bluuebunny/crossref_metadata_2025 huggingface dataset:
Histological analysis of direct organogenesis from micro-cross-sections of cultures of the banana
Authors: Li Jia , Huang Xue-Lin , Wei Yue-Rong , Huang Xia , Li Zhe , Li Xiao-Ju
Published: September 2006

The histological origin of organogenesis was studied during plant regeneration of banana (Musa AAA cv. Williams) via direct organogenesis from micro-cross-sections of the rhizome in modified Murashige–Skoog (MS) medium (including 10 µm 6-BAP, 1 µm IAA and 50 µm KN). The frequency of the organogenesis was dependent on the position from where the explant was cut. Generally, more adventitious shoots were obtained from explants cut from regions close to apical meristem. The origin of adventitious shoots was multicellular, from cell layers with active cell division in the epidermis of the rhizome axis. After 24 h of culture, a layer of epidermal cells close to the leaf sheath base was actively dividing, and as the time in culture increased, regions containing actively dividing cells became enlarged. By the fifth day of culture, regions of actively dividing cells covered the whole peripheral zone of cortex. Several meristemoid structures were formed from the peripheral zone of cortex after 7 days of culture. These structures developed into adventitious shoots by the ninth day of culture. Vigorous plantlets could be regenerated from the shoots when they were transferred to rooting medium containing MS basal salts supplemented with 30 g L–1 sucrose, 6.5 g L–1 agar, a vitamin/amino acid mixture, 1 µm NAA and 1 µm 6-BAP.
Combinational dormancy in seeds of the Western Australian endemic species Diplopeltis huegelii (Sapindaceae)
Authors: Turner S. R. , Merritt D. J. , Baskin J. M. , Baskin C. C. , Dixon K. W.
Published: September 2006

Seeds of the endemic Western Australian species Diplopeltis huegelii Endl. were successfully germinated after the presence of combinational dormancy was identified, following the observation of selected seed characteristics. D. huegelii seeds were found to have large, fully developed, peripheral coiled embryos (with no endosperm) that are 7–8 mm long when uncoiled. Seed-coat dormancy was overcome by dipping seeds in hot water for ≥15 s, but seeds also required a period of after-ripening before they would germinate readily. After-ripening occurred while intact seeds were stored dry at ambient laboratory conditions for 13 months or when scarified (hot-water treated) seeds were stored at 13, 23 or 50% RH at 23°C for 6 weeks. Scarified 13-month-old seeds germinated readily at 7/18, 13/26 and 18/33°C in a 12-h photoperiod and in constant darkness, whereas scarified 1-month-old seeds germinated to ≤43%. Thus, seed dormancy in this species is caused by a water-impermeable seed coat (physical dormancy, PY) and a (non-deep) physiologically dormant embryo (PD), i.e. combinational dormancy (PY + PD). This is only the second report of combinational dormancy in seeds of Sapindaceae and the first report in this family of the PD component of (PY + PD) being broken during dry storage.
Conservation biology of the rare species Conospermum undulatum and Macarthuria keigheryi in an urban bushland remnant
Authors: Close Dugald C. , Messina Giuseppe , Krauss Siegfried L. , Rokich Deanna P. , Stritzke Jennifer , Dixon Kingsley W.
Published: September 2006

We evaluated the utility of a focussed, short-duration research program for investigation of two rare species that occur within an urban bushland remnant, with application for improving conservation management and translocation outcomes. Conospermum undulatum Lindl. is listed as Threatened and Macarthuria keigheryi Lepschi is listed as Vulnerable under the (Australian) Federal Environment Protection and Biodiversity Conservation Act 1999. The C. undulatum population lacked evidence of juvenile plants, indicating either lack of a suitable germination cue or failure of seedling establishment. The M. keigheryi population was browsed heavily by feral rabbits where exposed and thrived when sheltered within unpalatable vegetation from rabbits. Seeds of M. keigheryi were rapidly removed in an ant cafeteria-style experiment, although seeds of the related Macarthuria australis and an ‘outgroup’ species, Gompholobium tomentosum, were removed at equally high rates. Seed viability was high in M. keigheryi, but variable in C. undulatum. Germination rates, in untreated fresh seed, were 11% for C. undulatum and 0% for M. keigheryi and increased to 27 and 3%, respectively, when treated with gibberellic acid. Maximum strike rates for cuttings of 33 and ~75% were obtained for C. undulatum and M. keigheryi, respectively. Cutting-grown plants of M. keigheryi flowered and seeded profusely in the nursery within 7 months, providing a highly effective seed-orchard resource for research and conservation seed banking. Genetic fingerprinting (AFLP) indicated that the C. undulatum population at Perth Airport was not genetically distinct from nearby C. undulatum populations, despite its relatively high variability in leaf morphology. All C. undulatum populations contained moderate to high levels of genetic variation, with the percentage of AFLP markers polymorphic ranging from 48.6 to 64.9%, and heterozygosity from 0.167 to 0.202. Overall, the knowledge gained from this program of short duration will enable informed management and will underpin successful population enhancement through future translocations.
Parameter estimation through inverse modelling and comparison of four leaching models using experimental data from two contrasting pesticide field trials in New Zealand
Authors: Sarmah A. K. , Close M. E. , Dann R. , Pang L. , Green S. R.
Published: September 2006

Predicting pesticide fate with a reasonable degree of precision using mathematical models requires a good choice of parameter values. When experimentally derived values are not readily available, or need to be measured individually for each compound through systematic laboratory experiments, the process not only becomes too time-consuming, but also may not yield reliable parameters due to the uncertainties encountered with laboratory measurements. The inverse modelling technique has therefore become an important tool in recent times, allowing calibration of models against experimental data and thus alleviating the lack of exactness, reproducibility, and objectivity often associated with laboratory-derived data and trial–error simulation. In this study, we used the inverse modelling package PEST interfaced with the GLEAMS, HYDRUS-1D, and LEACHM models to derive field-based mobility and degradation parameters for a selected number of pesticides, along with a bromide tracer, applied to 2 contrasting field sites in the south island of New Zealand. Given the broad range in soil properties at both sites and the climatic conditions (one drier than the other) used in testing, the models performed well. Based on the performance of the models, they can be ranked in the order LEACHM > HYDRUS-1D > GLEAMS. Bromacil appeared to be the most mobile among the compounds at both sites as well as having a greater persistency, followed by hexazinone and terbuthylazine, based on their optimised Koc values at the sites. For bromacil, median optimised Koc values were 22 and 35 mL/g at Nelson and Southland sites, respectively (compared with a best available value of 14 mL/g). However, T1/2 values for bromacil were much lower than the available best literature value of 207 days. The median Koc values for terbuthylazine were 114 and 87 mL/g at Nelson and Southland sites, respectively. These values were much lower than the best available literature value of 220 mL/g, and fall below the literature range (162–278 mL/g for terbuthylazine).
Minimising off-site movement of contaminants in furrow irrigation using polyacrylamide (PAM). I. Pesticides
Authors: Oliver Danielle P. , Kookana Rai S.
Published: September 2006

Off-site movement of pesticides from furrow-irrigated agriculture has been a concern in the Ord River Irrigation Area, Western Australia. After consultation with growers a range of management strategies were tested to assess the effectiveness of various practices to minimise off-site movement of pesticides during irrigation. This paper reports on the effectiveness of the additions of high molecular weight, anionic, polyacrylamide (PAM) to irrigation water to minimise off-site movement of endosulfan, chlorothalonil, bupirimate, and atrazine. Water leaving from 4 separate irrigation bays, which consisted of 25 furrows per irrigation bay (Expt 1) or 39 furrows per irrigation bay (Expt 2), was monitored over time. The average concentration of endosulfan α and β and bupirimate leaving the irrigation bays for the duration of the single irrigation event was generally always less for the PAM-treated irrigation bays than the control (control treatment). The addition of PAM to the irrigation water significantly decreased the cumulative runoff losses (g) of total endosulfan by 54% from 11.41 to 5.19 g/ha (P < 0.05), and of chlorothalonil by 49% from 53.65 to 27.32 g/ha (P < 0.001). There was no statistical difference in the load of atrazine or bupirimate leaving either treatment. Although the addition of PAM to irrigation water effectively decreased the off-site movement of 2 fairly strongly sorbed pesticides, endosulfan and chlorothalonil, it did not decrease the total load moving off-site of the more weakly sorbed pesticides, bupirimate and atrazine. The addition of PAM as a liquid to irrigation water was not found to increase the infiltration of a soluble pesticide, atrazine, into the soil profile. The mode of application of PAM, however, may affect water infiltration and hence vertical movement of soluble pesticides and requires further investigation.
Role of cocaine- and amphetamine-regulated transcript in estradiol-mediated neuroprotection
Authors: Xu Yun , Zhang Wenri , Klaus Judith , Young Jennifer , Koerner Ines , Sheldahl Laird C. , Hurn Patricia D. , Martínez-Murillo Francisco , Alkayed Nabil J.
Published: September 2006

Estrogen reduces brain injury after experimental cerebral ischemia in part through a genomic mechanism of action. Using DNA microarrays, we analyzed the genomic response of the brain to estradiol, and we identified a transcript, cocaine- and amphetamine-regulated transcript (CART), that is highly induced in the cerebral cortex by estradiol under ischemic conditions. Using
in vitro
and
in vivo
models of neural injury, we confirmed and characterized CART mRNA and protein up-regulation by estradiol in surviving neurons, and we demonstrated that i.v. administration of a rat CART peptide is protective against ischemic brain injury
in vivo
. We further demonstrated binding of cAMP response element (CRE)-binding protein to a CART promoter CRE site in ischemic brain and rapid activation by CART of ERK in primary cultured cortical neurons. The findings suggest that CART is an important player in estrogen-mediated neuroprotection and a potential therapeutic agent for stroke and other neurodegenerative diseases.
Activation of NF-κB by the intracellular expression of NF-κB-inducing kinase acts as a powerful vaccine adjuvant
Authors: Andreakos E. , Williams R. O. , Wales J. , Foxwell B. M. , Feldmann M.
Published: September 2006

There is a pressing need for adjuvants that will enhance the effectiveness of genetic vaccines. This is particularly important in cancer and infectious disease such as HIV and malaria for which successful vaccines are desperately needed. Here, we describe an approach to enhance immunogenicity that involves the activation of NF-κB by the transgenic expression of an intracellular signaling molecule, NF-κB-inducing kinase (NIK).In vitro, NIK increases dendritic cell antigen presentation in allogeneic and antigen-specific T cell proliferation assays by potently activating NF-κB and consequently up-regulating the expression of cytokines (TNF-α, IL-6, IL-12, IL-15, and IL-18), chemokines [IL-8, RANTES (regulated on activation, normal T cell expressed and secreted), macrophage inflammatory protein-1α, monocyte chemoattractant protein-1, and monocyte chemoattractant protein-3], MHC antigen-presenting molecules (class I and II), and costimulatory molecules (CD80 and CD86).In vivo, NIK enhances immune responses against a vector-encoded antigen and shifts them toward a T helper 1 immune response with increased IgG2a levels, T cell proliferation, IFN-γ production, and cytotoxic T lymphocyte responses more potently than complete Freund's adjuvant, a very efficacious T helper 1-inducing adjuvant. These findings define NIK, and possibly other inducers of NF-κB activation, as a potent adjuvant strategy that offers great potential for genetic vaccine development.
Intracellular IL-1α-binding proteins contribute to biological functions of endogenous IL-1α in systemic sclerosis fibroblasts
Authors: Kawaguchi Yasushi , Nishimagi Emi , Tochimoto Akiko , Kawamoto Manabu , Katsumata Yasuhiro , Soejima Makoto , Kanno Tokiko , Kamatani Naoyuki , Hara Masako
Published: September 2006

The aberrant production of precursor IL-1α (pre-IL-1α) in skin fibroblasts that are derived from systemic sclerosis (SSc) is associated with the induction of IL-6 and procollagen, which contributes to the fibrosis of SSc. However, little is understood about how intracellular pre-IL-1α regulates the expression of the other molecules in fibroblasts. We report here that pre-IL-1α can form a complex with IL-1α-binding proteins that is translocated into the nuclei of fibroblasts. Immunoprecipitation that used anti-human IL-1α Ab and35S-labeled nuclear extracts of fibroblasts showed three specific bands (≈31, 35, and 65 kDa). The 31-kDa molecule was identified as pre-IL-1α, and the 35- and 65-kDa molecules might be pre-IL-1α-binding proteins. A partial sequencing for the 10 aa from the N-terminals of the molecules showed 100% homology for HAX-1 (HS1-associated protein X-1) and IL-1 receptor type II (IL-1RII). Suppression of the genes of HAX-1 or IL-1RII induced the inhibitory effects of IL-1 signal transduction, including production of IL-6 and procollagen, by fibroblasts. In particular, pre-IL-1α was not translocated into the nucleus by an inhibition of HAX-1. These findings reveal that nuclear localization of pre-IL-1α depends on the binding to HAX-1 and that biological activities might be elicited by the binding to both HAX-1 and IL-1RII in SSc fibroblasts.
The cellular basis for parallel neural transmission of a high-frequency stimulus and its low-frequency envelope
Authors: Middleton Jason W. , Longtin André , Benda Jan , Maler Leonard
Published: September 2006

Sensory stimuli often have rich temporal and spatial structure. One class of stimuli that are common to visual and auditory systems and, as we show, the electrosensory system are signals that contain power in a narrow range of temporal (or spatial) frequencies. Characteristic of this class of signals is a slower variation in their amplitude, otherwise known as an envelope. There is evidence suggesting that, in the visual cortex, both narrowband stimuli and their envelopes are coded for in separate and parallel streams. The implementation of this parallel transmission is not well understood at the cellular level. We have identified the cellular basis for the parallel transmission of signal and envelope in the electrosensory system: a two-cell network consisting of an interneuron connected to a pyramidal cell by means of a slow synapse. This circuit could, in principle, be implemented in the auditory or visual cortex by the previously identified biophysics of cortical interneurons.
Differential microarray analysis of
Drosophila
mushroom body transcripts using chemical ablation
Authors: Kobayashi Masatomo , Michaut Lydia , Ino Ayako , Honjo Ken , Nakajima Taiki , Maruyama Yasushi , Mochizuki Hiroaki , Ando Mai , Ghangrekar Indrayani , Takahashi Kuniaki , Saigo Kaoru , Ueda Ryu , Gehring Walter J. , Furukubo-Tokunaga Katsuo
Published: September 2006

Mushroom bodies (MBs) are the centers for olfactory associative learning and elementary cognitive functions in the
Drosophila
brain. As a way to systematically elucidate genes preferentially expressed in MBs, we have analyzed genome-wide alterations in transcript profiles associated with MB ablation by hydroxyurea. We selected 100 genes based on microarray data and examined their expression patterns in the brain by
in situ
hybridization. Seventy genes were found to be expressed in the posterodorsal cortex, which harbors the MB cell bodies. These genes encode proteins of diverse functions, including transcription, signaling, cell adhesion, channels, and transporters. Moreover, we have examined developmental functions of 40 of the microarray-identified genes by transgenic RNA interference; 8 genes were found to cause mild-to-strong MB defects when suppressed with a MB-Gal4 driver. These results provide important information not only on the repertoire of genes that control MB development but also on the repertoire of neural factors that may have important physiological functions in MB plasticity.
Electrostatic interactions in the channel cavity as an important determinant of potassium channel selectivity
Authors: Bichet Delphine , Grabe Michael , Jan Yuh Nung , Jan Lily Yeh
Published: September 2006

Potassium channels are membrane proteins that allow the passage of potassium ions at near diffusion rates while severely limiting the flux of the slightly smaller sodium ions. Although studies thus far have focused on the narrowest part of the channel, known as the selectivity filter, channels are long pores with multiple ions that traverse the selectivity filter, the water-filled central cavity, and the rest of the pore formed by cytoplasmic domains. Here, we present experimental analyses on Kir3.2 (GIRK2), a G protein-activated inwardly rectifying potassium (Kir) channel, showing that a negative charge introduced at a pore-facing position in the cavity (N184) below the selectivity filter restores both K+selectivity and inward rectification properties to the nonselective S177W mutant channel. Molecular modeling demonstrates that the negative residue has no effect on the geometry of the selectivity filter, suggesting that it has a local effect on the cavity ion. Moreover, restoration of selectivity does not depend on the exact location of the charge in the central cavity as long as this residue faces the pore, where it is in close contact with permeant ions. Our results indicate that interactions between permeant ions and the channel cavity can influence ion selectivity and channel block by means of an electrostatic effect.
A therapeutic target for prostate cancer based on angiogenin-stimulated angiogenesis and cancer cell proliferation
Authors: Yoshioka Norie , Wang Li , Kishimoto Koji , Tsuji Takanori , Hu Guo-fu
Published: September 2006

Human angiogenin is progressively up-regulated in the prostate epithelial cells during the development of prostate cancer from prostate intraepithelial neoplasia (PIN) to invasive adenocarcinoma. Mouse angiogenin is the most up-regulated gene in AKT-induced PIN in prostate-restricted AKT transgenic mice. These results prompted us to study the role that angiogenin plays in prostate cancer. Here, we report that, in addition to its well established role in mediating angiogenesis, angiogenin also directly stimulates prostate cancer cell proliferation. Angiogenin undergoes nuclear translocation in PC-3 human prostate cancer cells grown both
in vitro
and in mice. Thus, knocking down angiogenin expression in PC-3 human prostate adenocarcinoma cells inhibits ribosomal RNA transcription,
in vitro
cell proliferation, colony formation in soft agar, and xenograft growth in athymic mice. Blockade of nuclear translocation of angiogenin by the aminoglycoside antibiotic neomycin inhibited PC-3 cell tumor growth in athymic mice and was accompanied by a decrease in both cancer cell proliferation and angiogenesis. These results suggest that angiogenin has a dual effect, angiogenesis and cancer cell proliferation, in prostate cancer and may serve as a molecular target for drug development. Blocking nuclear translocation of angiogenin could have a combined benefit of antiangiogenesis and chemotherapy in treating prostate cancer.
National Identity and History Writing in Ukraine
Authors: Kuzio Taras
Published: September 2006

Think Ukrainian. You are a successor to Princess Olha, Volodymyr the Great and Yaroslav the Wise, who are Equal to the Apostles. History requires from you confidence and trust in Ukraine. Think Ukrainian. Viktor Yushchenko, President of Ukraine. Presidential political advertisement, Channel 5 Television, 28 January 2006

The writing of history has a direct influence upon national identities. This is especially the case when historical writing and interpretation are contested, as they are among the three Eastern Slavic peoples (Russians, Ukrainians, and Belarusians). Where contestation is high, as in the Ukrainian- Russian relationship since the disintegration of the USSR, the writing and interpretation of history also impact upon their domestic and foreign policies and, most notably, their inter-state relations. Russian elites and the majority of Russians do not look upon Ukraine and Belarus as “foreign” countries.
Structural and functional features and significance of the physical linkage between ER and mitochondria
Authors: Csordás György , Renken Christian , Várnai Péter , Walter Ludivine , Weaver David , Buttle Karolyn F. , Balla Tamás , Mannella Carmen A. , Hajnóczky György
Published: September 2006

The role of mitochondria in cell metabolism and survival is controlled by calcium signals that are commonly transmitted at the close associations between mitochondria and endoplasmic reticulum (ER). However, the physical linkage of the ER–mitochondria interface and its relevance for cell function remains elusive. We show by electron tomography that ER and mitochondria are adjoined by tethers that are ∼10 nm at the smooth ER and ∼25 nm at the rough ER. Limited proteolysis separates ER from mitochondria, whereas expression of a short “synthetic linker” (<5 nm) leads to tightening of the associations. Although normal connections are necessary and sufficient for proper propagation of ER-derived calcium signals to the mitochondria, tightened connections, synthetic or naturally observed under apoptosis-inducing conditions, make mitochondria prone to Ca2+ overloading and ensuing permeability transition. These results reveal an unexpected dependence of cell function and survival on the maintenance of proper spacing between the ER and mitochondria.
Interleukin (IL)-22 and IL-17 are coexpressed by Th17 cells and cooperatively enhance expression of antimicrobial peptides
Authors: Liang Spencer C. , Tan Xiang-Yang , Luxenberg Deborah P. , Karim Riyez , Dunussi-Joannopoulos Kyriaki , Collins Mary , Fouser Lynette A.
Published: September 2006

Th17 cells are a distinct lineage of effector CD4+ T cells characterized by their production of interleukin (IL)-17. We demonstrate that Th17 cells also expressed IL-22, an IL-10 family member, at substantially higher amounts than T helper (Th)1 or Th2 cells. Similar to IL-17A, IL-22 expression was initiated by transforming growth factor β signaling in the context of IL-6 and other proinflammatory cytokines. The subsequent expansion of IL-22–producing cells was dependent on IL-23. We further demonstrate that IL-22 was coexpressed in vitro and in vivo with both IL-17A and IL-17F. To study a functional relationship among these cytokines, we examined the expression of antimicrobial peptides by primary keratinocytes treated with combinations of IL-22, IL-17A, and IL-17F. IL-22 in conjunction with IL-17A or IL-17F synergistically induced the expression of β-defensin 2 and S100A9 and additively enhanced the expression of S100A7 and S100A8. Collectively, we have identified IL-22 as a new cytokine expressed by Th17 cells that synergizes with IL-17A or IL-17F to regulate genes associated with skin innate immunity.
Integrin Signaling through Arg Activates p190RhoGAP by Promoting Its Binding to p120RasGAP and Recruitment to the Membrane
Authors: Bradley William D. , Hernández Samuel E. , Settleman Jeffrey , Koleske Anthony J.
Published: September 2006

The Rho family GTPases RhoA (Rho), Rac1, and Cdc42 are essential effectors of integrin-mediated cell attachment and spreading. Rho activity, which promotes formation of focal adhesions and actin stress fibers, is inhibited upon initial cell attachment to allow sampling of the new adhesive environment. The Abl-related gene (Arg) tyrosine kinase mediates adhesion-dependent inhibition of Rho through phosphorylation and activation of the Rho inhibitor p190RhoGAP-A (p190). p190 phosphorylation promotes its binding to p120RasGAP (p120). Here, we elucidate the mechanism by which p120 binding regulates p190 activation after adhesion. We show that p190 requires its p120-binding domain to undergo Arg-dependent activation in vivo. However, p120 binding does not activate p190RhoGAP activity in vitro. Instead, activation of p190 requires recruitment to the cell periphery. Integrin-mediated adhesion promotes relocalization of p190 and p120 to the cell periphery in wild-type fibroblasts, but not in arg−/−fibroblasts. A dominant-negative p120 fragment blocks p190:p120 complex formation, prevents activation of p190 by adhesion, and disrupts the adhesion-dependent recruitment of p190 to the cell periphery. Our results demonstrate that integrin signaling through Arg activates p190 by promoting its association with p120, resulting in recruitment of p190 to the cell periphery where it inhibits Rho.
Mechanically Induced Actin-mediated Rocketing of Phagosomes
Authors: Clarke Margaret , Müller-Taubenberger Annette , Anderson Kurt I. , Engel Ulrike , Gerisch Günther
Published: September 2006

Actin polymerization can be induced in Dictyostelium by compressing the cells to bring phagosomes filled with large particles into contact with the plasma membrane. Asymmetric actin assembly results in rocketing movement of the phagosomes. We show that the compression-induced assembly of actin at the cytoplasmic face of the plasma membrane involves the Arp2/3 complex. We also identify two other proteins associated with the mechanically induced actin assembly. The class I myosin MyoB accumulates at the plasma membrane–phagosome interface early during the initiation of the response, and coronin is recruited as the actin filaments are disassembling. The forces generated by rocketing phagosomes are sufficient to push the entire microtubule apparatus forward and to dislocate the nucleus.
Compositional depth profiling of polycrystalline thin films by grazing-incidence X-ray diffraction
Authors: Kötschau I. M. , Schock H. W.
Published: September 2006

This paper uses an innovative peak profile matching method to determine compositional depth profiles of Cu(In,Ga)(S,Se)2thin films and other suitable solid-solution compounds. A layer absorption model allows the generation of grazing-incidence diffraction patterns on the basis of the known diffractometer instrument function, compositional depth profiles and the corresponding mass absorption characteristics. In contrast to other methods, the modelling approach exploits the information stored in the shape evolution of the peak profile as a function of incidence angle. A small number of diffraction patterns of the same peak are sufficient to track depth-dependent shifts of the principal lattice parameters. The method is adapted to the specific properties of the chalcopyrite Cu(In,Ga)(S,Se)2system. In fact, the multinary chalcopyrite compounds grown by physical vapour deposition have some remarkable properties which allow the successful application of the method. Issues like surface roughness, refraction at low incidence angles and their effects upon relative intensities can be successfully circumvented by the modelling approach. Ambiguities in the modelling results are very small and can be minimized by comparison with complementary depth profiles using secondary ion mass spectrometry or cross-sectional energy-dispersive X-ray analysis.
Energy spectrometer on a diffractometer using a charge-coupled device X-ray detector
Authors: Abe Hiroshi , Saitoh Hiroyuki , Nakao Hironori , Ito Kazuki , Ohshima Ken-ichi
Published: September 2006

A charge-coupled device (CCD) X-ray detector for inelastic X-ray scattering was installed at beamline BL-4C of the Photon Factory at the High Energy Accelerator Research Organization in Japan. A wavelength-dispersive X-ray spectrometer was mounted on a six-circle diffractometer. Energy spectra were obtained by the CCD X-ray detector and a curved highly oriented pyrolytic graphite analyser. By the combination of energy spectroscopy and diffraction, simultaneous real-time data acquisition of both the momentum and the energy transfer was performed.
A new approach to wide-angle dynamical X-ray diffraction by deformed crystals
Authors: Podorov S. G. , Faleev N. N. , Pavlov K. M. , Paganin D. M. , Stepanov S. A. , Förster E.
Published: September 2006

A new approach is proposed for X-ray dynamical diffraction theory in distorted crystals. The theory allows one to perform dynamical diffraction simulations between Bragg peaks for non-ideal crystals, using a simple approach of two distorted waves. It can be directly applied for reciprocal-space simulation. The formalism is used to analyse high-resolution X-ray diffraction data, obtained for an InSb/InGaSb/InSb/InAs superlattice grown on top of a GaSb buffer layer on a (001) GaSb substrate.
SXD – the single-crystal diffractometer at the ISIS spallation neutron source
Authors: Keen David A. , Gutmann Matthias J. , Wilson Chick C.
Published: September 2006

SXD, the single-crystal diffractometer at the ISIS spallation neutron source, uses an array of two-dimensional position-sensitive detectors and the neutron time-of-flight technique to measure diffraction data throughout very large volumes of reciprocal space for each fixed orientation of a single-crystal sample. This paper describes SXD in detail, following major improvements to the instrument. Particular emphasis is placed on the range of science possible, using recent results as examples, and the opportunities for future experiments.
Folding a two-dimensional powder diffraction image into a one-dimensional scan: a new procedure
Authors: Cervellino Antonio , Giannini Cinzia , Guagliardi Antonietta , Ladisa Massimo
Published: September 2006

A new procedure aimed at folding a two-dimensional powder diffraction pattern into a one-dimensional scan is presented. The sample-to-detector distance is the only parameter that, in this approach, needs to be adjusted in a separate step by using the `standard' sample. The technique consists of three steps: tracking the beam centre by means of simulated annealing of the diffraction rings along the same axis, detector tilt and rotation determination by a Hankel Lanczos singular value decomposition and intensity integration by an adaptive binning algorithm. The X-ray powder diffraction (XRPD) intensity profile of the standard NIST Si 640c sample is used to test the performance. Results show the robustness of the method and its capability of efficiently tagging the pixels in a two-dimensional readout system by matching the ideal geometry of the detector to the real beam–sample–detector frame. The technique is a versatile and user-friendly tool for the one-dimensional folding of two-dimensional XRPD images.
Determination of microstructure and twinning relationship between martensitic variants in 53 at.%Ni–25 at.%Mn–22 at.%Ga ferromagnetic shape memory alloy
Authors: Cong D. Y. , Zhang Y. D. , Wang Y. D. , Esling C. , Zhao X. , Zuo L.
Published: September 2006

A recent study by high-resolution neutron powder diffraction provided accurate crystallographic information for the newly developed ferromagnetic shape memory alloy 53 at.%Ni–25 at.%Mn–22 at.%Ga. This made it possible to study by high-resolution electron backscatter diffraction the local microstructures and the twinning relationships between martensitic variants. The twin interfaces were also investigated and they are found to be coherent on the {112} planes.
Inferring orientation distributions in anisotropic powders of nano-layered crystallites from a single two-dimensional WAXS image
Authors: Méheust Yves , Knudsen Kenneth Dahl , Fossum Jon Otto
Published: September 2006

The wide-angle scattering of X-rays (WAXS) by anisotropic powders of nano-layered crystallites (nano-stacks) is addressed. Assuming that the orientation distribution probability functionfof the nano-stacks only depends on the deviation of the crystallites' orientation from a fixed reference direction, a relation providingffrom the dependence of a given diffraction peak's amplitude on the azimuthal angle is derived. The method is applied to two systems of sodium fluorohectorite (NaFH) clay particles, using synchrotron radiation and a WAXS setup with a two-dimensional detector. In the first system, which consists of dry-pressed NaFH samples, the orientation distribution probability function corresponds to a classical uniaxial nematic order. The second system is observed in bundles of polarized NaFH particles in silicon oil; in this case, the nano-stacks have their directors, on average, in a plane normal to the reference direction, andfis a function of the angle between a nano-stack's director and that of the plane. In both cases, a suitable Maier–Saupe function is obtained for the distributions, and the reference direction is determined with respect to the laboratory frame. The method only requires one scattering image. Consistency can be checked by determining the orientation distribution from several diffraction peaks independently.
Use of Patterson-based methods automatically to determine the structures of heavy-atom-containing proteins with up to 6000 non-hydrogen atoms in the asymmetric unit
Authors: Burla Maria Cristina , Caliandro Rocco , Carrozzini Benedetta , Cascarano Giovanni Luca , De Caro Liberato , Giacovazzo Carmelo , Polidori Giampiero , Siliqi Dritan
Published: September 2006

The Patterson superposition methods described by Burlaet al.[J. Appl. Cryst.(2006),39, 527–535], based on the use of the `multiple implication functions', have been enriched by supplementary filtering techniques based on some general (resolution-dependent) features of both the Patterson and the electron density maps. The method has been implemented in a modified version of the programSIR2004and tested using a set of 20 crystal structures selected from the Protein Data Bank, having a number of non-hydrogen atoms in the asymmetric unit larger than 2000, atomic resolution data and some heavy atoms (equal to or heavier than Ca). The new phasing procedure is able to solve most of the test structures, among which there are two proteins with more than 6000 non-hydrogen atoms in the asymmetric unit, so extending by far the complexity today commonly considered as the limit for Patterson-based methods (i.e.about 2000 non-hydrogen atoms).
Tailoring the structure of hybrid organic inorganic nanomaterials built on tetra- and polyfunctional alco-oxo-titanium clusters in polystyrene
Authors: Trabelsi Sondes , Fornasieri Giulia , Rozes Laurence , Janke Andreas , Mensch Axel , Sanchez Clément , Stamm Manfred
Published: September 2006

Functional titanium oxo-clusters Ti16O16(OEt)32−x(OPhCH=CH2)xwith different numbers of styrenic groups, wherex= 4 (tetra) andx= 16 (poly), have been synthesized and copolymerized with styrene. The resulting hybrid nanomaterials present three-dimensional networks in which the inorganic nano-fillers are covalently linked to the inorganic polymer. The influence of the number of functional groups borne by the oxo clusters on the structure of the resulting hybrid nanomaterials has been investigated by a combination of small-angle X-ray scattering, transmission electron microscopy and energy-filtering transmission electron microscopy. Compared with the tetra-functional clusters, the poly-functional clusters were better dispersed in the hybrid phase even at very high cluster content (between 5 and 10 wt%). Independently of the number of functional groups, three structural levels (i.e.largest, intermediate and primary clusters) have been revealed. The size of the aggregates has been found to be reduced by increasing the number of styrenic reactive groups.
XtalBase– a comprehensive data management system for macromolecular crystallography
Authors: Meining Winfried
Published: September 2006

The rate at which successful crystallization experiments and new structures of macromolecules are reported is growing at a fast pace. It is therefore desirable to collect data systematically, handle these data effectively and evaluate the accumulated knowledge in an automated fashion in order to optimize procedures for crystallization and data evaluation. A new web-based program,XtalBase, has been developed in order to aid the crystallographer in designing, preparing, documenting and evaluating crystallization experiments.XtalBasehosts a database of physicochemical data of compounds commonly used for the crystallization of macromolecules. Experimental conditions are constructed either from existing commercial screening sets, by random, by interpolation between start and end concentrations, or as sets of individually composed drops. Recipes needed for the preparation of solutions and drops are instantly calculated and displayed. The program allows for documenting observations in the form of scores, notes and pictures. The experimental data recorded within the program as well as data imported from the Biological Macromolecule Crystallization Database (BMCD) can be used to estimate a probability of success for crystallization conditions. The program enables the user statistically to correlate conditions with observations not only from their own experiments but from all experiments documented within the system.XtalBaseprovides facilities for storing a large variety of data, such as a sample history, collection and refinement parameters, coordinates, as well as publication data. Data can be imported and exportedviacustomizable templates. The system can be configured to execute programs, which are fed by data from the database, and to extract data from the program output. The administrative interface allows the customization of all data tables and fields. All data can be searched in a unified search facility. The program presents the basis for a consistently defined database of crystallization data combined with tools to handle crystallization and crystallographic dataviaa web browser. The program home page is http://www.xtalbase.net.
Silver behenate as a calibration standard of grazing-incidence small-angle X-ray scattering
Authors: Lee Byeongdu , Lo Chieh-Tsung , Seifert Soenke , Winans Randall E.
Published: September 2006

Grazing-incidence small-angle X-ray scattering (GISAXS) patterns of a silver behenate composite film, which has a typical layered structure, are described. The peak position of the film in the GISAXS pattern was varied depending on the incident angle, which was well described by taking into account the refraction and the reflection effects. Since the refractive index of samples depends on sample preparation, it is recommended that the measurement of silver behenate as a standard be done in conventional transmission mode to avoid any complexity.
Chlorartinite, a volcanic exhalation product also found in industrial magnesia screed
Authors: Sugimoto Kunihisa , Dinnebier Robert E. , Schlecht Thomas
Published: September 2006

The volcanic exhalation product chlorartinite, [Mg2(CO3)(H2O)(OH)]Cl·H2O, has recently been found to be a minor, and in some samples a major, component of magnesia floors for industrial use. In order to be able to perform quantitative phase analysis using the Rietveld method, its crystal structure was determined from high-resolution synchrotron powder diffraction data by the global optimization technique of simulated annealing and Rietveld refinement. The finalRpandRwpvalues are 5.23% and 6.56%, respectively. Chlorartinite crystallizes in the rhombohedral space groupR3c(No. 161), witha= 23.14422 (16) Å,c= 7.22333 (5) Å,V= 3350.84 (5) Å3,Z= 18. The building units of chlorartinite consist of MgO6octahedra forming 15-membered puckered rings which are interconnected by CO3triangular moieties. The rings are stacked to form a honeycomb-like three-dimensional framework structure with large isolated channels. Within the channels, free chlorine atoms and disordered water molecules are located.
Analysis of polydisperse bubbles in the aluminium–hydrogen system using a size-dependent contrast
Authors: Paskevicius M. , Buckley C. E.
Published: September 2006

The characterization of hydrogen defects in an aluminium–hydrogen system was performed previously [Buckleyet al.(2001).J. Appl. Cryst.34, 119–129] using small-angle scattering, inelastic neutron scattering and electron microscopy techniques. This analysis resulted in the determination of the relative change in lattice parameter as a result of hydrogen introduction into the Al matrix. However, this method relied on the average volume of the bubbles of hydrogen and also the pressure in a bubble of average volume. The characterization of the Al–H system has been improved by considering the size polydispersity of the hydrogen bubbles. The determination of a volume-fraction size distribution of the bubbles from small-angle scattering data has allowed a polydispersity analysis to be undertaken. A size-dependent contrast has been utilized in the modification of the volume-fraction size distribution into a more accurate form that accounts for varying concentrations of hydrogen within bubbles of different sizes. The determination of the size-dependent contrast is based upon an equation of state for molecular hydrogen which incorporates the compressibility of hydrogen under high pressures. The formation of alane (AlH3) is also investigated, as it can be formed by the chemisorption of hydrogen in aluminium under high pressures. The polydispersity analysis has allowed a more accurate description of the Al–H system and can be applied to similar scattering systems where the scattering length density is not constant over the whole scattering size regime.
Bond-valence parameters of lanthanides
Authors: Trzesowska Agata , Kruszynski Rafal , Bartczak Tadeusz J.
Published: September 2006

Ln—O and Ln—N bond-valence parameters have been computed in coordination complexes for lanthanides (Ln) at oxidation states other than +3 (CeIV, SmII, EuII and YbII). Moreover, Ln—Cl, Ln—S and Ln—C(π-bonded) bond-valence parameters are presented, as calculated for coordination compounds. In general, the bond-valence parameters decrease in the order Ln—O > Ln—C > Ln—N > Ln—Cl > Ln—S. It has been found that the values of bond-valence parameters decrease with increasing lanthanide atomic number for coordination compounds. As expected, the values of lanthanide–oxygen and lanthanide–nitrogen bond-valence parameters diminish with increasing lanthanide oxidation state. Several examples are given where the total valence of the lanthanide ion is apparently incorrectly assigned, as well as cases where bond-valence method calculations confirm the doubtful oxidation state assignment.
LnO
n
coordination polyhedra (Ln = La–Lu) in crystal structures
Authors: Vologzhanina A. V. , Pushkin D. V. , Serezhkin V. N.
Published: September 2006

Voronoi–Dirichlet (VD) polyhedra and the method of intersecting spheres were used to analyze the crystal structures of 2917 compounds containing 3903 crystallographically non-equivalent types of LnO
n
polyhedra (Ln = La–Lu). It was established that Ln coordination numbers (CN) vary from 3 to 12, and 20 types of coordination polyhedra are present in the structures. Despite the great diversity of CN and types of coordination polyhedra, the volume of the VD polyhedron was found to depend only on the identity of the Ln atom and its oxidation state.
Invariom structure refinement, electrostatic potential and toxicity of 4-O-methylalpinumisoflavone, O,O-dimethylalpinumisoflavone and 5-O-methyl-4-O-(3-methylbut-2-en-1-yl)alpinumisoflavone
Authors: Kingsford-Adaboh Robert , Dittrich Birger , Hübschle Christian B. , Gbewonyo Winfred S. K. , Okamoto Hideki , Kimura Masaro , Ishida Hiroyuki
Published: September 2006

The accurate X-ray single-crystal structures of the isoflavone compounds 4-O-methylalpinumisoflavone, O,O-dimethylalpinumisoflavone and 5-O-methyl-4-O-(3-methylbut-2-en-1-yl)alpinumisoflavone {alpinumisoflavone = 5-hydroxy-7-(4-hydroxyphenyl)-2,2-dimethyl-2H,6H-benzo[1,2-b:5,4-b′]dipyran-6-one} from data sets measured at cryogenic temperature have been obtained from invariom modelling using theoretically predicted Hansen and Coppens multipole-model form factors, which describe the aspherical electron density distribution. Molecular dipole moments and electrostatic potentials obtained from invariom modelling are discussed and compared with results from ab initio theoretical calculations. All three studied compounds are solvent extracts of root bark or seed powder of Millettia thonningii (leguminosae), a plant molluscicide and cercaricide used in Franco West Africa as medication against various diseases. The compounds' toxicities to brine shrimp have been determined and their different potencies tentatively related to conformation differences, intramolecular contacts, dipole moments and electrostatic potential features.
π-Bond cooperativity and anticooperativity effects in resonance-assisted hydrogen bonds (RAHBs)
Authors: Bertolasi Valerio , Pretto Loretta , Gilli Gastone , Gilli Paola
Published: September 2006

Bond cooperativity effects, which are typical of `resonant' chains or rings of π-conjugated hydrocarbons, can also occur in hydrogen-bonded systems in the form of σ-bond and π-bond cooperativity or anticooperativity. σ-Bond cooperativity is associated with the long chains of O—H...O bonds in water and alcohols while σ-bond anticooperativity occurs when the cooperative chain is interrupted by a local defect reversing the bond polarity. π-Bond cooperativity is the driving force controlling resonance-assisted hydrogen bonds (RAHBs), while π-bond anticooperativity has never been considered so far and is investigated here by studying couples of hydrogen-bonded β-enolone and/or β-enaminone six-membered rings fused through a common C=O or C—C bond. The effect is studied by X-ray crystal structure determination of five compounds [(2Z)-1-(2-hydroxyphenyl)-3-phenyl-1,3-propanedione enol (1), (2Z)-1-(2-hydroxy-5-chlorophenyl)-3-phenyl-1,3-propanedione enol (2), (2Z)-1-(2-hydroxy-5-methylphenyl)-3-phenyl-1,3-propanedione enol (3), (2Z)-1-(2-hydroxy-4-methyl-5-chlorophenyl)-3-phenyl-1,3-propanedione enol (4) and dimethyl(2E)-3-hydroxy-2-{[(4-chlorophenyl)amino]carbonyl}pent-2-enedioate (5)] and by extensive analysis of related fragments found in the CSD (Cambridge Structural Database). It is shown that fusion through the C=O bond is always anticooperative and such to weaken the symmetric O—H...O...H—O and N—H...O...H—N bonds formed, but not the asymmetric O—H...O...H—N bond. Fusion through the C—C bond may produce either cooperative or anticooperative hydrogen bonds, the former being more stable than the latter and giving rise to a unique resonance-assisted ten-membered ring running all around the two fused six-membered rings, which can be considered a type of tautomerism never described before.