bluuebunny/crossref_metadata_2025 huggingface dataset:
Adult and larval associations of the alpine stonefly genus Riekoperla McLellan (Plecoptera:Gripopterygidae) using mitochondrial DNA
Authors: Mynott J. H. , Webb J. M. , Suter P. J.
Published: July 2011

The current taxonomic understanding of the genus Riekoperla McLellan, 1971 (Gripopterygidae) is poor, with 15 of the 28 species and subspecies having unknown or uncertain larval associations. Sequences of a 657 bp fragment from the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) were obtained from 122 specimens of 13 species collected throughout the alpine areas of New South Wales and Victoria, Australia. Of these, sequence data associated adults and larvae for the following 10 species: R. alpina McLellan, 1971, R. cf. intermedia, R. compressa Theischinger, 1985, R. hynesorum Theischinger, 1985, R. karki McLellan, 1971, R. montana Theischinger, 1985, R. reticulata (Kimmins, 1951), R. rugosa (Kimmins, 1951), R. trapeza Theischinger, 1985, and R. tuberculata McLellan, 1971. Adults of R. intermedia Theischinger, 1985, R. triloba triloba McLellan, 1971 and R. williamsi McLellan, 1971 were sequenced but no larvae were associated with them. The 13 species were reciprocally monophyletic and had minimum interspecific sequence divergences ranging from 7.2–19.5%, higher than the maximum intraspecific sequence divergences (0.6–5.8%). The combination of morphology and molecular data enabled rapid life stage association for alpine Riekoperla species and this method should be used more frequently for other environmentally significant aquatic insects.
Unidirectional introgression within the genus Dolomedes (Araneae:Pisauridae) in southern New Zealand
Authors: Lattimore Vanessa L. , Vink Cor J. , Paterson Adrian M. , Cruickshank Robert H.
Published: July 2011

We investigated the genetic structure of mitochondrial DNA (COI) and nuclear DNA (actin 5C) for variation within and among populations of two nurseryweb spider species: Dolomedes aquaticus Goyen, 1888 and D. minor Koch, 1876. Specimens were collected from intermediately disturbed braided rivers located in southern South Island, New Zealand. The genetic variation was compared against morphological characteristics to identify traits, both genetically and phenotypically, that indicate past occurrences of introgression. Haplotypes clearly assignable to D. aquaticus were also present in specimens of D. minor, supporting previous research suggesting introgression of mtDNA from D. aquaticus to D. minor. No evidence was found to indicate introgression from D. minor to D. aquaticus, suggesting that the introgression is asymmetrical and that the isolation mechanisms that may be in place to prevent such an occurrence are more successful within one species. In addition, the distribution patterns of identical haplotypes were found to provide an indication for when and where introgression took place.
Protecting the innocent: studying short-range endemic taxa enhances conservation outcomes
Authors: Harvey Mark S. , Rix Michael G. , Framenau Volker W. , Hamilton Zoë R. , Johnson Michael S. , Teale Roy J. , Humphreys Garth , Humphreys William F.
Published: July 2011

A major challenge confronting many contemporary systematists is how to integrate standard taxonomic research with conservation outcomes. With a biodiversity crisis looming and ongoing impediments to taxonomy, how can systematic research continue to document species and infer the ‘Tree of Life’, and still maintain its significance to conservation science and to protecting the very species it strives to understand? Here we advocate a systematic research program dedicated to documenting short-range endemic taxa, which are species with naturally small distributions and, by their very nature, most likely to be threatened by habitat loss, habitat degradation and climate change. This research can dovetail with the needs of industry and government to obtain high-quality data to inform the assessment of impacts of major development projects that affect landscapes and their biological heritage. We highlight how these projects are assessed using criteria mandated by Western Australian legislation and informed by guidance statements issued by the Environmental Protection Authority (Western Australia). To illustrate slightly different biological scenarios, we also provide three case studies from the Pilbara region of Western Australia, which include examples demonstrating a rapid rise in the collection and documentation of diverse and previously unknown subterranean and surface faunas, as well as how biological surveys can clarify the status of species thought to be rare or potentially threatened. We argue that ‘whole of biota’ surveys (that include all invertebrates) are rarely fundable and are logistically impossible, and that concentrated research on some of the most vulnerable elements in the landscape – short-range endemics, including troglofauna and stygofauna – can help to enhance conservation and research outcomes.
Structural plasticity of perisynaptic astrocyte processes involves ezrin and metabotropic glutamate receptors
Authors: Lavialle Monique , Aumann Georg , Anlauf Enrico , Pröls Felicitas , Arpin Monique , Derouiche Amin
Published: July 2011

The peripheral astrocyte process (PAP) preferentially associates with the synapse. The PAP, which is not found around every synapse, extends to or withdraws from it in an activity-dependent manner. Although the pre- and postsynaptic elements have been described in great molecular detail, relatively little is known about the PAP because of its difficult access for electrophysiology or light microscopy, as they are smaller than microscopic resolution. We investigated possible stimuli and mechanisms of PAP plasticity. Immunocytochemistry on rat brain sections demonstrates that the actin-binding protein ezrin and the metabotropic glutamate receptors (mGluRs) 3 and 5 are compartmentalized to the PAP but not to the GFAP-containing stem process. Further experiments applying ezrin siRNA or dominant-negative ezrin in primary astrocytes indicate that filopodia formation and motility require ezrin in the membrane/cytoskeleton bound (i.e., T567-phosphorylated) form. Glial processes around synapses in situ consistently display this ezrin form. Possible motility stimuli of perisynaptic glial processes were studied in culture, based on their similarity with filopodia. Glutamate and glutamate analogues reveal that rapid (5 min), glutamate-induced filopodia motility is mediated by mGluRs 3 and 5. Ultrastructurally, these mGluR subtypes were also localized in astrocytes in the rat hippocampus, preferentially in their fine PAPs. In vivo, changes in glutamatergic circadian activity in the hamster suprachiasmatic nucleus are accompanied by changes of ezrin immunoreactivity in the suprachiasmatic nucleus, in line with transmitter-induced perisynaptic glial motility. The data suggest that (
i
) ezrin is required for the structural plasticity of PAPs and (
ii
) mGluRs can stimulate PAP plasticity.
How to Make a 29% Increase Look Bigger: The Unit Effect in Option Comparisons
Authors: Pandelaere Mario , Briers Barbara , Lembregts Christophe
Published: July 2011

Quantitative information can appear in different units (e.g., 7-year warranty = 84-month warranty). This article demonstrates that attribute differences appear larger on scales with a higher number of units; expressing quality information on such an expanded scale makes consumers switch to a higher-quality option. Testifying to its practical importance, expressing the energy content of snacks in kilojoules rather than kilocalories increases the choice of a healthy snack. The unit effect occurs because consumers focus on the number rather than the type of units in which information is expressed (numerosity effect). Therefore, reminding consumers of alternative units in which information can be expressed eliminates the unit effect. Finally, the unit effect moderates relative thinking: consumers are more sensitive to relative attribute differences when the attribute is expressed on expanded scales. The relation with anchoring and implications for temporal discounting and loyalty programs are discussed.
Heat and momentum transport of ion internal transport barrier plasmas on the Large Helical Device
Authors: Nagaoka K. , Ida K. , Yoshinuma M. , Takeiri Y. , Yokoyama M. , Morita S. , Tanaka K. , Ido T. , Shimizu A. , Tamura N. , Funaba H. , Murakami S. , Goto M. , Takahashi H. , Suzuki C. , Suzuki Y. , Ikeda K. , Osakabe M. , Tsumori K. , Nakano H. , Kaneko O. , Yamada H.
Published: July 2011

The peaked ion-temperature profile with steep gradient, the so-called ion internal transport barrier (ion ITB), was formed in the neutral beam heated plasmas on the Large Helical Device and the high-ion-temperature regime of helical plasmas has been significantly extended. The ion thermal diffusivity in the ion ITB plasma decreases down to the neoclassical transport level. The heavy ion beam probe observed the smooth potential profile with negative radial electric field (ion root) in the core region where the ion thermal diffusivity decreases significantly. The large toroidal rotation was also observed in the ion ITB core and the transport of toroidal momentum was analysed qualitatively. The decrease in momentum diffusivity with ion temperature increase was observed in the ion ITB core. The toroidal rotation driven by ion-temperature gradient, the so-called intrinsic rotation, is also identified.
Tokamak plasma edge modelling including the main chamber wall
Authors: Baelmans M. , Börner P. , Dekeyser W. , Reiter D.
Published: July 2011

Quantifying main chamber wall recycling, erosion and resulting material migration, at least on the basis of known or empirical far scrape-off layer (SOL) processes, is still highly uncertain, despite its relevance for ITER and fusion reactor design studies. This affects, for example, the design problem of first mirror performance of many optical diagnostics in the harsh ITER environment. Poor computational access is not least due to a fundamental technical limitation in apparently all current tokamak edge plasma fluid codes, which implicates a wide computationally unresolved gap between the outermost plasma layer treated in codes and the real vessel wall. We show how the current ITER version of the B2-EIRENE code (SOLPS-4.3) can be extended to cover also this far SOL, on the same footing as the rest of the plasma transport model. We discuss consequences of this new model for estimating plasma power and particle sink terms caused by a fairly realistic wall in ITER based on the conventional Bohm criterion along all plasma–wall interfaces.

Corrections were made to this article on 14 July 2011. The authors have been assigned to the correct affiliations.
Estimation of Mixture Models using Cross‐Validation Optimization: Implications for Crop Yield Distribution Modeling
Authors: Woodard Joshua D. , Sherrick Bruce J.
Published: July 2011

A critical issue in identifying an appropriate characterization of crop yield distributions is that the best‐fitting distribution in an in‐sample framework is not necessarily the best choice out‐of‐sample. This study provides a methodology for estimating flexible and efficient mixture models using cross‐validation that alleviates many of these associated model selection issues. The method is illustrated in an application to the rating of group risk insurance products. Results indicate that nonparametric models often fit best in‐sample but are inefficient and consistently overstate true rates, and vice versa for parametric models. The proposed model provides unbiased rates and also has desirable efficiency properties.
A novel signal processing approach for the detection of copy number variations in the human genome
Authors: Stamoulis Catherine , Betensky Rebecca A.
Published: July 2011

Motivation: Human genomic variability occurs at different scales, from single nucleotide polymorphisms (SNPs) to large DNA segments. Copy number variations (CNVs) represent a significant part of our genetic heterogeneity and have also been associated with many diseases and disorders. Short, localized CNVs, which may play an important role in human disease, may be undetectable in noisy genomic data. Therefore, robust methodologies are needed for their detection. Furthermore, for meaningful identification of pathological CNVs, estimation of normal allelic aberrations is necessary.

Results: We developed a signal processing-based methodology for sequence denoising followed by pattern matching, to increase SNR in genomic data and improve CNV detection. We applied this signal-decomposition-matched filtering (SDMF) methodology to 429 normal genomic sequences, and compared detected CNVs to those in the Database of Genomic Variants. SDMF successfully detected a significant number of previously identified CNVs with frequencies of occurrence ≥10%, as well as unreported short CNVs. Its performance was also compared to circular binary segmentation (CBS). through simulations. SDMF had a significantly lower false detection rate and was significantly faster than CBS, an important advantage for handling large datasets generated with high-resolution arrays. By focusing on improving SNR (instead of the robustness of the detection algorithm), SDMF is a very promising methodology for identifying CNVs at all genomic spatial scales.

Availability: The data are available at http://tcga-data.nci.nih.gov/tcga/ The software and list of analyzed sequence IDs are available at http://www.hsph.harvard.edu/~betensky/ A Matlab code for Empirical Mode Decomposition may be found at: http://www.clear.rice.edu/elec301/Projects02/empiricalMode/code.html

Contact:  caterina@mit.edu
RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
Authors: Hu Qian-Nan , Deng Zhe , Hu Huanan , Cao Dong−Sheng , Liang Yi−Zeng
Published: July 2011

Summary: Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism.

Availability: RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder.

Contact:  qnhu@whu.edu.cn
First Report of Phytophthora nicotianae on Bulb Onion in the United States
Authors: French J. M. , Stamler R. A. , Randall J. J. , Goldberg N. P.
Published: July 2011

Phytophthora nicotianae (synonym P. parasitica) Breda de Haan was isolated from recently harvested onion bulbs (Allium cepa) in cold storage from a commercial field in southern New Mexico. Deteriorating, water-soaked tissue from the center of four bulbs was plated onto water agar and incubated at room temperature. After 72 h, cultures of Phytophthora (identified by the presence of coenocytic hyphae and papillate sporangia) were isolated and transferred to V8 agar amended with ampicillin (250 mg/liter), rifampicin (10 mg/liter), and pimaricin (0.2% wt/vol). Isolates were identified as P. nicotianae based on morphological characteristics and DNA analysis. Sporangia were sharply papilliate, noncaducous, and ovoid to spherical. The average sporangium size was 45.9 × 39.9 μm with a length-to-width ratio of 1.15. Clamydospores, both terminal and intercalary, were spherical to ovoid and averaged 37.2 × 35.2 μm (2). PCR from whole-cell extracts was performed on four cultured isolates from the infected onion tissue using previously described primers ITS4 and ITS6, which amplify the 5.8S rDNA and ITS1 and ITS2 internal transcribed spacers (1,4). A band of approximately 890 bp was amplified and directly sequenced (GenBank Accession No. HQ398876). A BLAST search of the NCBI total nucleotide collection revealed a 100% similarity to multiple P. nicotianae isolates previously sequenced (1). To confirm the pathogenicity of the isolates, onion seedlings were inoculated with 25 ml of P. nicotionae zoospore solution (15,000 zoospores/ml). Necrosis of leaf tissue and seedling death was observed 5 days postinoculation. P. nicotianae was reisolated from the infected onion seedlings and the ITS region was sequenced to confirm its identity. P. nicotianae was previously reported in bulb onion from Australia, Taiwan (Formosa), and Zimbabwe (Rhodesia) (2). P. nicotianae was reported on bunching onions (A. fistulosum) in Hawaii in 1989 (3). Onions are an important crop in New Mexico with a total production value of 47 million dollars in 2008 (NM Agriculture Statistics 2008). This discovery of a potentially significant postharvest disease poses a threat to the onion industry in New Mexico. To our knowledge, this is the first report of P. nicotianae in bulb onion in the United States and the first report of P. nicotianae in New Mexico on any crop.

References: (1) D. E. L. Cooke and J. M. Duncan. Mycol. Res. 101:667, 1997. (2) D. C. Erwin and O. K. Ribeiro. Page 56 in: Phytophthora Diseases Worldwide. The American Phytopathological Society, St Paul, MN, 1996. (3) R. D. Raabe et al. Information Text Series No. 22. University of Hawaii. Hawaii Inst. Trop. Agric. Human Resources, 1981. (4) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, 1990.
First Report of Phaeoacremonium mortoniae Associated with Grapevine Decline in Iran
Authors: Mohammadi H.
Published: July 2011

In July 2009, a survey was conducted in individually owned rooted vineyards in Iran to determine fungal pathogens associated with grapevine decline. Symptoms of grapevine decline such as slow dieback, stunted growth, small chlorotic leaves, and reduced foliage were observed on 7-year-old grapevines (cv. Askari) in Bavanat (Fars Province, southwestern Iran). Internal wood symptoms such as black spots and dark brown-to-black vascular streaking were observed in cross and longitudinal sections of stems and trunks. Wood samples were collected from symptomatic trunks and cordons. The bark of each fragment was removed and 10 thin cross sections (2 to 3 mm thick) were cut from symptomatic vascular tissue of the samples. These disks were immersed in 1.5% sodium hypochlorite solution for 4 min, washed thrice with sterile distilled water, and plated onto malt extract agar (MEA) supplemented with 100 mg liter–1 of streptomycin sulfate. Plates were incubated at 25°C in darkness. All colonies were transferred to potato dextrose agar (PDA) and incubated at 25°C. Five isolates of a Phaeoacremonium sp. were obtained. Single-spore isolates were transferred to PDA, MEA, and oatmeal agar (OA) media and incubated at 25°C for 8 to 16 days in the dark (2). Colonies reached a radius of 9.5 to 12 mm after 8 days of incubation. Colonies were flat and yellowish white on PDA and OA and white-to-pale gray after 16 days of incubation on MEA. Conidiophores were short and unbranched, 14 to 38.5 (23.5) μm long, and often ending in a single terminal phialide. Phialides were terminal or lateral and mostly monophialidic. Conidia were hyaline, oblong to ellipsoidal or reniform, 2 to 6.5 (4.9) μm long, and 1.1 to 1.7 (1.4) μm wide. On the basis of these characteristics, the isolates were identified as Phaeoacremonium mortoniae (1,2). Additionally, identity of the PMH1 isolate was confirmed by sequencing a fragment of the -tubulin gene with primers T1 and Bt2b (GenBank Accession No. JF831449). The sequence of this isolate was identical to the sequence of P. mortoniae (GenBank Accession No. HM116767). Pathogenicity tests were conducted on 2-month-old grapevine seedlings of cv. Askari by watering the roots with 25 ml of a conidial suspension (107 conidia ml–1) harvested from 21-day-old cultures grown on MEA. Controls were inoculated with 25 ml of sterile distilled water. Fifteen replicates were used for each isolate with an equal number of noninoculated plants. All plants were grown under greenhouse conditions (25 to 30°C). Two months after inoculation, inoculated seedlings showed reduced growth, chlorotic leaves, epinasty, severe defoliation, and finally wilting, while control seedlings remained healthy. The fungus was reisolated from internal tissues of the stems of inoculated seedlings. To my knowledge, this is the first report of P. mortoniae causing grapevine decline in Iran.

References: (1) M. Groenewald et al. Mycol. Res. 105:651, 2001. (2) L. Mostert et al. Stud. Mycol. 54:1, 2006.
Characterization of Phytophthora spp. on Floriculture Crops in North Carolina
Authors: Olson H. A. , Benson D. M.
Published: July 2011

Isolates of Phytophthora in floriculture crops were collected from North Carolina commercial greenhouse facilities in 2007 and 2008, identified, and characterized for mating type and mefenoxam sensitivity. In all, 163 isolates from 13 host species at 11 locations were identified primarily as Phytophthora nicotianae (59%), P. drechsleri (23%), P. cryptogea (9%), and P. tropicalis (4%). Multiple Phytophthora spp. were found at five locations. DNA sequencing was more reliable for differentiating P. cryptogea and P. drechsleri. Only the A1 mating type of P. drechsleri was collected; however, both mating types of P. nicotianae, P. cryptogea, and P. tropicalis were found. Overall, 66% of Phytophthora isolates were resistant or intermediate in resistance to mefenoxam at 1 μg a.i./ml. Three groups of P. drechsleri isolates had effective concentration of mefenoxam providing 50% growth inhibition (EC50) estimates over 700 μg a.i./ml. EC50 estimates for P. nicotianae ranged from 246 to 435 μg a.i./ml. Isolates of P. nicotianae exhibited phenotypic heterogeneity at several locations, suggesting multiple separate introductions to the facilities. In contrast, P. nicotianae and P. drechsleri isolates from two locations were phenotypically identical to a previous survey, suggesting that the facilities have Phytophthora spp. established onsite.
Phosphorylation of Ser-80 of VP1 and Ser-254 of VP2 is essential for human BK virus propagation in tissue culture
Authors: Chen Pei-Lain , Hsu Pang-Hung , Fang Chiung-Yao , Chang Chi-Fang , Ou Wei-Chih , Wang Meilin , Chang Deching
Published: July 2011

BK virus (BKV) infection may cause polyomavirus-associated nephropathy in patients with renal transplantation. Recently, the phosphorylated amino acids on the structural proteins VP1, VP2 and VP3 of BKV have been identified by liquid chromatography–tandem mass spectrometry in our laboratory. In this study, we further analysed the biological effects of these phosphorylation events. Phosphorylation of the BKV structural proteins was demonstrated by [32P]orthophosphate labelling in vivo. Site-directed mutagenesis was performed to replace all of the phosphorylated amino acids. The mutated BKV genomes were transfected into Vero cells for propagation analysis. The results showed that expression of the early protein LT and of the late protein VP1 by the mutants VP1-S80A, VP1-S80-133A, VP1-S80-327A, VP1-S80-133-327A and VP2-S254A was abolished. However, propagation of other mutants was similar to that of wild-type BKV. The results suggest that phosphorylation of Ser-80 of VP1 and Ser-254 of VP2 is crucial for BKV propagation.
Rice Ethylene-Response AP2/ERF Factor OsEATB Restricts Internode Elongation by Down-Regulating a Gibberellin Biosynthetic Gene
Authors: Qi Weiwei , Sun Fan , Wang Qianjie , Chen Mingluan , Huang Yunqing , Feng Yu-Qi , Luo Xiaojin , Yang Jinshui
Published: July 2011

Plant height is a decisive factor in plant architecture. Rice (Oryza sativa) plants have the potential for rapid internodal elongation, which determines plant height. A large body of physiological research has shown that ethylene and gibberellin are involved in this process. The APETALA2 (AP2)/Ethylene-Responsive Element Binding Factor (ERF) family of transcriptional factors is only present in the plant kingdom. This family has various developmental and physiological functions. A rice AP2/ERF gene, OsEATB (for ERF protein associated with tillering and panicle branching) was cloned from indica rice variety 9311. Bioinformatic analysis suggested that this ERF has a potential new function. Ectopic expression of OsEATB showed that the cross talk between ethylene and gibberellin, which is mediated by OsEATB, might underlie differences in rice internode elongation. Analyses of gene expression demonstrated that OsEATB restricts ethylene-induced enhancement of gibberellin responsiveness during the internode elongation process by down-regulating the gibberellin biosynthetic gene, ent-kaurene synthase A. Plant height is negatively correlated with tiller number, and higher yields are typically obtained from dwarf crops. OsEATB reduces rice plant height and panicle length at maturity, promoting the branching potential of both tillers and spikelets. These are useful traits for breeding high-yielding crops.
Growth Arrest by Trehalose-6-Phosphate: An Astonishing Case of Primary Metabolite Control over Growth by Way of the SnRK1 Signaling Pathway
Authors: Delatte Thierry L. , Sedijani Prapti , Kondou Youichi , Matsui Minami , de Jong Gerhardus J. , Somsen Govert W. , Wiese-Klinkenberg Anika , Primavesi Lucia F. , Paul Matthew J. , Schluepmann Henriette
Published: July 2011

The strong regulation of plant carbon allocation and growth by trehalose metabolism is important for our understanding of the mechanisms that determine growth and yield, with obvious applications in crop improvement. To gain further insight on the growth arrest by trehalose feeding, we first established that starch-deficient seedlings of the plastidic phosphoglucomutase1 mutant were similarly affected as the wild type on trehalose. Starch accumulation in the source cotyledons, therefore, did not cause starvation and consequent growth arrest in the growing zones. We then screened the FOX collection of Arabidopsis (Arabidopsis thaliana) expressing full-length cDNAs for seedling resistance to 100 mm trehalose. Three independent transgenic lines were identified with dominant segregation of the trehalose resistance trait that overexpress the bZIP11 (for basic region/leucine zipper motif) transcription factor. The resistance of these lines to trehalose could not be explained simply through enhanced trehalase activity or through inhibition of bZIP11 translation. Instead, trehalose-6-phosphate (T6P) accumulation was much increased in bZIP11-overexpressing lines, suggesting that these lines may be insensitive to the effects of T6P. T6P is known to inhibit the central stress-integrating kinase SnRK1 (KIN10) activity. We confirmed that this holds true in extracts from seedlings grown on trehalose, then showed that two independent transgenic lines overexpressing KIN10 were insensitive to trehalose. Moreover, the expression of marker genes known to be jointly controlled by SnRK1 activity and bZIP11 was consistent with low SnRK1 or bZIP11 activity in seedlings on trehalose. These results reveal an astonishing case of primary metabolite control over growth by way of the SnRK1 signaling pathway involving T6P, SnRK1, and bZIP11.
Mechanisms of Molecular Mimicry of Plant CLE Peptide Ligands by the Parasitic NematodeGlobodera rostochiensis
Authors: Guo Yongfeng , Ni Jun , Denver Robert , Wang Xiaohong , Clark Steven E.
Published: July 2011

Nematodes that parasitize plant roots cause huge economic losses and have few mechanisms for control. Many parasitic nematodes infect plants by reprogramming root development to drive the formation of feeding structures. How nematodes take control of plant development is largely unknown. Here, we identify two host factors involved in the function of a receptor ligand mimic, GrCLE1, secreted by the potato cyst nematode Globodera rostochiensis. GrCLE1 is correctly processed to an active form by host plant proteases. Processed GrCLE1 peptides bind directly to the plant CLE receptors CLV2, BAM1, and BAM2. Involvement of these receptors in the ligand-mimicking process is also supported by the fact that the ability of GrCLE1 peptides to alter plant root development in Arabidopsis (Arabidopsis thaliana) is dependent on these receptors. Critically, we also demonstrate that GrCLE1 maturation can be entirely carried out by plant factors and that the availability of CLE processing activity may be essential for successful ligand mimicry.
OsPHF1 Regulates the Plasma Membrane Localization of Low- and High-Affinity Inorganic Phosphate Transporters and Determines Inorganic Phosphate Uptake and Translocation in Rice
Authors: Chen Jieyu , Liu Yu , Ni Jun , Wang Yifeng , Bai Youhuang , Shi Jing , Gan Jian , Wu Zhongchang , Wu Ping
Published: July 2011

PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (PHF1) is known to regulate the plasma membrane localization of PHT1;1, a high-affinity inorganic phosphate (Pi) transporter in Arabidopsis (Arabidopsis thaliana). OsPHF1, a rice (Oryza sativa) gene homologous to AtPHF1, was isolated and found to regulate the localization of both low- and high-affinity Pi transporters to the plasma membrane. Three OsPHF1 allelic mutants carrying one-point mutations at the fifth WD-repeat motif and two at the transmembrane helix, respectively, showed arsenate resistance and severely reduced Pi accumulation. The data indicate that mutation of OsPHF1 results in the endoplasmic reticulum retention of the low-affinity Pi transporter OsPT2 and high-affinity Pi transporter OsPT8. Mutation of OsPHF1 also reduced Pi accumulation in plants exhibiting excessive shoot Pi accumulation due to the overexpression of OsPHR2. However, the transcript level of OsPHF1 itself is not controlled by OsPHR2. Overexpression of OsPHF1 increased Pi accumulation in both roots and shoots in a solution culture with Pi-supplied condition. These results indicate that the role of OsPHF1 is unique in the localization of both low- and high-affinity Pi transporters on the plasma membrane in rice and determines Pi uptake and translocation in rice. The similar function of PHF1 required to facilitate PHT1 transit through the endoplasmic reticulum between Arabidopsis and rice provides an example of expectations from what one would deduce from sequence comparisons to extend knowledge from Arabidopsis to crops.
Systematic confirmation study of reported prostate cancer risk‐associated single nucleotide polymorphisms in Chinese men
Authors: Liu Fang , Hsing Ann W. , Wang Xiang , Shao Qiang , Qi Jun , Ye Yu , Wang Zhong , Chen Hongyan , Gao Xin , Wang Guozeng , Chu Lisa W. , Ding Qiang , OuYang Jun , Gao Xu , Huang Yichen , Chen Yanbo , Gao Yu Tang , Zhang Zuo‐Feng , Rao Jianyu , Shi Rong , Wu Qijun , Wang Meilin , Zhang Zhengdong , Zhang Yuanyuan , Jiang Haowen , Zheng Jie , Hu Yanlin , Guo Ling , Lin Xiaoling , Tao Sha , Jin Guangfu , Sun Jielin , Lu Daru , Lilly Zheng S. , Sun Yinghao , Mo Zengnan , Xu Jianfeng
Published: July 2011

More than 30 prostate cancer (PCa) risk‐associated loci have been identified in populations of European descent by genome‐wide association studies. We hypothesized that a subset of these loci might be associated with PCa risk in Chinese men. To test this hypothesis, 33 single nucleotide polymorphisms (SNP), one each from the 33 independent PCa risk‐associated loci reported in populations of European descent, were investigated for their associations with PCa risk in a case‐control study of Chinese men (1108 cases and 1525 controls). We found that 11 of the 33 SNP were significantly associated with PCa risk in Chinese men (P < 0.05). The reported risk alleles were associated with increased risk for PCa, with allelic odds ratios ranging from 1.12 to 1.44. The most significant locus was located on 8q24 region 2 (rs16901979, P = 5.14 × 10−9) with a genome‐wide significance (P < 10−8), and three loci reached the Bonferroni correction significance level (P < 1.52 × 10−3), including 8q24 region 1 (rs1447295, P = 7.04 × 10−6), 8q24 region 5 (rs10086908, P = 9.24 × 10−4) and 8p21 (rs1512268, P = 9.39 × 10−4). Our results suggest that a subset of the PCa risk‐associated SNP discovered by genome‐wide association studies among men of European descent is also associated with PCa risk in Chinese men. This finding provides evidence of ethnic differences and similarity in genetic susceptibility to PCa. Genome‐wide association studies in Chinese men are needed to identify Chinese‐specific PCa risk‐associated SNP. (Cancer Sci 2011; 102: 1916–1920)
GIMEMA AIDA 0493 amended protocol for elderly patients with acute promyelocytic leukaemia. Long‐term results and prognostic factors
Authors: Latagliata Roberto , Breccia Massimo , Fazi Paola , Vignetti Marco , Di Raimondo Francesco , Sborgia Marco , Vincelli Donatella , Candoni Anna , Salvi Flavia , Rupoli Serena , Martinelli Giovanni , Kropp Maria Grazia , Tonso Anna , Venditti Adriano , Melillo Lorella , Cimino Giuseppe , Petti Maria Concetta , Avvisati Giuseppe , Lo‐Coco Francesco , Mandelli Franco ,   for the GIMEMA Acute Leukaemia Working Party
Published: July 2011

To reduce toxicity in elderly patients with acute promyelocytic leukaemia, in 1997 the Gruppo Italiano Malattie Ematologiche Dell’Adulto (GIMEMA) started an amended protocol for patients aged >60 years, with the same induction [all‐trans retinoic acid (ATRA) + idarubicin] as in younger patients, followed by a single consolidation course (idarubicin + cytarabine) and maintenance with intermittent ATRA. Among 60 enrolled patients, 54 (90%) achieved haematological remission and six died during induction. Four additional patients died in complete remission (CR) from haemorrhage (2) and infection (2) prior or during consolidation therapy. Eleven patients relapsed at a median time of 17·5 months from CR. The 5‐year overall survival (OS), disease‐free survival (DFS) and cumulative incidence of relapse (CIR) rates were 76·1%, 64·6% and 27·4%, respectively. Univariate analysis identified a performance score (PS) = 2 as the only significant adverse prognostic factor for both OS (P = 0·017) and DFS (P = 0·0003). Male sex had an unfavourable impact on DFS (P = 0·021) and on CIR (P = 0·019), but not on OS (P = 0·234). In multivariate analysis for DFS, only PS = 2 retained prognostic significance (HR = 4·5, P = 0·0083). In conclusion, the amended GIMEMA protocol is effective, with similar relapse rate and inferior toxicity compared to the original AIDA 0493. However, considering the recent availability of effective new agents, a less aggressive approach should be tested in this setting.
p.Tyr365Cys change in factor VIII: haemophilia A, but not as we know it
Authors: Bowyer Annette E. , Goodeve Anne , Liesner Ri , Mumford Andrew D. , Kitchen Steve , Makris Mike
Published: July 2011

Haemophilia A is caused by a reduction in clotting factor VIII (FVIII). FVIII coagulant activity (FVIII:C) can be measured by three methods; the one‐stage activated partial thromboplastin time‐based clotting assay, the two‐stage Xa generation‐based clotting assay and the chromogenic Xa generation‐based assay. The FVIII:C of most patients with haemophilia A are concordant regardless of the assay method employed. Up to a third of patients show assay discrepancy, usually with the two‐stage and chromogenic assays being much lower than the one‐stage assay. Very rarely, patients have been reported with lower one‐stage compared to two‐stage and chromogenic assays, but here we report that the mutation p.Tyr365Cys accounts for most of these patients and, at least in the UK, is not rare. We have identified this mutation in 23 different families. Affected male index individuals had a lower mean one‐stage FVIII:C of 27 iu/dl compared to two‐stage FVIII:C mean of 77 iu/dl. Affected individuals had minimal or absent bleeding symptoms and when these were present they were usually in patients with another co‐inherited bleeding disorder. Affected individuals often had surgery without the need to correct the one‐stage FVIII:C.
Short‐term warfarin reversal for elective surgery – using low‐dose intravenous vitamin K: safe, reliable and convenient*
Authors: Burbury Kate L. , Milner Alvin , Snooks Belinda , Jupe David , Westerman David A.
Published: July 2011

Peri‐procedural management of warfarin reflects an intricate balance between the restoration of haemostasis and appropriate thromboprophylaxis. This prospective single‐arm study assessed the safety and efficacy of a convenient schedule, incorporating low‐dose intravenous vitamin K (vitKIV) for short‐term warfarin reversal prior to elective surgery, as well as vitK‐dependent factor levels (vitK‐Factors) and International Normalized Ratio (INR) pre‐ and post‐vitKIV. One seventy eight patients on long‐term warfarin received 3 mg vitKIV 12–18 h pre‐procedure with no adverse reactions. 167/178 (94%) achieved an INR ≤ 1·5 post‐vitKIV on the day of surgery, while all achieved INR ≤ 1·7. Four patients had procedure‐associated major bleeding, but importantly had achieved a pre‐procedure INR < 1·5 and vitK‐Factors >0·30 iu/ml. No patient suffered a symptomatic thromboembolism during the 6‐week follow‐up. Median days to re‐establish a therapeutic INR were 4 (range 2–11). VitKIV near normalized all vitK‐Factors, with a uniform pattern of depletion and repletion in association with an increase and decrease in INR, respectively; and from the data, INR < 1·5 correlated with vitK‐Factors >0·30 iu/ml. Low‐dose vitKIV for short‐term warfarin reversal was reliable and safe, and successfully lowered the INR to an acceptable level for planned surgery, with no excess of bleeding, thromboembolism, delayed discharge, or resistance to warfarin. The protocol was simple and convenient for both the patients and the healthcare institution.
Emotional availability and attachment across generations: variations in patterns associated with infant health risk status
Authors: Cassibba R. , van IJzendoorn M. H. , Coppola G.
Published: July 2011

Background  The presence of limits or distortions in the children's communicative behaviours (due to a chronic illness) may interfere with the possibility to build secure attachment relationships. Moreover, the distress that the atypical chronic illness condition brings to family life may interfere the intergenerational transmission of attachment.

Methods  This study evaluated the associations between maternal attachment representations, emotional availability and mother–child attachment in a clinical and in a comparison group. Forty infants (23 female) in their 14th month of life and their mothers participated in this study, 20 dyads with clinical infants (10 premature infants and 10 infants affected by atopic dermatitis) and 20 full‐term and healthy comparison infants. The Adult Attachment Interview, the Emotional Availability Scales (EAS) and the Strange Situation Procedure were used to assess, respectively, the security of mothers' attachment representations, the emotional availability and the quality of mother–child attachment.

Results  We found that the two groups (clinical vs. comparison) did not differ with respect to the Adult Attachment Interview and the Emotional Availability Scales measures. A significant difference was found in the distribution of the infant–mother attachment patterns, with a higher incidence of insecure infants in the clinical group. In the typically developing group, more secure maternal attachment representations predicted more emotional availability in mother–infant interactions, which predicted more secure infant–mother attachments. However, we did not find similar support for intergenerational transmission of attachment in the clinical group.

Conclusions  We speculate that constant concerns about the child's health condition and communicative difficulties of clinical infants may hamper or even mitigate the intergenerational transmission of attachment.
Cerebral palsy registers and high‐quality data: an evaluation of completeness of the4Childregister using capture–recapture techniques
Authors: Surman G. , da Silva A. A. M. , Kurinczuk J. J.
Published: July 2011

Background As the survival of very preterm and low‐birthweight infants increases, so does the importance of monitoring the birth prevalence of childhood impairments; disease registers provide a means to do so for these rare conditions. High levels of ascertainment for disease research registers have become increasingly difficult to achieve in the face of additional challenges posed by consent and confidentiality issues.4Child –Four Counties Database of Cerebral Palsy, Vision Loss and Hearing Loss in Children has been collecting data and monitoring these three major childhood impairments since 1984.

Methods This study used capture–recapture and related techniques to identify areas which are particularly affected by low ascertainment, to estimate the magnitude of missing cases on the4Childregister and to provide birth prevalence estimates of cerebral palsy which allow for these missing cases.

Results Estimates suggest that while overall around 27% of cerebral palsy cases were not reported to4Child, ascertainment for severely motor‐impaired children (93% complete) and those born in two of the four counties was good (Oxfordshire: 90%, Northamptonshire: 94%). After allowing for missing cases, adjusted estimates of cerebral palsy birth prevalence for 1984–1993 were 3.0 per 1000 live births versus 2.5 per 1000 live births in 1994–2003.

Conclusions Capture–recapture techniques can identify areas of poor ascertainment and add to information around the provision of cerebral palsy birth prevalence estimates. Despite variation in ascertainment over time, capture–recapture estimates supported a decline in cerebral palsy birth prevalence between the earlier and later study periods in the four English counties of the geographical area covered by4Child.
Developing a programme for healthy growth and nutrition during infancy: understanding user perspectives
Authors: Lakshman R. , Landsbaugh J. R. , Schiff A. , Cohn S. , Griffin S. , Ong K. K.
Published: July 2011

Background  Avoiding excess energy intake and rapid weight gain during infancy may be effective in preventing childhood obesity. We developed a programme for healthy growth and nutrition in formula milk‐fed babies. The aim of this study was to understand users' perspectives about the programme and planned trial.

Methods  We conducted three focus group discussions (10 mothers) and nine individual interviews (seven health visitors, one midwife and one mother) discussing the programme materials and trial protocol. All sessions were transcribed verbatim and a thematic analysis was performed using the framework approach.

Results  Mothers reported receiving conflicting messages about infant feeding and were keen for consistent advice. They welcomed the support that the programme would offer to mothers who gave their babies formula milk, but some were sceptical about the feasibility of limiting formula milk quantities. They suggested that recommended quantities should be presented as general guidelines rather than rigid rules. Some mothers said that it was too early to intervene to prevent obesity, that babies could not be overfed and that the risks of formula milk feeding had been exaggerated. Because of the routine advice to feed on demand, babies were fed in response to crying, and crying was equated with ‘hunger’. Some mothers said that growth was genetically determined so they ignored the growth charts. Health visitors used the growth charts to assess adequate weight gain rather than to identify excess weight gain. Health visitors said that mothers would need a lot of education and support to limit formula milk quantities.

Conclusions  Efforts to prevent childhood obesity by avoiding excess weight gain during infancy have to address mothers' beliefs that babies cannot be overfed, that crying always signals hunger and that growth is determined by genes rather than nutrition. Mothers and healthcare providers have different motivations and understanding these are important in the development of any intervention.
The neuropeptide calcitonin gene‐related peptide affects allergic airway inflammation by modulating dendritic cell function
Authors: Rochlitzer S. , Veres T. Z. , Kühne K. , Prenzler F. , Pilzner C. , Knothe S. , Winkler C. , Lauenstein H.‐D. , Willart M. , Hammad H. , Müller M. , Krug N. , Lambrecht B. N. , Braun A.
Published: July 2011

Background The neuropeptide calcitonin gene‐related peptide (CGRP) is released in the lung by sensory nerves during allergic airway responses. Pulmonary dendritic cells (DC) orchestrating the allergic inflammation could be affected by CGRP.

Objective To determine the immunomodulatory effects of CGRP on DC function and its impact on the induction of allergic airway inflammation.

Methods CGRP receptor expression on lung DC was determined by RT‐PCR and immunofluorescence staining. The functional consequences of CGRP receptor triggering were evaluated in vitro using bone marrow‐derived DC. DC maturation and the induction of ovalbumin (OVA)‐specific T cell responses were analysed by flow cytometry. The in vivo relevance of the observed DC modulation was assessed in a DC‐transfer model of experimental asthma. Mice were sensitized by an intrapharyngeal transfer of OVA‐pulsed DC and challenged with OVA aerosol. The impact of CGRP pretreatment of DC on airway inflammation was characterized by analysing differential cell counts and cytokines in bronchoalveolar lavage fluid (BALF), lung histology and cytokine responses in mediastinal lymph nodes.

Results RT‐PCR, immunofluorescence and cAMP assay demonstrated the expression of functionally active CGRP receptors in lung DC. RT‐PCR revealed a transcriptional CGRP receptor down‐regulation during airway inflammation. CGRP specifically inhibited the maturation of in vitro generated DC. Maturation was restored by blocking with the specific antagonist CGRP8−37. Consequently, CGRP‐pretreated DC reduced the activation and proliferation of antigen‐specific T cells and induced increased the numbers of T regulatory cells. The transfer of CGRP‐pretreated DC diminished allergic airway inflammation in vivo, shown by reduced eosinophil numbers and increased levels of IL‐10 in BALF.

Conclusions and Clinical Relevance CGRP inhibits DC maturation and allergen‐specific T cell responses, which affects the outcome of the allergic airway inflammation in vivo. This suggests an additional mechanism by which nerve‐derived mediators interfere with local immune responses. Thus, CGRP as an anti‐inflammatory mediator could represent a new therapeutic tool in asthma therapy.

Cite this as: S. Rochlitzer, T. Z. Veres, K. Kühne, F. Prenzler, C. Pilzner, S. Knothe, C. Winkler, H.‐D. Lauenstein, M. Willart, H. Hammad, M. Müller,
N. Krug, B. N. Lambrecht and A. Braun, Clinical & Experimental Allergy, 2011 (41) 1609–1621.
Glucose activation of islets of Langerhans up-regulates Toll-like receptor 5: possible mechanism of protection
Authors: Weile C , Josefsen K , Buschard K
Published: July 2011

Toll-like receptors are pattern-recognition receptors of the innate immune system that are activated during viral, bacterial or other infections, as well as during disease progression of type 1 and type 2 diabetes. Toll-like receptor 5 (TLR-5) specifically recognizes bacterial infection through binding of flagellin from pathogenic bacteria such as Salmonella and Listeria species. We have found that the expression of TLR5 is up-regulated by glucose activation of isolated islets of Langerhans, in contrast to other investigated TLRs (TLR-2, -3, -4, -6 and -9. Stimulation of islets with 10 mm glucose increased the levels of TLR5 mRNA 10-fold (P = 0·03) and the TLR-5 protein levels twofold (P = 0·04). Furthermore, the protein level of downstream signalling molecule myeloid differentiation primary response gene 88 (MyD88) increased 1·6-fold (P = 0·01). Activation of TLR-5 in islets lead to a marked reduction of both stimulated and basal secretion of insulin, as well as an increase in production of nitric oxide, proinflammatory cytokines, anti-inflammatory heat-shock protein and major histocompatibility complex (MHC) class I transporter. We observe no effects of TLR-5 activation on islet survival. We suggest that this regulation by TLR-5 might be beneficial during serious infection such as sepsis by limiting the activity of beta cells during peaks of insulin demand to counteract beta cell damage.