bluuebunny/crossref_metadata_2025 huggingface dataset:
Subcellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein
Authors: You Jaehwan , Dove Brian K. , Enjuanes Luis , DeDiego Marta L. , Alvarez Enrique , Howell Gareth , Heinen Paul , Zambon Maria , Hiscox Julian A.
Published: November 2005

The coronavirus nucleocapsid (N) protein is a viral RNA-binding protein with multiple functions in terms of virus replication and modulating cell signalling pathways. N protein is composed of three distinct regions containing RNA-binding motif(s), and appropriate signals for modulating cell signalling. The subcellular localization of severe acute respiratory syndrome coronavirus (SARS-CoV) N protein was studied. In infected cells, SARS-CoV N protein localized exclusively to the cytoplasm. In contrast to the avian coronavirus N protein, overexpressed SARS-CoV N protein remained principally localized to the cytoplasm, with very few cells exhibiting nucleolar localization. Bioinformatic analysis and deletion mutagenesis coupled to confocal microscopy and live-cell imaging, revealed that SARS-CoV N protein regions I and III contained nuclear localization signals and region II contained a nucleolar retention signal. However, cytoplasmic localization was directed by region III and was the dominant localization signal in the protein.
Inhibition of hepatitis B virus replication by various RNAi constructs and their pharmacodynamic properties
Authors: Peng Jinliang , Zhao Yonggang , Mai Junhua , Pang Weng Ka , Wei Xiaohui , Zhang Peizuo , Xu Yuhong
Published: November 2005

The strategy of RNA interference (RNAi)-based gene silencing has been suggested to have great potential in treating viral diseases. It provides new hope of being able to complement the limited therapeutic options currently available for chronic hepatitis B virus (HBV) infection. To advance such a strategy towards clinical use, the effects of various parameters on the anti-HBV efficiency of RNAi need to be well-defined. In this study, the efficacy and pharmacodynamic properties of different RNAi target sequences and constructs were examined. Several sequences were found to be effective in cell and animal models, achieving inhibition rates of approximately 80–90 %. Methyl-modified small interfering RNA (siRNA) molecules were found to be more stable inside cells than natural siRNA molecules and offered longer-lasting inhibitory effects. Both were effective at rather low doses (an equimolar ratio with HBV preS2–S protein expression vector). Plasmid DNA vectors were less dose-responsive, but their effectiveness in vivo lasted longer, for approximately 1 month. By analysing these different parameters and their possible mechanisms, some important issues in RNAi therapeutics that should assist the future development of clinical applications have been addressed.
Presence of broadly reactive and group-specific neutralizing epitopes on newly described isolates of Crimean-Congo hemorrhagic fever virus
Authors: Ahmed Asim A. , McFalls Jeanne M. , Hoffmann Christian , Filone Claire Marie , Stewart Shaun M. , Paragas Jason , Khodjaev Shabot , Shermukhamedova Dilbar , Schmaljohn Connie S. , Doms Robert W. , Bertolotti-Ciarlet Andrea
Published: November 2005

Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the genus Nairovirus of the family Bunyaviridae, causes severe disease in humans with high rates of mortality. The virus has a tripartite genome composed of a small (S), a medium (M) and a large (L) RNA segment; the M segment encodes the two viral glycoproteins, GN and GC. Whilst relatively few full-length M segment sequences are available, it is apparent that both GN and GC may exhibit significant sequence diversity. It is unknown whether considerable antigenic differences exist between divergent CCHFV strains, or whether there are conserved neutralizing epitopes. The M segments derived from viral isolates of a human case of CCHF in South Africa (SPU 41/84), an infected tick (Hyalomma marginatum) in South Africa (SPU 128/81), a human case in Congo (UG 3010), an infected individual in Uzbekistan (U2-2-002) and an infected tick (Hyalomma asiaticum) in China (Hy13) were sequenced fully, and the glycoproteins were expressed. These novel sequences showed high variability in the N-terminal region of GN and more modest differences in the remainder of GN and in GC. Phylogenetic analyses placed these newly identified strains in three of the four previously described M segment groups. Studies with a panel of mAbs specific to GN and GC indicated that there were significant antigenic differences between the M segment groups, although several neutralizing epitopes in both GN and GC were conserved among all strains examined. Thus, the genetic diversity exhibited by CCHFV strains results in significant antigenic differences that will need to be taken into consideration for vaccine development.
Type I interferons protect mice against enterovirus 71 infection
Authors: Liu Ming-Liang , Lee Yi-Ping , Wang Ya-Fang , Lei Huan-Yao , Liu Ching-Chuan , Wang Shih-Min , Su Ih-Jen , Wang Jen-Reng , Yeh Trai-Ming , Chen Shun-Hua , Yu Chun-Keung
Published: November 2005

In this study, the contribution of type I interferons (IFNs) to protection against infection with enterovirus 71 (EV71) was investigated using a murine model where the virus was administrated to neonatal Institute of Cancer Research (ICR) mice by either the intraperitoneal (i.p.) or the oral route. In i.p. inoculated mice, post-infection treatment of dexamethasone (5 mg kg−1 at 2 or 3 days after infection) exacerbated clinical symptoms and increased the tissue viral titre. In contrast, polyriboinosinic : polyribocytidylic acid [poly(I : C); 10 or 100 μg per mouse at 12 h before infection], a potent IFN inducer, improved the survival rate and decreased the tissue viral titres after EV71 challenge, which correlated with an increase in serum IFN-α concentration, the percentage of dendritic cells, their expression of major histocompatibility complex class II molecule and IFN-α in spleen. Treatment with a neutralizing antibody for type I IFNs (104 neutralizing units per mouse, 6 h before and 12 h after infection) resulted in frequent deaths and higher tissue viral load in infected mice compared with control mice. In contrast, an early administration of recombinant mouse IFN-αA (104 U per mouse for 3 days starting at 0, 1 or 3 days after infection) protected the mice against EV71 infection. In vitro analysis of virus-induced death in three human cell lines showed that human type I IFNs exerted a direct protective effect on EV71. It was concluded that type I IFNs play an important role in controlling EV71 infection and replication.
Coxsackie B virus infection of mice: inoculation by the oral route protects the pancreas from damage, but not from infection
Authors: Bopegamage Shubhada , Kovacova Jana , Vargova Agnesa , Motusova Jana , Petrovicova Anna , Benkovicova Maria , Gomolcak Pavol , Bakkers Judith , van Kuppeveld Frank , Melchers Willem J. G. , Galama Jochem M.
Published: November 2005

The pathogenesis of coxsackie B virus (CVB) infections is generally studied in mice by intraperitoneal (i.p.) injection, whereas the gastrointestinal tract is the natural porte d'entrée in humans. The present study was undertaken to compare systematically the influence of infection route on morbidity and pathology. Swiss Albino mice were infected with CVB3 (Nancy) at different doses (5×103, 5×105, 5×107, 5×109 TCID50), given either i.p. or orally. Virus could be isolated from several organs (heart, spleen and pancreas), indicating systemic infection, irrespective of the infection route. Virus titres were 1–2 logs higher after i.p. infection, but kinetics were largely independent of infection route. Organs became negative for virus isolation after 21 days, with the exception of spleen tissue, which remained positive for up to 49 days. Thereafter, virus was detected only by immunohistochemistry and PCR up to 98 days post-infection (oral route). Histopathology showed mild inflammation and necrosis in heart tissue of all mice during the acute phase, with repair at later stages. Strikingly, pancreatic lesions were confined to the exocrine pancreas and observed only after i.p. infection. Under all experimental conditions, the pancreatic islets were spared. In contrast, immunohistochemistry showed the presence of viral VP1, protein 3A and alpha interferon (IFN-α) in exocrine as well as endocrine pancreas of all mice, irrespective of route and dose of infection. It is concluded that infection via the oral route protects the pancreas from damage, but not from infection, a process in which IFN-α is not the only factor involved.
Yunnan orbivirus, a new orbivirus species isolated from Culex tritaeniorhynchus mosquitoes in China
Authors: Attoui Houssam , Jaafar Fauziah Mohd , Belhouchet Mourad , Aldrovandi Nicolas , Tao Sanju , Chen Boquan , Liang Guodong , Tesh Robert B. , de Micco Philippe , de Lamballerie Xavier
Published: November 2005

An orbivirus designated Yunnan orbivirus (YUOV) was isolated from Culex tritaeniorhynchus mosquitoes collected in the Yunnan province of China. Electron microscopy showed particles with typical orbivirus morphology. The YUOV genome was sequenced completely and compared with previously characterized orbivirus genomes. Significant identity scores were detected between proteins encoded by the segments (Seg-1 to Seg-10) of YUOV and those encoded by their homologues in insect-borne and tick-borne orbiviruses. Analysis of VP1 (Pol) and VP2 (T2, which correlates with the virus serogroup) indicated that YUOV is a new species of the genus Orbivirus that is unrelated to the other insect-borne orbiviruses. The replication of YUOV in mosquito cell lines was restricted to Aedes albopictus cells and the virus failed to replicate in mammalian cell lines. However, intraperitoneal injection of virus into naïve mice resulted in productive, non-lethal virus replication and viraemia. Infected mice developed serum neutralizing antibodies and were protected against a new infection challenge. Sequence analysis of clones from the segments encoding outer coat proteins (Seg-3 and Seg-6) of YUOV recovered from mouse blood did not show significant changes in the sequences. The availability of the complete genome sequence will facilitate the development of sequence-specific PCR assays for the study of YUOV epidemiology in the field.
Evolution of human immunodeficiency virus type 2 coreceptor usage, autologous neutralization, envelope sequence and glycosylation
Authors: Shi Yu , Brandin Eleonor , Vincic Elzbieta , Jansson Marianne , Blaxhult Anders , Gyllensten Katarina , Moberg Lars , Broström Christina , Fenyö Eva Maria , Albert Jan
Published: November 2005

To investigate why human immunodeficiency virus type 2 (HIV-2) is less virulent than HIV-1, the evolution of coreceptor usage, autologous neutralization, envelope sequence and glycosylation was studied in sequentially obtained virus isolates and sera from four HIV-2-infected individuals. Neutralization of primary HIV-2 isolates was tested by a cell line-based assay and IgG purified from patients' sera. Significant autologous neutralization was observed for the majority (39 of 54) of the HIV-2 serum–virus combinations tested, indicating that neutralization escape is rare in HIV-2 infection. Furthermore, sera from 18 HIV-2 patients displayed extensive heterologous cross-neutralization when tested against a panel of six primary HIV-2 isolates. This indicates that HIV-2 is intrinsically more sensitive to antibody neutralization than HIV-1. In line with earlier reports, HIV-2 isolates could use several alternative receptors in addition to the major coreceptors CCR5 and CXCR4. Intrapatient evolution from CCR5 use to CXCR4 use was documented for the first time. Furthermore, CXCR4 use was linked to the immunological status of the patients. Thus, all CXCR4-using isolates, except one, were obtained from patients with CD4 counts below 200 cells μl−1. Sequence analysis revealed an association between coreceptor usage and charge of the V3 loop of the HIV-2 envelope, as well as an association between the rate of disease progression and the glycosylation pattern of the envelope protein. Furthermore, HIV-2 isolates had fewer glycosylation sites in the V3 domain than HIV-1 (two to three versus four to five). It is proposed here that HIV-2 has a more open and accessible V3 domain than HIV-1, due to differences in glycan packing, and that this may explain its broader coreceptor usage and greater sensitivity to neutralizing antibodies.
Detection of Epstein–Barr virus BGLF4 protein kinase in virus replication compartments and virus particles
Authors: Wang Jiin-Tarng , Yang Pei-Wen , Lee Chung-Pei , Han Chia-Hong , Tsai Ching-Hwa , Chen Mei-Ru
Published: November 2005

BGLF4 is the only serine/threonine protein kinase identified in Epstein–Barr virus (EBV); it is known to phosphorylate viral DNA polymerase processivity factor, EA-D (BMRF1), EBNA-LP, EBNA-2, cellular EF-1δ and nucleoside analogue ganciclovir. However, the expression and biological functions of BGLF4 have not yet been clearly demonstrated in EBV-infected cells. To reveal authentic functions of BGLF4 protein within viral-replicating cells, a panel of specific monoclonal antibodies was generated and characterized. The major immunogenic regions of BGLF4 were mapped to aa 27–70 and 327–429. Using these antibodies, the expression kinetics and localization of BGLF4 were analysed in reactivated EBV-positive lymphoid and epithelial cells. BGLF4 was expressed as a phosphoprotein at the early lytic stage and was detected predominantly in the nucleus of EBV-positive cells, but small amounts of BGLF4 were observed in cytosolic and heavy membrane fractions at the late phase of virus replication. Additionally, it was demonstrated that BGLF4 co-localizes with viral DNA polymerase processivity factor, EA-D (BMRF1), in the virus replication compartment and that it is a virion component. Finally, possible functional domains at the N terminus of BGLF4 were analysed and it was found that aa 1–26 of BGLF4 are dispensable for EA-D phosphorylation, whereas deletion of aa 27–70 reduced kinase activity.
Analysis of the full-length genome of hepatitis E virus isolates obtained from wild boars in Japan
Authors: Nishizawa Tsutomu , Takahashi Masaharu , Endo Kazunori , Fujiwara Shinji , Sakuma Nobuo , Kawazuma Fumiaki , Sakamoto Hirotsugu , Sato Yukihiro , Bando Masashi , Okamoto Hiroaki
Published: November 2005

Two (2·3 %) of 87 wild-caught boars in Japan had detectable hepatitis E virus (HEV) RNA. The two boar HEV isolates (wbJTS1 and wbJYG1) obtained in the present study and a previously reported isolate (wbJSG1) whose partial sequence had been determined were sequenced over the entire genome. The wbJSG1, wbJTS1 and wbJYG1 isolates comprised 7225 or 7226 nt, excluding the poly(A) tail, and segregated into genotype 3. They differed by 8·5–11·2 % from each other and by 8·6–18·4 % from 17 reported genotype 3 HEV isolates, including one boar isolate, in the full-length sequence. When compared with 191 reported genotype 3 HEV isolates whose partial sequences were known, these three boar isolates were closer to Japanese isolates than to isolates of non-Japanese origin (89·2±2·6 vs 85·9±2·2 %;P<0·0001). A proportion of wild boars in Japan are infected with markedly heterogeneous HEV strains that are indigenous to Japan and may serve as reservoirs of HEV.
At5PTase13 Modulates Cotyledon Vein Development through Regulating Auxin Homeostasis
Authors: Lin Wen-Hui , Wang Yuan , Mueller-Roeber Bernd , Brearley Charles A. , Xu Zhi-Hong , Xue Hong-Wei
Published: November 2005

Phosphatidylinositol signaling pathway and the relevant metabolites are known to be critical to the modulation of different aspects of plant growth, development, and stress responses. Inositol polyphosphate 5-phosphatase is a key enzyme involved in phosphatidylinositol metabolism and is encoded by an At5PTase gene family in Arabidopsis thaliana. A previous study shows that At5PTase11 mediates cotyledon vascular development probably through the regulation of intracellular calcium levels. In this study, we provide evidence that At5PTase13 modulates the development of cotyledon veins through its regulation of auxin homeostasis. A T-DNA insertional knockout mutant, At5pt13-1, showed a defect in development of the cotyledon vein, which was rescued completely by exogenous auxin and in part by brassinolide, a steroid hormone. Furthermore, the mutant had reduced auxin content and altered auxin accumulation in seedlings revealed by the DR5:β-glucuronidase fusion construct in seedlings. In addition, microarray analysis shows that the transcription of key genes responsible for auxin biosynthesis and transport was altered in At5pt13-1. The At5pt13-1 mutant was also less sensitive to auxin inhibition of root elongation. These results suggest that At5PTase13 regulates the homeostasis of auxin, a key hormone controlling vascular development in plants.
Heat Stability of Maize Endosperm ADP-Glucose Pyrophosphorylase Is Enhanced by Insertion of a Cysteine in the N Terminus of the Small Subunit
Authors: Linebarger Carla R. Lyerly , Boehlein Susan K. , Sewell Aileen K. , Shaw Janine , Hannah L. Curtis
Published: November 2005

ADP-glucose pyrophosphorylase (AGPase) is a key regulatory enzyme in starch biosynthesis. However, plant AGPases differ in several parameters, including spatial and temporal expression, allosteric regulation, and heat stability. AGPases of cereal endosperms are heat labile, while those in other tissues, such as the potato (Solanum tuberosum) tuber, are heat stable. Sequence comparisons of heat-stable and heat-labile AGPases identified an N-terminal motif unique to heat-stable enzymes. Insertion of this motif into recombinant maize (Zea mays) endosperm AGPase increased the half-life at 58°C more than 70-fold. Km values for physiological substrates were unaffected, although Kcat was doubled. A cysteine within the inserted motif gives rise to small subunit homodimers not found in the wild-type maize enzyme. Placement of this N-terminal motif into a mosaic small subunit containing the N terminus from maize endosperm and the C terminus from potato tuber AGPase increases heat stability more than 300-fold.
Induction of Thioredoxin Is Required for Nodule Development to Reduce Reactive Oxygen Species Levels in Soybean Roots
Authors: Lee Mi-Young , Shin Ki-Hye , Kim Yun-Kyoung , Suh Ji-Yeon , Gu Young-Yun , Kim Mi-Ran , Hur Yoon-Sun , Son Ora , Kim Jin-Sun , Song Eunsook , Lee Myeong-Sok , Nam Kyoung Hee , Hwang Keum Hee , Sung Mi-Kyung , Kim Ho-Jung , Chun Jong-Yoon , Park Miey , Ahn Tae-In , Hong Choo Bong , Lee Suk-Ha , Park Hong Jae , Park Jong-Sug , Verma Desh Pal S. , Cheon Choong-Ill
Published: November 2005

Nodules are formed on legume roots as a result of signaling between symbiotic partners and in response to the activities of numerous genes. We cloned fragments of differentially expressed genes in spot-inoculated soybean (Glycine max) roots. Many of the induced clones were similar to known genes related to oxidative stress, such as thioredoxin and β-carotene hydroxylase. The deduced amino acid sequences of full-length soybean cDNAs for thioredoxin and β-carotene hydroxylase were similar to those in other species. In situ RNA hybridization revealed that the thioredoxin gene is expressed on the pericycle of 2-d-old nodules and in the infected cells of mature nodules, suggesting that thioredoxin is involved in nodule development. The thioredoxin promoter was found to contain a sequence resembling an antioxidant responsive element. When a thioredoxin mutant of yeast was transformed with the soybean thioredoxin gene it became hydrogen peroxide tolerant. These observations prompted us to measure reactive oxygen species levels. These were decreased by 3- to 5-fold in 7-d-old and 27-d-old nodules, coincident with increases in the expression of thioredoxin and β-carotene hydroxylase genes. Hydrogen peroxide-producing regions identified with cerium chloride were found in uninoculated roots and 2-d-old nodules, but not in 7-d-old and 27-d-old nodules. RNA interference-mediated repression of the thioredoxin gene severely impaired nodule development. These data indicate that antioxidants such as thioredoxin are essential to lower reactive oxygen species levels during nodule development.
Arabidopsis Calcium-Dependent Protein Kinase AtCPK32 Interacts with ABF4, a Transcriptional Regulator of Abscisic Acid-Responsive Gene Expression, and Modulates Its Activity
Authors: Choi Hyung-in , Park Hee-Jin , Park Ji Hye , Kim Sunmi , Im Min-Young , Seo Hyo-Hyun , Kim Yong-Woo , Hwang Inhwan , Kim Soo Young
Published: November 2005

The phytohormone abscisic acid (ABA) regulates stress-responsive gene expression during vegetative growth. The ABA regulation of many genes is mediated by a subfamily of basic leucine zipper class transcription factors referred to as ABFs (i.e. ABF1–ABF4), whose transcriptional activity is induced by ABA. Here we show that a calcium-dependent protein kinase is involved in the ABA-dependent activation process. We carried out yeast two-hybrid screens to identify regulatory components of ABF4 function and isolated AtCPK32 as an ABF4-interacting protein. AtCPK32 has autophosphorylation activity and can phosphorylate ABF4 in vitro. Mutational analysis indicated that serine-110 of ABF4, which is highly conserved among ABF family members, may be phosphorylated by AtCPK32. The serine-110 residue is essential for ABF4-AtCPK32 interaction, and transient expression assay revealed that it is also required for the normal transcriptional function of ABF4. The expression patterns and subcellular localization of AtCPK32 are similar to those of ABF4. Furthermore, its overexpression affects both ABA sensitivity and the expression of a number of ABF4-regulated genes. Together, our data demonstrate that AtCPK32 is an ABA signaling component that regulates the ABA-responsive gene expression via ABF4.
Populus euphraticaDisplays Apoplastic Sodium Accumulation, Osmotic Adjustment by Decreases in Calcium and Soluble Carbohydrates, and Develops Leaf Succulence under Salt Stress
Authors: Ottow Eric A. , Brinker Monika , Teichmann Thomas , Fritz Eberhard , Kaiser Werner , Brosché Mikael , Kangasjärvi Jaakko , Jiang Xiangning , Polle Andrea
Published: November 2005

Populus euphratica Olivier is known to exist in saline and arid environments. In this study we investigated the physiological mechanisms enabling this species to cope with stress caused by salinity. Acclimation to increasing Na+ concentrations required adjustments of the osmotic pressure of leaves, which were achieved by accumulation of Na+ and compensatory decreases in calcium and soluble carbohydrates. The counterbalance of Na+/Ca2+ was also observed in mature leaves from field-grown P. euphratica trees exposed to an environmental gradient of increasing salinity. X-ray microanalysis showed that a primary strategy to protect the cytosol against sodium toxicity was apoplastic but not vacuolar salt accumulation. The ability to cope with salinity also included maintenance of cytosolic potassium concentrations and development of leaf succulence due to an increase in cell number and cell volume leading to sodium dilution. Decreases in apoplastic and vacuolar Ca2+ combined with suppression of calcineurin B-like protein transcripts suggest that Na+ adaptation required suppression of calcium-related signaling pathways. Significant increases in galactinol synthase and alternative oxidase after salt shock and salt adaptation point to shifts in carbohydrate metabolism and suppression of reactive oxygen species in mitochondria under salt stress.
Protection against Photooxidative Injury of Tobacco Leaves by 2-Alkenal Reductase. Detoxication of Lipid Peroxide-Derived Reactive Carbonyls
Authors: Mano Jun'ichi , Belles-Boix Enric , Babiychuk Elena , Inzé Dirk , Torii Yoshimitsu , Hiraoka Eiji , Takimoto Koichi , Slooten Luit , Asada Kozi , Kushnir Sergei
Published: November 2005

Degradation of lipid peroxides leads to the formation of cytotoxic 2-alkenals and oxenes (collectively designated reactive carbonyls). The novel NADPH-dependent oxidoreductase 2-alkenal reductase (AER; EC 1.3.1.74) from Arabidopsis (Arabidopsis thaliana), which is encoded by the gene At5g16970, catalyzes the reduction of the α,β-unsaturated bond of reactive carbonyls, and hence is presumed to function in antioxidative defense in plants. Here we show that Arabidopsis AER (At-AER) has a broad substrate spectrum to biologically relevant reactive carbonyls. Besides 2-alkenals, the enzyme recognized as substrates the lipid peroxide-derived oxenes 9-oxo-octadeca-(10E),(12Z)-dienoic acid and 13-oxo-octadeca-(9E),(11Z)-dienoic acid, as well as the potent genotoxin 4-oxo-(2E)-nonenal, altogether suggesting AER has a key role in the detoxification of reactive carbonyls. To validate this conclusion by in vivo studies, transgenic tobacco (Nicotiana tabacum) plants that had 100- to 250-fold higher AER activity levels than control plants were generated. The engineered plants exhibited significantly less damage from either (1) the exogenously administered 4-hydroxy-(2E)-nonenal, (2) treatment with methyl viologen plus light, or (3) intense light. We further show that the At-AER protein fused with the Aequorea victoria green fluorescent protein localizes in cytosol and the nucleus in Bright-Yellow 2 cells. These results indicate that reactive carbonyls mediate photooxidative injury in leaf cells, and At-AER in the cytosol protects the cells by reducing the α,β-unsaturated bond of the photoproduced reactive carbonyls.
New similarity index for crystal structure determination from X-ray powder diagrams
Authors: Hofmann Detlef Walter Maria , Kuleshova Ludmila
Published: November 2005

A new similarity index for automated comparison of powder diagrams is proposed. In contrast to traditionally used similarity indices, the proposed method is valid in cases of large deviations in the cell constants. The refinement according to this index closes the gap between crystal structure prediction and automated crystal structure determination. The opportunities of the new procedure have been demonstrated by crystal structure solution of un-indexed powder diagrams of some organic pigments (PY111, PR181 and Me-PR170).
A systematic topological search for the framework of ZSM-10
Authors: Foster M. D. , Treacy M. M. J. , Higgins J. B. , Rivin I. , Balkovsky E. , Randall K. H.
Published: November 2005

The application of a new technique for zeolite framework structure solution is described that exhaustively enumerates every possible topology consistent with known unit-cell dimensions and space-group symmetry. It is shown that computer-generated on-line databases of hypothetical crystal structures can radically augment structure building in the pre-refinement stage.
In situdata collection and structure refinement from microcapillary protein crystallization
Authors: Yadav Maneesh K. , Gerdts Cory J. , Sanishvili Ruslan , Smith Ward W. , Roach L. Spencer , Ismagilov Rustem F. , Kuhn Peter , Stevens Raymond C.
Published: November 2005

In situX-ray data collection has the potential to eliminate the challenging task of mounting and cryocooling often fragile protein crystals, reducing a major bottleneck in the structure determination process. An apparatus used to grow protein crystals in capillaries and to compare the background X-ray scattering of the components, including thin-walled glass capillaries against Teflon, and various fluorocarbon oils against each other, is described. Using thaumatin as a test case at 1.8 Å resolution, this study demonstrates that high-resolution electron density maps and refined models can be obtained fromin situdiffraction of crystals grown in microcapillaries.
Solving centrosymmetrical zeolites from powder diffraction data by combining the direct-methods origin-free modulus sum function with the isomorphous replacement technique. X
Authors: Rius-Palleiro Jordi , Peral Inmaculada , Margiolaki Irene , Torrelles Xavier
Published: November 2005

A new two-stage strategy for the solution of zeolite crystal structures with centrosymmetrical frameworks is proposed; this strategy exploits the information contained in multiple powder diffraction patterns. In the first stage, the structure-directing agent (SDA),i.e.the template molecule, is located by combining the isomorphous replacement technique with direct methods. In the second stage, the framework atoms are found by applying direct methods strengthened with additional information coming from the located SDA. All phase refinements are based on the maximization of the origin-free modulus sum function as implemented in the direct-methods programXLENS[Rius (2004).Z. Kristallogr.219, 826–832], with data resolution limits equal to 3.2 Å for the first and 2.21 Å for the second stage. The viability of this new two-stage strategy is illustrated with the solution of the novel zeolite ITQ-32, containing nine Si atoms in the asymmetric unit, from synchrotron powder diffraction data. Especially important is the confirmation that the intensity differences involved in the SDA isomorphous replacement are significantly greater than the experimentally measured errors.
Dislocation densities and crystallite size distributions in nanocrystalline ball-milled fluorides,MF2(M= Ca, Sr, Ba and Cd), determined by X-ray diffraction line-profile analysis
Authors: Ribárik G. , Audebrand N. , Palancher H. , Ungár T. , Louër D.
Published: November 2005

The dislocation densities and crystallite size distributions in ball-milled fluorides,MF2(M= Ca, Sr, Ba and Cd), of the fluorite structure type have been determined as a function of milling time by X-ray diffraction line-profile analysis. The treatment has been based on the concept of dislocation contrast to explain strain anisotropy by means of the modified Williamson–Hall and Warren–Averbach approaches and a whole-profile fitting method using physically based functions. In most cases, the measured and calculated patterns are in perfect agreement; however, in some specific cases, the first few measured profiles appear to be narrower than the calculated ones. This discrepancy is interpreted as the result of an interference effect similar to that described by Rafaja, Klemm, Schreiber, Knapp & Kužel [J. Appl. Cryst.(2004),37, 613–620]. By taking into account and correcting for this interference effect, the microstructure of ball-milled fluorides is determined in terms of dislocation structure and size distributions of coherent domains. A weak coalescence of the crystallites is observed at longer milling periods. An incubation period in the evolution of microstrains is in correlation with the homologous temperatures of the fluorides.
Upgrade of the 32 m small-angle neutron scattering instrument SANS-U
Authors: Okabe Satoshi , Nagao Michihiro , Karino Takeshi , Watanabe Satoshi , Adachi Tomohiro , Shimizu Hirohiko , Shibayama Mitsuhiro
Published: November 2005

The small-angle neutron scattering instrument, SANS-U, owned by the Institute for Solid State Physics, The University of Tokyo, has been upgraded. The SANS-U is a 32 m SANS instrument installed in 1991 at the guide hall of the JRR-3M research reactor of the Japan Atomic Energy Research Institute, and has been serving for inter-university cooperative research use since 1993. The major upgrades include (i) replacement of the two-dimensional area detector by a multi-wire type position-sensitive proportional counter, (ii) renewal of the operating system from a VAX and sequencers to an integrated PXI system controlled byLabVIEW-RTsoftware, (iii) a focusing collimation system, and (iv) a variety of accessory equipment. These upgrades provide a wide dynamic range of neutron counting, user-friendly operation and real-time circular averaging of two-dimensional data.
An examination of the thermal expansion of urea using high-resolution variable-temperature X-ray powder diffraction
Authors: Hammond Robert , Pencheva Klimentina , Roberts Kevin J. , Mougin Patricia , Wilkinson Derek
Published: November 2005

Variable-temperature high-resolution capillary-mode powder X-ray diffraction is used to assess changes in unit-cell dimensions as a function of temperature over the range 188–328 K. No evidence was found for any polymorphic transformations over this temperature range and thermal expansion coefficients for urea were found to be αa= (5.27 ± 0.26) × 10−5 K−1and αc= (1.14 ± 0.057) × 10−5 K−1.
Effects of torsions on the integrated intensity of diffracted X-rays from silicon crystals
Authors: Saka Takashi
Published: November 2005

A very sensitive method to detect long-range strain in otherwise perfect crystalline material has been proposed [Saka (2003).J. Appl. Cryst.36, 249–254]. In this method, the specimen was rotated around the scattering vector. By rotating the specimen, the integrated intensity of higher-order reflections was significantly increased from that in the initial vertical position. The results obtained were explained by assuming that the specimen was bent around an axis on the surface of the specimen, with the axis deviating slightly from the direction parallel to the edge of the specimen. In the present paper, it is shown that the results can be clearly explained by a model where the specimen is uniformly bent with a small torsion around the axes parallel to the specimen edges. The present model is highly probable, as the axes of the bending and torsion are parallel to the edges of the specimen.
Periodic transition of microcrystals on the host (110) face of KLu(WO4)2crystals
Authors: Wang Kunpeng , Zhang Jianxiu , Wang Jiyang , Yu Wentao , Zhang Huaijin , Wang Zhengping
Published: November 2005

The interesting morphology of the (110) face of laser-active potassium lutetium tungstate, KLu(WO4)2(KLuW), crystals has been investigated with an Opton polarizing microscope. Three microcrystals with regular shapes are formed on the edge of the host (110) surface; furthermore, their shapes have a 180° rotation relationship with each other. It is suggested that the three microcrystals may be the representatives of different growth stages, indicating that a periodic transition occurs during the process of crystal growth. In addition, the morphologies of the steps spreading from the three microcrystals and the inner growth sources are very different. The shape of the observed microcrystal is predicted and the formation mechanisms are carefully analyzed. The observed periodic transition morphologies are thought to imply some profound physical background. Unfortunately, until now no universally accepted theory has been able to elucidate the periodic transition phenomena.
A refractive focusing lens system for small-angle neutron scattering
Authors: Mildner D. F. R. , Hammouda B. , Kline S. R.
Published: November 2005

Simple neutron optics measurements have been performed using optical-quality concave lenses as a function of neutron wavelength on a 30 m SANS instrument. The variation in the width of the beam spot on the detector at wavelengths different from the focused condition has been observed. The movement of the beam on the detector when the centerline of the lens combination is shifted from the incident-beam centerline has also been observed. These results are compared with theoretical predictions.
Exact model calculations of the total radial distribution functions for the X-ray diffraction case and systems of complicated chemical composition
Authors: Korsunskiy V. I. , Neder R. B.
Published: November 2005

An algorithm to simulate the radial distribution functions (RDFs) for systems of complex chemical composition is presented which takes into account the exact formulae of the RDF theory in the case of X-ray diffraction. The representation of the partial RDFs of the structural models by histograms allows the method to be used for a wide set of models, for example structures generated with stochastic simulations like the Monte Carlo method. The sensitivity of the results in relation to histogram step size and histogram noise is investigated. A step size of about half the full width at half-maximum (FWHM) of the partial RDF peaks is sufficiently small to make the algorithm reasonably insensitive to the particular step size and to histogram noise. A solution is proposed to calculate the RDF for powders of nanocrystalline particles with complex structures, for which not all interatomic distances can be defined accurately.
The clients’ perspective on change during treatment for an alcohol problem: qualitative analysis of follow‐up interviews in the UK Alcohol Treatment Trial
Authors: Orford Jim , Hodgson Ray , Copello Alex , John Bev , Smith Melanie , Black Rachel , Fryer Kate , Handforth Linda , Alwyn Tina , Kerr Cicely , Thistlethwaite Gill , Slegg Gary ,   UKATT Research Team
Published: November 2005

Aim  To develop a model of change during and following professional treatment for drinking problems, grounded in clients’ accounts.

Participants  Subsets of consecutively selected clients of the UK Alcohol Treatment Trial (UKATT), followed‐up at 3 months (n = 211) and 12 months (n = 198) after randomization.

Location  Five statutory and non‐statutory alcohol problems treatment agencies in three areas of England and Wales.

Data  Open‐ended interviews conducted according to a brief interview guide, leading to 400–800‐word post‐interview reports used for analysis (tape‐recordings used for auditing purposes).

Analysis  Reports analysed by a team according to grounded theory principles, involving an iterative process with successive refinement of interviewing and analysis with each successive batch of data.

Findings  A model of change from the clients’ perspective was developed. Treatment was seen by clients as facilitating various changes in ways of thinking and/or increased support of various kinds from family and friends, along with new ways of acting in relation to drinking or more generally. For many those changes had led to an appreciation of the benefits accruing to them. Treatment was seen as part of a broader treatment system which included pretreatment assessment, forms of help additional to the trial treatment, plus an element of self‐directed change during and following treatment. Taken with awareness of worsening alcohol‐related harms, triggering events and external influence to seek treatment (the catalyst system), to which clients continued to refer following treatment, the change process is depicted as a complex, ongoing set of systems in which a trial treatment is embedded.

Conclusions  Models of change should be broadened so that treatment is seen as a complex system of parts, facilitating a nexus of cognitive, social and behavioural changes, embedded within a broader system of events and processes catalysing change. Such a model helps explain the relative absence of between‐treatments outcome differences in UKATT and in the alcohol problems treatment and more general psychotherapy research literatures.
Financial stress, smoking cessation and relapse: results from a prospective study of an Australian national sample
Authors: Siahpush Mohammad , Carlin John B.
Published: November 2005

Aims  Our aim was to examine the association between financial stress and subsequent smoking cessation among smokers, and relapse among ex‐smokers.

Design and participants  Data came from the first two waves of the Household Income and Labour Dynamics in Australia (HILDA) survey. The size of the subsample of smokers was 2076, and that of ex‐smokers was 2717. Data collection was based on face‐to‐face interviews.

Measurement  Eight questionnaire items (e.g. difficulty paying electricity, gas or telephone bills and going without meals due to shortage of money) were used to construct a nine‐point financial stress index.

Findings  Smokers with more financial stress were less likely to quit, with the odds of quitting reducing by 13% (95% CI: 4–21%; P = 0.008) per unit of the financial stress index. Ex‐smokers with more financial stress were more likely to relapse (P < 0.001).

Conclusions  Special programmes may have to be implemented to counter the potentially adverse effects of tobacco price increases on smokers who have financial stress and fail to quit smoking.
Prospective prediction of children's smoking transitions: role of parents’ and older siblings’ smoking
Authors: Bricker Jonathan B. , Peterson Jr Arthur V. , Leroux Brian G. , Andersen M. Robyn , Rajan K. Bharat , Sarason Irwin G.
Published: November 2005

Aims To use a novel social epidemic probability model to investigate longitudinally the extent to which parents’ and older siblings’ smoking predict children's smoking transitions.

Design Parents’ and older siblings’ smoking status was assessed when children were in 3rd grade (baseline). Three smoking transitions were assessed over the period of child/adolescent smoking acquisition (up to 12th grade): (1) transition from never smoking to trying smoking, (2) transition from trying to monthly smoking and (3) transition from monthly to daily smoking. 

Setting Forty Washington State school districts participating in the long term Hutchinson Smoking Prevention Project (HSPP).

Participants and measurements Participants were the 5520 families for whom data on both parents’ and older siblings’ baseline smoking status, as well as on children's smoking transitions, were available. 

Findings The probability that a smoking parent influenced their child to make the first transition to trying smoking was 32% (95% CI: 27%, 36%); to make the second transition from trying to monthly smoking, 15% (95% CI: 10%, 19%); and to make the third transition from monthly to daily smoking, 28% (95% CI: 21%, 34%). The probability that an older sibling influenced a child to make the first transition to trying smoking was 29% (95% CI: 17%, 39%); to make the second transition from trying to monthly smoking, 0% (95% CI: 0%, 8%); and to make the third transition from monthly to daily smoking, 20% (95% CI: 4%, 33%).

Conclusions In contrast to previous research, the results provide new evidence suggesting that family smoking influences both initiation and escalation of children's smoking. Results also quantify, in terms of probabilities, the importance of parents’ and older siblings’ smoking on children's three major smoking transitions. Parents’ smoking, as well as older siblings’ smoking, are important behaviors to target in preventing adolescents from making smoking transitions.
Longitudinal trajectories of heavy drinking in adults in the United States of America
Authors: Karlamangla Arun , Zhou Kefei , Reuben David , Greendale Gail , Moore Alison
Published: November 2005

Aims  To estimate age, period, cohort and other demographic influences on heavy alcohol consumption and trajectories of heavy drinking in American adults.

Design  Prospective cohort of 14 127 participants, aged 25–74 years at baseline. Generalized estimating equations to model longitudinal change in the probability of heavy drinking and its association with demographic factors.

Setting  National, population‐based sample of non‐institutionalized civilians.

Measurements  Heavy alcohol consumption (usual number of drinks per occasion ≥ five for men; ≥ four for women) at baseline (1971–74) and three follow‐ups until 1992.

Findings  Heavy alcohol consumption declined with increasing age (age effect) and tracked national average consumption (period effect). There was no cohort effect. Higher probability of heavy drinking was associated with male gender (relative risk: RR = 2.4), being not married (RR = 1.4), having less than high school education (RR = 1.7), having annual income below the median (RR = 1.5), not living in the South‐east (RR = 1.7), and smoking (RR = 3.4). Getting married and quitting smoking during the study were each associated with reduction in heavy drinking (RR = 0.55 and 0.61, respectively). Slower age‐related decline in the probability of heavy drinking was seen in men (P < 0.0001), married individuals (P = 0.03), and smokers (P = 0.05).

Conclusions  Demographic predictors of trends in heavy drinking are different from those for trends in average alcohol consumption. The likelihood of heavy drinking declined more slowly with increasing age in men and smokers, suggesting that the negative health effects of alcohol in older ages may be greatest in these groups.
Lion (Panthera leo) home ranges and livestock conflicts in Waza National Park, Cameroon
Authors: Bauer H. , de Iongh H. H.
Published: November 2005

An isolated population of approximately 50 lions (Panthera leo L.) in Waza National Park, Cameroon, caused considerable damage to livestock. Home range sizes of five collared lions were assessed, the mean was very large: 630 km2. The lions differed in their stock raiding behaviour, with two male habitual problem animals, one female nonproblem animal and two female seasonal problem animals that left the Park in the wet season. Together, they were inferred to kill over 100 heads of cattle annually.
Population structure and behaviour of crop‐raiding elephants in Kibale National Park, Uganda
Authors: Chiyo Patrick I. , Cochrane Erica P.
Published: November 2005

We examined patterns of crop raiding by elephants across gender and age classes in relation to elephant life history and sociobiology and estimated the quantitative contribution of crops to elephant diet in Kibale National Park (KNP). Elephant dung‐boli sizes were used to estimate age and sex, while the presence of crop remains in the dung of crop‐raiding elephants was used as evidence of repeated raiding. To estimate the expected proportion of elephants raiding per age class, the age distribution of raiders was compared with the age distribution of all KNP elephants. Elephants raiding crops were predominantly males. They began raiding in expected proportions at 10–14 years while a higher than expected proportion raided crops at 20–24 years. These results suggest that crop raiding is initiated at an age when male elephants leave their families and a large proportion of elephants raid when they are approaching reproductive competition. Evidence from dung of crop raiders, suggests that repeated raiding increases with age. Crop raiders derived 38% of their daily forage from the short time spent raiding, consistent with expectations of foraging theory. Males may be more likely to learn crop raiding because they are socially more independent and experience intense mating competition than females.
Cellular immunity in healthy volunteers treated with an octavalent conjugatePseudomonas aeruginosavaccine
Authors: Zuercher A W , Imboden M A , Jampen S , Bosse D , Ulrich M , Chtioui H , Lauterburg B H , Lang A B
Published: November 2005

Humoral immunity in response to an octavalent O-polysaccharide-toxin A conjugate Pseudomonas aeruginosa vaccine is well studied, and a phase III clinical study in cystic fibrosis (CF) patients is currently ongoing. In contrast, little is known about cellular immunity induced by this vaccine. Fifteen healthy volunteers were immunized on days 1 and 60. Parameters of cellular immunity were studied before vaccination on day 1, and on day 74. Analyses included flow cytometry of whole blood and antigen-induced proliferation of and cytokine production by lymphocyte cultures. The effects of immunization on the composition of peripheral blood lymphocytes as determined by flow cytometry were minor. In contrast, after immunization a highly significant increase of proliferation in response to stimulation with detoxified toxin A was noted: the stimulation index rose from 1·4 on day 1 to 42·2 on day 74 (restimulation with 0·4 µg/ml; P = 0·003). Immunization led to significant production of interferon (IFN)-γ and tumour necrosis factor (TNF)-α by antigen-stimulated lymphocytes. In contrast, no significant induction of interleukin (IL)-4 or IL-10 was observed. In conclusion, immunization of healthy volunteers led to activation of cellular immunity including strong antigen-specific proliferation and cytokine production. In CF patients priming of the cellular immune system towards a Th1-like pattern would be of potential advantage. Therefore, confirmatory analyses in immunized CF patients with and without chronic infection with P. aeruginosa are foreseen.