision making is unlikely to be practically attainable. The results also indicated that, contrary to “folk wisdom,” spore loads of a few hundred spores per square meter do not lead to appreciable crop loss in resistant cultivars and are therefore acceptable. We conclude that scope exists for including dispersal information in decision making for potato late blight with resistant potato cultivars but not for susceptible cultivars. The modeling framework used in this study can be extended to investigate the scope for inclusion of dispersal information in decision support for other aerially transmitted pathogens.
Will Routine Annual Influenza Prevention and Control Systems Serve the United States Well in a Pandemic?
Authors: Ringel Jeanne S. , Moore Melinda , Zambrano John , Lurie Nicole
Published: June 2009

Objective: To assess the extent to which the systems in place for prevention and control of routine annual influenza could provide the information and experience needed to manage a pandemic.

Methods: The authors conducted a qualitative assessment based on key informant interviews and the review of relevant documents.

Results: Although there are a number of systems in place that would likely serve the United States well in a pandemic, much of the information and experience needed to manage a pandemic optimally is not available.

Conclusions: Systems in place for routine annual influenza prevention and control are necessary but not sufficient for managing a pandemic, nor are they used to their full potential for pandemic preparedness. Pandemic preparedness can be strengthened by building more explicitly upon routine influenza activities and the public health system’s response to the unique challenges that arise each influenza season (eg, vaccine supply issues, higher than normal rates of influenza-related deaths). (Disaster Med Public Health Preparedness. 2009;3(Suppl 2):S160–S165)
Disparities between observed and predicted impacts of climate change on winter bird assemblages
Authors: La Sorte Frank A. , Lee Tien Ming , Wilman Hamish , Jetz Walter
Published: June 2009

Understanding how climate change affects the structure and function of communities is critical for gauging its full impact on biodiversity. To date, community-level changes have been poorly documented, owing, in part, to the paucity of long-term datasets. To circumvent this, the use of ‘space-for-time’ substitution—the forecasting of temporal trends from spatial climatic gradients—has increasingly been adopted, often with little empirical support. Here we examine changes from 1975 to 2001 in three community attributes (species richness, body mass and occupancy) for 404 assemblages of terrestrial winter avifauna in North America containing a total of 227 species. We examine the accuracy of space-for-time substitution and assess causal associations between community attributes and observed changes in annual temperature using a longitudinal study design. Annual temperature and all three community attributes increased over time. The trends for the three community attributes differed significantly from the spatially derived predictions, although richness showed broad congruence. Correlations with trends in temperature were found with richness and body mass. In the face of rapid climate change, applying space-for-time substitution as a predictive tool could be problematic with communities developing patterns not reflected by spatial ecological associations.
Telomere shortening and survival in free-living corvids
Authors: Salomons H. M. , Mulder G. A. , van de Zande L. , Haussmann M. F. , Linskens M. H. K. , Verhulst S.
Published: June 2009

Evidence accumulates that telomere shortening reflects lifestyle and predicts remaining lifespan, but little is known of telomere dynamics and their relation to survival under natural conditions. We present longitudinal telomere data in free-living jackdaws (
Corvus monedula
) and test hypotheses on telomere shortening and survival. Telomeres in erythrocytes were measured using pulsed-field gel electrophoresis. Telomere shortening rates within individuals were twice as high as the population level slope, demonstrating that individuals with short telomeres are less likely to survive. Further analysis showed that shortening rate in particular predicted survival, because telomere shortening was much accelerated during a bird's last year in the colony. Telomere shortening was also faster early in life, even after growth was completed. It was previously shown that the lengths of the shortest telomeres best predict cellular senescence, suggesting that shorter telomeres should be better protected. We test the latter hypothesis and show that, within individuals, long telomeres shorten faster than short telomeres in adults and nestlings, a result not previously shown
in vivo
. Moreover, survival selection in adults was most conspicuous on relatively long telomeres. In conclusion, our longitudinal data indicate that the shortening rate of long telomeres may be a measure of ‘life stress’ and hence holds promise as a biomarker of remaining lifespan.
Will male advertisement be a reliable indicator of paternal care, if offspring survival depends on male care?
Authors: Kelly Natasha B. , Alonzo Suzanne H.
Published: June 2009

Existing theory predicts that male signalling can be an unreliable indicator of paternal care, but assumes that males with high levels of mating success can have high current reproductive success, without providing any parental care. As a result, this theory does not hold for the many species where offspring survival depends on male parental care. We modelled male allocation of resources between advertisement and care for species with male care where males vary in quality, and the effect of care and advertisement on male fitness is multiplicative rather than additive. Our model predicts that males will allocate proportionally more of their resources to whichever trait (advertisement or paternal care) is more fitness limiting. In contrast to previous theory, we find that male advertisement is always a reliable indicator of paternal care and male phenotypic quality (e.g. males with higher levels of advertisement never allocate less to care than males with lower levels of advertisement). Our model shows that the predicted pattern of male allocation and the reliability of male signalling depend very strongly on whether paternal care is assumed to be necessary for offspring survival and how male care affects offspring survival and male fitness.
The expression of melanin-based plumage is separately modulated by exogenous oxidative stress and a melanocortin
Authors: Galván Ismael , Alonso-Alvarez Carlos
Published: June 2009

Melanin-based traits involved in animal communication have been traditionally viewed as occurring under strict genetic control. However, it is generally accepted that both genetic and environmental factors influence melanin production. Medical studies suggest that, among environmental factors influencing melanization, oxidative stress could play a relevant role. On the other hand, genetic control would be exerted by the melanocortin system, and particularly by the alpha-melanocyte-stimulating hormone (α-MSH), which triggers the production of eumelanins (black pigments). To determine how the melanocortin system and an exogenous source of oxidative stress interact in the expression of melanin-based plumage, developing red-legged partridges (Alectoris rufa) were manipulated. Some partridges were injected with α-MSH, while other birds received a pro-oxidant molecule (diquat) in drinking water. Controls and birds receiving both treatments were also studied. Both α-MSH- and diquat-treated individuals presented larger eumelanin-based traits than controls, but α-MSH+diquat-treated birds showed the largest traits, suggesting that oxidative stress and melanocortins promote additive but independent effects. Diquat also induced a decline in the level of a key intracellular antioxidant (glutathione), which is associated with high expression of eumelanin-based signals in other bird species. Some scenarios for the evolution of melanin-based traits in relation to oxidative stress are proposed.
Simulating flow separation from continuous surfaces: routes to overcoming the Reynolds number barrier
Authors: Leschziner Michael , Li Ning , Tessicini Fabrizio
Published: June 2009

This paper provides a discussion of several aspects of the construction of approaches that combine statistical (Reynolds-averaged Navier–Stokes, RANS) models with large eddy simulation (LES), with the objective of making LES an economically viable method for predicting complex, high Reynolds number turbulent flows. The first part provides a review of alternative approaches, highlighting their rationale and major elements. Next, two particular methods are introduced in greater detail: one based on coupling near-wall RANS models to the outer LES domain on a single contiguous mesh, and the other involving the application of the RANS and LES procedures on separate zones, the former confined to a thin near-wall layer. Examples for their performance are included for channel flow and, in the case of the zonal strategy, for three separated flows. Finally, a discussion of prospects is given, as viewed from the writer's perspective.
Experiment and simulation on interface shapes of an yttrium aluminium garnet miniature molten zone formed using the laser-heated pedestal growth method for single-crystal fibers
Authors: Chen P. Y. , Chang C. L. , Huang K. Y. , Lan C. W. , Cheng W. H. , Huang S. L.
Published: June 2009

A two-dimensional simulation was employed to study the melt/air and melt/solid interface shapes of the miniature molten zone formed in a laser-heated pedestal growth (LHPG) system. Using a non-orthogonal body-fitting grid system with the control-volume finite-difference method, the interface shape can be determined both efficiently and accurately. During stable growth, the dependence of the molten-zone length and shape on the heating CO2laser is examined in detail under both the maximum and the minimum allowed powers with various growth speeds. The effect of gravity on the miniature molten zone is also simulated and the possibility of horizontally oriented LHPG is revealed. Such a horizontal system is good for the growth of long crystal fibers.
Crystal structure of defect-containing semiconductor nanocrystals – an X-ray diffraction study
Authors: Buljan Maja , Desnica Uroš V. , Radić Nikola , Dražić Goran , Matěj Zdeněk , Valeš Václav , Holý Václav
Published: June 2009

Defects of crystal structure in semiconductor nanocrystals embedded in an amorphous matrix are studied by X-ray diffraction and a full-profile analysis of the diffraction curves based on the Debye formula. A new theoretical model is proposed, describing the diffraction from randomly distributed intrinsic and extrinsic stacking faults and twin blocks in the nanocrystals. The application of the model to full-profile analysis of experimental diffraction curves enables the determination of the concentrations of individual defect types in the nanocrystals. The method has been applied for the investigation of self-organized Ge nanocrystals in an SiO2matrix, and the dependence of the structure quality of the nanocrystals on their deposition and annealing parameters was obtained.
Simulation of small-angle X-ray scattering from thylakoid membranes
Authors: Kirkensgaard J. J. K. , Holm J. K. , Larsen J. K. , Posselt D.
Published: June 2009

Small-angle X-ray scattering (SAXS) patterns are calculated from a three-dimensional model of photosynthetic thylakoid membranes. The intricate structure of the thylakoids is represented by sampling random `electron density points' on geometric surfaces. The simulation setup works as a virtual instrument, allowing direct comparison with experimental data. The simulations qualitatively reproduce experimental data and thus clarify the structural origin of the scattering features. This is used to explain recent SAXS measurements and as a guideline for new experiments and future quantitative modeling. The setup has general applicability for model testing purposes when modeling scattering from membrane systems of complex geometries.
Microbeam X-ray diffraction from twisted lamellar crystals: theory and computer simulation
Authors: Luchnikov Valeriy A. , Ivanov Dimitri A.
Published: June 2009

The diffraction peak position, width and intensity distribution are calculated for the case of a helicoidally twisted crystalline lamella, both analytically and numerically. It is shown that the diffraction 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. The equatorial peaks, which are close to the normal direction to the lamellar basal plane, are characterized by the highest azimuthal width. By contrast, the reflections positioned close to the lamellar surface have the smallest azimuthal width. For non-equatorial peaks in the proximity of the twisting axis the intensity has an unusual asymmetric shape. The shape of the microbeam, as well as its position and direction with respect to the lamella, influences the shape of the diffraction peaks in reciprocal space and their appearance in two-dimensional diffractograms. The proposed approach can be useful, for example, for the interpretation of microbeam diffractograms of banded polymer spherulites.
Transformations for monoclinic crystal symmetry in texture analysis
Authors: Matthies Siegfried , Wenk Hans-Rudolf
Published: June 2009

Monoclinic crystals can be described in two settings: in the first setting theC2rotation axis is parallel to thezaxis and in the second setting it is parallel to theyaxis. Transformations of lattice parameters, Miller and zone indices, and atomic coordinates is straightforward; the situation is far more complex for texture analysis with orientation distributions and corresponding representations. This article gives explicit transformations that need to be applied, not only for texture analysis but also for calculations of physical properties of materials with preferred orientation. In texture research the relationship between the Cartesian crystal coordinate system and the unit cell must be unambiguously defined and a uniform convention is desirable.
On the polymorphism of benzocaine; a low-temperature structural phase transition for form (II)
Authors: Chan Eric J. , Rae A. David , Welberry T. Richard
Published: June 2009

A low-temperature structural phase transition has been observed for form (II) of benzocaine (BZC). Lowering the temperature doubles the b-axis repeat and changes the space group from P212121 to P1121 with γ now 99.37 °. The structure is twinned, the twin rule corresponding to a 21 screw rotation parallel to a. The phase transition is associated with a sequential displacement parallel to a of zigzag bi-layers of ribbons perpendicular to b*. No similar phase transition was observed for form (I) and this was attributed to the different packing symmetries of the two room-temperature polymorphic forms.
Analysis of ion-migration paths in inorganic frameworks by means of tilings and Voronoi–Dirichlet partition: a comparison
Authors: Anurova Nataly A. , Blatov Vladislav A.
Published: June 2009

Two methods using Voronoi–Dirichlet polyhedra (Voronoi–Dirichlet partition) or tiles (tiling) based on partitioning space are compared to investigate cavities and channels in crystal structures. The tiling method was applied for the first time to study ion conductivity in 105 ternary, lithium–oxygen-containing compounds, Li
a

X

b
O
z
, that were recently recognized as fast-ion conductors with the Voronoi–Dirichlet partition method. The two methods were found to be similar in predicting the occurrence of ionic conductivity, however, their conclusions on the dimensionality of conductivity were different in two cases. It is shown that such a contradiction can indicate a high anisotropy of conductivity. Both advantages and restrictions of the methods are discussed with respect to fast-ion conductors and zeolites.
Structures of the pseudo-trigonal polymorphs of Cu2(OH)3Cl. Corrigendum
Authors: Malcherek Thomas , Schlüter Jochen
Published: June 2009

An error in the paper by Malcherek & Schlüter (2009), Acta Cryst. B65, 334–341, is corrected.
Mesenchymal cells inhibit expansion but not cytotoxicity exerted by gamma–delta T cells
Authors: Petrini I. , Pacini S. , Petrini M. , Fazzi R. , Trombi L. , Galimberti S.
Published: June 2009

Background  Multipotent mesenchymal stromal cells (MSCs) exert a relevant immunosuppressive activity by inhibiting T‐ and B‐lymphocytes, natural killer (NK) cells and dendritic cell expansion. Nevertheless, a possible activity on gamma/delta T cells has still not been evaluated.

Gamma–delta T lymphocytes play an important role in the control of cancer and they have been shown to be implicated in graft‐vs.‐host disease. Thus, modulation of activation and proliferation of these cells could be relevant for therapeutic purposes.

Materials and methods  Peripheral blood mononuclear cells from 21 healthy donors were used as source for gamma–delta T cells, expanded in presence of 10 IU mL−1 interleukin‐2 (IL‐2) and 1 μM zoledronate. MSCs were recovered from patients undergoing routine total hip replacement surgery, and characterised by flow cytometry. Cytotoxicity on multiple myeloma and melanoma cell lines was assessed by measuring dilution of the carboxyfluorescein diacetate succinimydylester dye (CFSE). Gamma–delta T cells were then incubated with MSCs in contact cultures, and with addition of MSC‐conditioned medium.

Results  In this article we confirmed that (1) in vitro expanded gamma–delta T cells play a significant anti‐proliferative effect on multiple myeloma and melanoma cells and (2) multipotent mesenchymal stromal cells effectively suppress the ex vivo expansion of T cells carrying a specific T‐cell receptor gene (TCR) rearrangement, Vgamma9/Vdelta2, induced by the combination of IL‐2 and zoledronate, without interfering with their cytotoxic activity.

Discussion  These findings contribute to explain the activity of ex vivo expanded mesenchymal cells, suggesting that MSCs would interact with gamma–delta T lymphocytes.

Conclusion  This effect could be relevant in separating graft‐vs.‐host from the graft‐vs.‐tumour effect, especially considering the possibility of modulating T‐lymphocytes activity by the immunomodulating drugs now available.
Renal artery stenosis predicts adverse cardiovascular and renal outcome in patients with peripheral artery disease
Authors: Amighi J. , Schlager O. , Haumer M. , Dick P. , Mlekusch W. , Loewe C. , Böhmig G. , Koppensteiner R. , Minar E. , Schillinger M.
Published: June 2009

Background  Patients with symptomatic peripheral artery disease (PAD) are considered cardiovascular high‐risk patients. Our aim was to investigate whether incidental renal artery stenosis (RAS) increases the risk for adverse cardiovascular and renal outcomes in these patients.

Materials and methods  We prospectively enrolled 487 consecutive patients admitted for revascularization of symptomatic PAD and performed a renal overview angiogram categorizing RAS as absent (0–29%), moderate (30–59%) and severe (≥ 60%) respectively. Clinical follow‐up was for median 15 months (IQR 12–22) for the occurrence of major adverse events [MAE: composite of death, myocardial infarction (MI), stroke, percutaneous coronary intervention, coronary bypass surgery, amputation and kidney failure]. Glomerular filtration rates (GFR) were obtained at 12 months to quantify the course of renal function.

Results  A severe RAS was found in 76 patients (15·6%). Overall MAE occurred in 121 patients (24·8%), the composite endpoint of MI, stroke, amputation and death occurred in 101 patients (20·7%). Patients with a severe RAS had a 1·87‐fold increased adjusted risk for MAE (95% CI 1·12–3·12, P = 0·017), a 2·51‐fold increased adjusted risk for occurrence of the composite endpoint of MI, stroke, amputation and death (95% CI 1·45–4·34, P = 0·001) and a 2·93‐fold increased risk for death (95% CI 1·41–6·08, P = 0·004), compared to those of patients without RAS respectively. We observed a significant association between the decrease of GFR over the 12‐month follow‐up period and the severity of RAS by multivariable analysis (P = 0·044).

Conclusion  Severe RAS in patients with symptomatic PAD is an independent predictor of major adverse cardiovascular events, adverse renal outcome and mortality.
Effects of AT1‐ and β‐adrenergic receptor antagonists on TGF‐β1‐induced fibrosis in transgenic mice
Authors: Seeland U. , Schäffer A. , Selejan S. , Hohl M. , Reil J.‐C. , Müller P. , Rosenkranz S. , Böhm M.
Published: June 2009

Background Transforming growth factor‐β1 (TGF‐β1) is involved in interstitial remodelling promoting collagen synthesis and suppressing collagen degradation by inhibition of collagenases. TGF‐β1 mediates angiotensin II‐dependent effects and modulates β1‐adrenergic signalling. To study the effect of neuroendocrine antagonism on TGF‐β‐induced hypertrophic and fibrotic phenotype, we treated TGF‐β1 (Cys223,225Ser) transgenic mice (TGF‐β1‐TG) with either the β1‐receptor blocker metoprolol (MET), the angiotensin II type I (AT1)‐receptor antagonist telmisartan (TEL) or an antibody blocking TGF‐β1 signalling (TGFβ1‐sR‐Ab).

Material and Methods Transforming growth factor‐β1‐TG mice (8 weeks) overexpressing TGF‐β1 were treated with either TEL (10 mg kg−1), MET (350 mg kg−1) or a soluble TGF‐β1 receptor antibody (1 mg kg−1) for 6 weeks. Morphological analyses of interstitium and cardiomyocytes were related to expression of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) by immunoblotting and zymography.

Results In TGF‐β1‐TG mice, myocardial interstitial total collagen content was fourfold elevated compared to that of controls (P < 0·05) and was lowered under the treatment with TEL (P < 0·05). Protein expression of TIMP‐1 and ‐4 was increased in TGF‐β1‐TG but inhibited by TEL (TIMP‐1 and TIMP‐4) and MET (TIMP‐1), while collagenase activity was decreased in TGF‐β1‐TG and normalized by treatment with TEL (MMP‐1 and MMP‐13) and MET (MMP‐1) (P < 0·05). Morphometric measurements of cardiomyocyte diameter and area demonstrated similar antihypertrophic effects for all treatment groups.

Conclusion The AT1‐antagonist TEL reduced myocardial hypertrophy and interstitial fibrosis in TGF‐β1‐TG mice by normalizing MMP/TIMP ratio. β1‐Adrenergic inhibition by MET as well as TGF‐β1 antagonism induced antihypertrophic rather than antifibrotic effects. Inhibition of both renin‐angiotensin system and β1‐adrenergic system may exert different but synergistic effects to reduce myocardial remodelling.
Elevated tryptase levels selectively cluster in myeloid neoplasms: a novel diagnostic approach and screen marker in clinical haematology
Authors: Sperr W. R. , El‐Samahi A. , Kundi M. , Girschikofsky M. , Winkler S. , Lutz D. , Endler G. , Rumpold H. , Agis H. , Sillaber C. , Jäger U. , Valent P.
Published: June 2009

Background Recent data suggest that tryptase, a mast cell enzyme, is expressed in neoplastic cells in myeloid leukaemias. In several of these patients, increased serum tryptase levels are detectable.

Materials and methods We have determined serum tryptase levels in 914 patients with haematological malignancies, including myeloproliferative disorders (n = 156), myelodysplastic syndromes (MDS,n = 241), acute myeloid leukaemia (AML,n = 317), systemic mastocytosis (SM,n = 81), non‐Hodgkin′s lymphoma (n = 59) and acute lymphoblastic leukaemia (n = 26). Moreover, tryptase was measured in 136 patients with non‐neoplastic haematological disorders, 102 with non‐haematological disorders and 164 healthy subjects.

Results In healthy subjects, the median serum tryptase was 5·2 ng mL−1. Elevated serum tryptase levels were found to cluster in myeloid neoplasm, whereas almost all patients with lymphoid neoplasms exhibited normal tryptase. Among myeloid neoplasms, elevated tryptase levels (> 15 ng mL−1) were recorded in > 90% of patients with SM, 38% with AML, 34% with CML and 25% with MDS. The highest tryptase levels, often > 1000 ng mL−1, were found in advanced SM and core‐binding‐factor leukaemias. In most patients with non‐neoplastic haematological disorders and non‐haematological disorders analysed in our study, tryptase levels were normal, the exception being a few patients with end‐stage kidney disease and helminth infections, in whom a slightly elevated tryptase was found.

Conclusions In summary, tryptase is a new diagnostic marker of myeloid neoplasms and a useful test in clinical haematology.
Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale‐free network
Authors: Hayashi Yohei , Senda Toshiya , Sano Norihiko , Horikoshi Masami
Published: June 2009

A rapid increase in research on the relationship between histone modifications and their subsequent reactions in the nucleus has revealed that the histone modification system is complex, and robust against point mutations. The prevailing theoretical framework (the histone code hypothesis) is inadequate to explain either the complexity or robustness, making the formulation of a new theoretical framework both necessary and desirable. Here, we develop a model of the regulatory network of histone modifications in which we encode histone modifications as nodes and regulatory interactions between histone modifications as links. This network has scale‐free properties and subnetworks with a pseudo–mirror symmetry structure, which supports the robustness of the histone modification network. In addition, we show that the unstructured tail regions of histones are suitable for the acquisition of this scale‐free property. Our model and related insights provide the first framework for an overall architecture of a histone modification network system, particularly with regard to the structural and functional roles of the unstructured histone tail region. In general, the post‐translational “modification webs” of natively unfolded regions (proteins) may function as signal routers for the robust processing of the large amounts of signaling information.
Geology in the Falkland Islands
Authors: CLARK RICHARD , EDWARDS EMMA , LUXTON STEPHEN , & TOM SHIPP , WILSON PETER
Published: June 2009

In the next few years we are likely to hear and learn much about the offshore geology of the Falkland Islands as exploratory drilling for hydrocarbons begins. The offshore geology may become better known than the onshore, of which there has been little detailed investigation in the 200+ years since settlements were established. Here we outline the history of geological investigations and present information gathered during recent fieldwork.
The birth of the continents: new clues from inclusions in diamonds
Authors: ROLLINSON HUGH
Published: June 2009

Tiny inclusions found in diamonds may hold the clue to the origin of the Earth's continental crust. This is the new idea proposed by a group of Earth scientists from Australia and Russia studying a diamond pipe in Siberia.
Protecting the Jurassic: global boundary stratotypes and conservation
Authors: & KEVIN PAGE , MELENDEZ GUILLERMO
Published: June 2009

Who decides where the boundaries lie?
Excursion guide 11: Mount St Helens
Authors: WALTHAM TONY
Published: June 2009

The 1980 eruption of the Mount St Helens volcano produced a huge crater, massive debris flows and truly remarkable blast effects. All the features are still very visible, and the site offers easy access for an unforgettable visit.
Granites are not diapiric!
Authors: Petford Nick , Clemens John D.
Published: June 2009

How are granite magmas transported from their source regions in the deep crust, through 10–40 km of overlying solid rock and emplaced close to the Earth's surface? What are the mechanical processes that allow this to take place and how long does it all take? These problems have challenged and preoccupied geologists since the days of Hutton. In the ensuing 200 years or so, a range of ideas from the plausible to the eccentric have been put forward to explain the granite phenomenon. As a result of developments in our understanding of the physical behaviour of granitic magmas and their host rocks over the last decade, we are now in a position to begin to offer some more informed and realistic models of the processes involved.