bluuebunny/crossref_metadata_2025 huggingface dataset:
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells
Authors: Li Meng , Paik Hyun-il Henry , Balch Curt , Kim Yoosung , Li Lang , Huang Tim H-M. , Nephew Kenneth P. , Kim Sun
Published: June 2008

Motivation: In the human genome, ‘CpG islands’, CG-rich regions located in or near gene promoters, are normally unmethylated. However, in cancer cells, CpG islands frequently gain methylation, resulting in silencing of growth-limiting tumor suppressor genes. To our knowledge, the potential relationship between CpG island hypermethylation, transcription factor (TF) binding in local promoter regions and transcriptional control has not been previously explored in a genome-wide context.

Results: In this study, we utilized bioinformatics tools and TF binding site(TFBs) databases to globally analyze sequences methylated in a laboratory model for the development of drug-resistant cancer. Our results demonstrated that four TFBS were enriched in hypermethylated sequences. More interestingly, overrepresentation of these TFBS was observed in hyper-/hypo-methylated sequences where significant changes in methylation levels were observed in drug-resistant cancer cells. In summary, we believe that these findings offer a means to further explore the relationship between DNA methylation and gene expression in drug resistance and tumorigenesis.

Contact:  sunkim2@indiana.edu; knephew@indiana.edu
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data
Authors: Sobreira Tiago J. P. , Gruber Arthur
Published: June 2008

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Availability: GenSeed is available under the GNU General Public License at http://www.coccidia.icb.usp.br/genseed/

Contact:  argruber@usp.br

Supplementary information:  Supplementary data are available at http://www.coccidia.icb.usp.br/genseed/
Management of the Spread of Tomato spotted wilt virus in Tobacco Crops with Insecticides Based on Estimates of Thrips Infestation and Virus Incidence
Authors: Chatzivassiliou E. K.
Published: June 2008

Tomato spotted wilt virus (TSWV) causes serious losses in the tobacco-producing areas of northern Greece. Following a destructive epidemic of TSWV in the prefecture of Kilkis in 2003, a coordinated disease management scheme was developed in collaboration with the local tobacco farmers' associations on 1,000 ha in 2004 and 500 ha in 2005 of tobacco crops of the cv. Virginia. Insecticides first were evaluated for efficiency to control Thrips tabaci, the only TSWV vector present in tobacco crops in Greece. Field data on T. tabaci infestation, population fluctuation, and TSWV incidence were used to coordinate insecticide applications. T. tabaci overwinters in the soil covered by wild flora close to infested fields. The first adults of each season were recorded on blue sticky traps in week 13 and viruliferous individuals were found on weeds close to the tobacco fields in week 16 of both years. Tobacco seedlings were protected against thrips by a preventive drench application of carbofuran to soil in seedling beds, followed by two methomyl and one malathion foliage applications. To achieve an effective decrease of primary inoculum in the fields, malathion was applied to weeds on the field borders before transplanting the tobacco seedlings. In the tobacco crops, carbofuran was applied directly after transplanting. Early transplanted (week 19 to 20) seedlings were sprayed with methomyl. Subsequently, two rounds of foliar applications were started in week 23, consisting of cypermethrin, followed by malathion and methomyl, followed by one or two malathion sprays. At transplanting (week 19 to 23 or 22 in 2004 or 2005, respectively), 340 ± 160 (mean + standard deviation, n = 4 weeks) and 230 ± 130 (n = 3) T. tabaci individuals per trap were recorded in 2004 and 2005, respectively, and 52% of the thrips trapped in the neighboring flora in 2004 were TSWV infected. Afterwards, T. tabaci populations did not increase significantly until harvest (up to 350 individuals were counted per trap). In a control field of an oriental tobacco cultivar in which no insecticides were applied, up to 5,000 and 3,300 thrips were found per trap in 2004 and 2005, respectively. The final incidence of tobacco plants with TSWV infection fluctuated from 10 to 20% in the Virginia tobacco crops whereas, in the control crop, it was 60 and 85% in 2004 and 2005, respectively. This study showed that a well-coordinated collective plan based on data on infection pressure by TSWV and the vector population fluctuation during the growing season can represent an effective way of combating epidemics in tobacco.
Molecular Characterization of Meloidogyne hispanica (Nematoda, Meloidogynidae) by Phylogenetic Analysis of Genes Within the rDNA in Meloidogyne spp.
Authors: Landa Blanca B. , Rius Juan E. Palomares , Vovlas Nicola , Carneiro Regina M. D. G. , Maleita Carla M. N. , de O. Abrantes Isabel M. , Castillo Pablo
Published: June 2008

In the past, the distribution of Meloidogyne hispanica, the Seville root-knot nematode, appeared to be restricted to the southern part of Spain and Prunus spp.; however, its distribution has been confirmed to be worldwide because it occurs in all continents (Europe, Africa, Asia, Australia, and North, Central, and South America). Differentiation of M. hispanica from other Meloidogyne spp., mainly M. arenaria, can be very difficult using morphological and biological traits data. These species are quite similar and can be regularly confused in inaccurate taxonomic comparisons. In this study, species-specific polymerase chain reaction (PCR) and phylogenetic analysis of sequences from three ribosomal (r)DNA regions (18S, internal transcribed spacer [ITS]1-5.8S-ITS2, and D2-D3 of 28S) were used to characterize three M. hispanica isolates from different geographical origins (Brazil, Portugal, and Spain). Molecular analyses showed identical sequences for all three isolates for the three rDNA regions. Maximum parsimony analysis of the three rDNA regions and the species-specific PCR demonstrated and supported the differentiation of M. hispanica from M. incognita, M. javanica, and M. arenaria and from all described root-knot nematode species.
Genetics of Leaf Rust Resistance in Brambling Wheat
Authors: Zhang J. X. , Singh R. P. , Kolmer J. A. , Huerta-Espino J. , Jin Y. , Anderson J. A.
Published: June 2008

The CIMMYT-developed spring wheat ‘Brambling’ has a high level of adult-plant resistance (APR) to leaf rust caused by Puccinia triticina. Our objectives were to determine the genetic basis of resistance in seedlings and adult plants and the magnitude of genotype × environment effects on the expression of APR. Brambling was crossed with spring wheat ‘Jupateco 73S’ that is highly susceptible to current predominant P. triticina races in Mexico and the United States. The F1, F2:3, F4:5, F4:6, and F5:7 recombinant inbred lines (RILs) were evaluated under artificial field epidemics in Mexico and St. Paul, MN. The RILs also were tested with five races of P. triticina in greenhouse seedling experiments. A DNA marker was used to postulate the presence of slow-rusting gene Lr34 in the RILs. F1 data suggested strong dominant effect of the APR genes in Brambling. The proportion of homozygous susceptible lines in each generation indicated the presence of three effective resistance genes in adult plants of Brambling in tests in Mexico and three or four genes in tests in St. Paul. The RILs segregated for seedling genes Lr14a and Lr23 and adult-plant slow-rusting gene Lr34 derived from Brambling and Lr17a from Jupateco 73S. Gene Lr23 conditioned APR to P. triticina races present in the St. Paul nursery and accounted for the additional effective gene at this location. Expression of APR was influenced by the environment in the RILs, even though Brambling displayed a consistent response, indicating that stability of APR can be achieved by combinations of slow-rusting resistance genes.
Reduction ofXylella fastidiosaTransmission Through Pecan Scion Wood by Hot-Water Treatment
Authors: Sanderlin R. S. , Melanson R. A.
Published: June 2008

Pecan (Carya illinoinensis) bacterial leaf scorch disease, caused by the bacterium Xylella fastidiosa, causes leaf loss and reduction in yield of pecans. One of the ways that the pathogen infects newly developing trees is by graft-transmission through infected scion wood. Submersion of pecan scion wood in 46°C water for 30 min greatly reduced transmission of X. fastidiosa following grafting. During a 2-year study with potted rootstock grafted to either hot-water-treated or nontreated scion wood collected from limbs of ‘Cape Fear’ pecan infected with X. fastidiosa, the pathogen was detected in 21% of the trees that developed from the nontreated scion wood and 0.7% of the trees from the hot-water-treated scions. The hot-water treatment of 46°C for 30 min did not affect graft success. Likewise, scion diameter had no effect on success of grafting or on the efficacy of hot-water treatment. Similar hot-water treatments have been efficacious in elimination of X. fastidiosa and some other pathogens from grapevine cuttings. The use of the hot-water treatment demonstrated in this report could be helpful to individual pecan growers and nurseries that use scion wood that may be infected with X. fastidiosa to reduce the occurrence of pecan bacterial leaf scorch disease in new trees.
Bacterial Stem Rot of Poinsettia Caused by a Dickeya sp. (Pectobacterium chrysanthemi) in China
Authors: Rungnapha K. , Yu S. H. , Xie G. L.
Published: June 2008

In December 2006, a rot symptom of unknown etiology was observed on stems of plants (Euphorbia pulcherrima cv. Fu-xing) at a flower nursery in the Zhejiang Province of China where we had previously reported leaf spot of poinsettia caused by Xanthomonas campestris (2). Chlorotic spots anywhere along the stem and purplish black petioles were the first noticeable symptoms. The spots rapidly coalesced, forming large irregular chlorotic areas. Petioles turned black and shriveled and affected leaves wilted. Infected tissues were soft and water soaked. Ten bacterial strains were isolated from the diseased samples and five were selected for identification. They were similar to those of the standard reference strains of Pectobacterium chrysanthemi (Dickeya sp.), LMG 2804 from Belgium and ZUPB20056 from China, in phenotypic tests based on the Biolog Microbial Identification System, version 4.2 (Biolog Inc., Hayward, CA), pathogenicity tests, gas chromatography of fatty acid methyl esters (FAME) using the Microbial Identification System (MIDI Inc, Newark, DE) with aerobic bacterial library (TABA50), and transmission electron microscopy (TEM,KYKY-1000B, Japan). All strains tested were gram-negative facultative anaerobic rods measuring 1.5 to 3.6 × 0.6 to 1.1 μm, with peritrichous flagella. Colonies were gray-white and slightly raised with smooth margins on nutrient agar. They were negative for trehalose and positive for phosphatase production and reducing substances from sucrose. A hypersensitive reaction was observed on tobacco cv. Benshi, 24 h after inoculation. All five isolates, LMG 2804, and ZUPB20056 were identified as P. chrysanthemi (Dickeya sp.) with a Biolog similarity index of 0.58 to 0.83, 0.68, and 0.72 and a FAME similarity index of 0.52 to 0.80, 0.59, and 0.70, respectively. Identification as P. chrysanthemi (Dickeya sp.) was confirmed by PCR with specific primers used by Nassar et al (3). Koch's postulates were completed with the inoculation of 12 4-month-old intact poinsettia plants of cv. Fu-xing with cell suspensions containing 108 CFU/ml by a pinprick at the base of the stem. All five strains induced stem infection similar to those observed in natural infections. No symptoms were noted on the two control plants inoculated with sterilized distilled water by the same method. The bacterium was reisolated from symptomatic stems of poinsettia plants. P. chrysanthemi (Dickeya sp.) was first reported in United States as the cause of bacterial stem rot of poinsettia in 1972 (1). To our knowledge, this is the first report of poinsettia stem rot caused by P. chrysanthemi (Dickeya sp.) in China. The disease cycle and the control strategies of the bacterial stem rot of poinsettia in the regions are being further studied.

References: (1) H. A. J. Hoitink et al. Plant Dis. Rep. 56:480, 1972. (2) B. Li et al. Plant Pathol. 55:293, 2006. (3) A. A. Nassar et al. Appl. Environ. Microbiol. 62:2228, 1996.
Occurrence of Ourmia melon virus in the Guilan Province of Northern Iran
Authors: Gholamalizadeh R. , Vahdat A. , Hossein-Nia S. V. , Elahinia A. , Bananej K.
Published: June 2008

A survey was conducted in 2005 and 2006 in the major cucurbit-growing areas in Guilan Province (northern Iran). Leaf samples were collected from plants of melon (Cucumis melo L.) (n = 119) and squash (Cucurbita sp.) (n = 150) showing various virus-like symptoms (mosaic, yellowing, chlorotic spot, and irregular ring spot) on leaves. All samples collected from 16 different regions were screened for the presence of 10 cucurbit viruses by double-antibody sandwich (DAS)-ELISA using polyclonal antibodies provided by H. Lecoq (INRA, Avignon, France) and V. Lisa (CNR, Torino, Italy). Virus-free cucurbits (melon, squash, and cucumber) grown in insect-proof cages were used as negative controls. Positive and negative controls were included in all tests. Ourmia melon virus (OuMV, genus Ourmiavirus) was the most prevalent virus in melon and was detected in 59% of the samples. OuMV was also detected in 20 of 150 (13%) squash samples. OuMV was detected in 4 of the 16 areas surveyed (Rasht, Somehsara, Masal, and Rood-Bar). The identification of OuMV was confirmed through differential host range reaction. Crude sap from symptomatic leaves was used to inoculate Chenopodium quinoa and Gomphrena globosa as local lesion hosts. Squash, melon, and cucumber were subsequently inoculated by using a single local lesion. Typical yellowing and chlorotic spot symptoms were observed after 40 to 45 days on melon and squash and leaf curling was observed on Nicotiana rustica. The OuMV presence in these symptomatic test plants was confirmed by DAS-ELISA and the tests were negative with Cucurbit aphid-borne yellows virus (CABYV) and Zucchini yellow mosaic virus (ZYMV) antisera. No symptoms were observed on Datura stramonium, Capsicum annum, Phaseolus vulgaris, Pisum sativum, Raphanus sativus, and Beta vulgaris, and OuMV was not detected by DAS-ELISA in these plants. Although showing no symptoms, OuMV-inoculated Vicia faba plants reacted positively in DAS-ELISA. The number of multiple infections of OuMV with other common cucurbit viruses was relatively high (46%), most frequently with ZYMV and CABYV. Since the first report of OuMV from melon in Azerbaijan-E-Gharbi Province, western Iran (1), there has been no report of OuMV occurrence in any other region of Iran or any other country in the world, and the sequence of OuMV remains to be determined. Our results show that OuMV is naturally spreading into other regions of Iran.

Reference: (1) V. Lisa et al. Ann. Appl. Biol. 112:291, 1988.
First Report of Crown and Root Rot Caused by Phytophthora capsici on Hydroponically Grown Cucumbers in Norway
Authors: Herrero M. L. , Brurberg M. B. , Hermansen A.
Published: June 2008

In December 2004, symptoms of root and crown rot were observed on cucumbers (Cucumis sativus L.) in a greenhouse in Norway. Cucumbers were the only crop of the greenhouse that used rockwool as a growing substrate in a hydroponical system. The first symptoms were detected in propagation material. One week after planting, symptoms of root and crown rot were observed and approximately 10% of the plants died. Later, losses of 50% in some greenhouses were observed. A yield reduction as much as 65% was estimated in the winter period (January and February). The two main cucumber cultivars planted were Armada and Lopez. In February 2005, Phytophthora capsici (Leonian) (1) was isolated on potato dextrose agar from a sample of cv. Lopez. The isolate produced deciduous, papillate sporangia (occasionally with two or three papilla) and pedicels that were sometimes longer than the sporangia. Sequencing of amplicons of the internal transcribed spacer region (ITS) rDNA and of the mitochondrial cytochrome c oxidase subunit 1 (Cox1) gene (2) confirmed the identification. Three isolates collected through 2005 from the same greenhouse were crossed with tester strains of P. cryptogea. Formation of oogonia and amphigynous antheridia was always observed in crosses with mating type A2; thus, all isolates were the A1 mating type. All three isolates grew well at 35°C and did not produce chlamydospores. A pathogenicity test was performed with one isolate of P. capsici. Four plants of cucumber cvs. Indira and Jessica were grown in a growth chamber at 24°C. Plants at the two-leaf stage were drenched with 20 ml of a zoospore suspension of 106 zoospores per ml per plant. After 18 days, all plants of both cultivars developed symptoms of crown rot or wilted and died. P. capsici was reisolated from inoculated plants of both cultivars. The pathogenicity test was repeated in the same way, but in a greenhouse with temperatures that ranged between 18 and 29°C. In addition, four plants of both cultivars at the four-leaf stage were inoculated with a suspension of 105 zoospores per ml. After 1 week, all plants developed crown rot or were irreversibly wilted, independently of the plant age or the zoospore concentration. To our knowledge, this is the first report of P. capsici in Norway.

References: (1) D. C. Erwin and O. K. Ribeiro. Phytophthora Diseases Worldwide. The American Phytopathological Society St. Paul MN, 1996. (2) L. P. N. M. Kroon et al. Phytopathology 94:613, 2004.
In Vitro Rearing of Perkinsiella saccharicida and the Use of Leaf Segments to Assay Fiji disease virus Transmission
Authors: Hughes G. L. , Allsopp P. G. , Brumbley S. M. , Johnson K. N. , O'Neill S. L.
Published: June 2008

Fiji leaf gall (FLG) is caused by the Reovirus, Fiji disease virus (FDV), which is transmitted to sugarcane by planthoppers of the genus Perkinsiella. Low vector transmission rates and slow disease symptom development make experimentation within the FDV-Perkinsiella-sugarcane system inherently difficult. A laboratory-based technique was devised to rear the vector using sugarcane leaves as a food source. Planthoppers were reared on sugarcane leaf segments embedded in agarose enclosed within plastic containers. To provide a nondestructive assay for determination of the inoculation potential of planthoppers, FDV was detected by reverse transcription-polymerase chain reaction (RT-PCR) in newly infected sugarcane leaf segments following exposure to viruliferous planthoppers. Leaf segment inoculation correlated with development of FLG symptoms in whole plants that were fed on by the same planthoppers. Analysis of FDV RNAs within the planthopper, measured by quantitative RT-PCR (qRT-PCR), indicated that FDV RNA concentration was associated with successful inoculation of the leaf segment, transmission of FDV to sugarcane and subsequent development of FLG in plants. Quantification of FDV RNA within planthoppers provided an additional measure to assess vector competence in individuals.
One hundred million years of skin feeding? Extended parental care in a Neotropical caecilian (Amphibia: Gymnophiona)
Authors: Wilkinson Mark , Kupfer Alexander , Marques-Porto Rafael , Jeffkins Hilary , Antoniazzi Marta M , Jared Carlos
Published: June 2008

Maternal dermatophagy, the eating of maternal skin by offspring, is an unusual form of parental investment involving co-evolved specializations of both maternal skin and offspring dentition, which has been recently discovered in an African caecilian amphibian. Here we report the discovery of this form of parental care in a second, distantly related Neotropical species
Siphonops annulatus,
where it is characterized by the same syndrome of maternal and offspring specializations. The detailed similarities of skin feeding in different caecilian species provide strong evidence of its homology, implying its presence in the last common ancestor of these species. Biogeographic considerations, the separation of Africa and South American land masses and inferred timescales of amphibian diversification all suggest that skin feeding is an ancient form of parental care in caecilians, which has probably persisted in multiple lineages for more than 100 Myr. These inferences support the hypotheses that (i) maternal dermatophagy is widespread in oviparous direct-developing caecilians, and (ii) that viviparous caecilians that feed on the hypertrophied maternal oviduct evolved from skin-feeding ancestors. In addition to skin-feeding, young
S. annulatus
were observed to congregate around, and imbibe liquid exuded from, the maternal cloacal opening.
Multiple coiling of an elastic sheet in a tube
Authors: Romero V , Witten T.A , Cerda E
Published: June 2008

A piece of paper coiled up in a tube hugs the wall in order to minimize its elastic energy. However, a moment's observation shows that the paper fails to make complete contact near its ends. Here, we show that the detached region in the inner part of the coil touches down the tube wall in an angle that is independent of the system size, thickness and stiffness of the surface. This angle is universal for any coiled sheet whose unstressed state is initially flat. Our results show how the shape and stress distribution for this detached region define the geometry and mechanical equilibrium for the rest of the sheet. In particular, we find scaling relations to describe the structure of the outer part of the coil, in contact with the tube wall, as a function of the number of times the sheet is coiled,
N
.
AMegaraptor-like theropod (Dinosauria: Tetanurae) in Australia: support for faunal exchange across eastern and western Gondwana in the Mid-Cretaceous
Authors: Smith Nathan D , Makovicky Peter J , Agnolin Federico L , Ezcurra Martín D , Pais Diego F , Salisbury Steven W
Published: June 2008

The fossil record of Australian dinosaurs in general, and theropods in particular, is extremely sparse. Here we describe an ulna from the Early Cretaceous Eumeralla Formation of Australia that shares unique autapomorphies with the South American theropodMegaraptor.We also present evidence for the spinosauroid affinities ofMegaraptor. This ulna represents the first Australian non-avian theropod with unquestionable affinities to taxa from other Gondwanan landmasses, suggesting faunal interchange between eastern and western Gondwana during the Mid-Cretaceous. This evidence counters claims of Laurasian affinities for Early Cretaceous Australian dinosaur faunas, and for the existence of a geographical or climatic barrier isolating Australia from the other Gondwanan continents during this time. The temporal and geographical distribution ofMegaraptorand the Eumeralla ulna is also inconsistent with traditional palaeogeographic models for the fragmentation of Gondwana, but compatible with several alternative models positing connections between South America and Antarctica in the Mid-Cretaceous.
Kin recognition in zebrafish: a 24-hour window for olfactory imprinting
Authors: Gerlach Gabriele , Hodgins-Davis Andrea , Avolio Carla , Schunter Celia
Published: June 2008

Distinguishing kin from non-kin profoundly impacts the evolution of social behaviour. Individuals able to assess the genetic relatedness of conspecifics can preferentially allocate resources towards related individuals and avoid inbreeding. We have addressed the question of how animals acquire the ability to recognize kin by studying the development of olfactory kin preference in zebrafish (
Danio rerio
). Previously, we showed that zebrafish use an olfactory template to recognize even unfamiliar kin through phenotype matching. Here, we show for the first time that this phenotype matching is based on a learned olfactory imprinting process in which exposure to kin individuals on day 6 post fertilization (pf) is necessary and sufficient for imprinting. Larvae that were exposed to kin before or after but not
on
day 6 pf did not recognize kin. Larvae isolated from all contact with conspecifics did not imprint on their own chemical cues; therefore, we see no evidence for kin recognition through self-matching in this species. Surprisingly, exposure to non-kin odour during the sensitive phase of development did not result in imprinting on the odour cues of unrelated individuals, suggesting a genetic predisposition to kin odour. Urine-born peptides expressed by genes of the immune system (MHC) are important messengers carrying information about ‘self’ and ‘other’. We suggest that phenotype matching is acquired through a time-sensitive learning process that, in zebrafish, includes a genetic predisposition potentially involving MHC genes expressed in the olfactory receptor neurons.
Disrupting TwoArabidopsis thalianaXylosyltransferase Genes Results in Plants Deficient in Xyloglucan, a Major Primary Cell Wall Component
Authors: Cavalier David M. , Lerouxel Olivier , Neumetzler Lutz , Yamauchi Kazuchika , Reinecke Antje , Freshour Glenn , Zabotina Olga A. , Hahn Michael G. , Burgert Ingo , Pauly Markus , Raikhel Natasha V. , Keegstra Kenneth
Published: June 2008

Xyloglucans are the main hemicellulosic polysaccharides found in the primary cell walls of dicots and nongraminaceous monocots, where they are thought to interact with cellulose to form a three-dimensional network that functions as the principal load-bearing structure of the primary cell wall. To determine whether two Arabidopsis thaliana genes that encode xylosyltransferases, XXT1 and XXT2, are involved in xyloglucan biosynthesis in vivo and to determine how the plant cell wall is affected by the lack of expression of XXT1, XXT2, or both, we isolated and characterized xxt1 and xxt2 single and xxt1 xxt2 double T-DNA insertion mutants. Although the xxt1 and xxt2 mutants did not have a gross morphological phenotype, they did have a slight decrease in xyloglucan content and showed slightly altered distribution patterns for xyloglucan epitopes. More interestingly, the xxt1 xxt2 double mutant had aberrant root hairs and lacked detectable xyloglucan. The reduction of xyloglucan in the xxt2 mutant and the lack of detectable xyloglucan in the xxt1 xxt2 double mutant resulted in significant changes in the mechanical properties of these plants. We conclude that XXT1 and XXT2 encode xylosyltransferases that are required for xyloglucan biosynthesis. Moreover, the lack of detectable xyloglucan in the xxt1 xxt2 double mutant challenges conventional models of the plant primary cell wall.
Mums, Dummies and ‘Dirty Dids’: The Dummy as a Symbolic Representation of Mothering?
Authors: Whitmarsh Judy
Published: June 2008

The bio medical expert literature, although contested, associates the use of dummies, soothers or pacifiers, with illness, dental malformation, impaired speech and language, and working‐class mothering. This article suggests this negative perspective has filtered, via experts and the media, into public narratives of ‘good’ mothering. Interviews with 20 disadvantaged mothers demonstrate the complex negotiations undertaken to integrate dummy use into their personal ‘good‐mothering’ narratives. Representing their hitherto ignored voices in the dummy debate allows a consideration of the context of, and influences on, dummy use. The article argues that rather than a symbol of inadequate working‐class mothering, dummy use is a complex, highly negotiated, situated mothering practice.
All Work and no Play? Understanding the Needs of Children with Caring Responsibilities
Authors: Aldridge Jo
Published: June 2008

This article draws on research with children who provide care for parents with serious mental health problems and signals ongoing research that uses photographic participation methods with these groups of vulnerable children. The intention of this article is to highlight the need to move away from popular and simplistic representations of children with caring responsibilities (young carers) as victims of their parents’ illnesses, as ‘little angels’ whose caring work is condoned through rewards or as (exploited) informal domestic workers whose childhoods are inevitably compromised by the caring activity they undertake. Recommendations are made for generating deeper understanding about the lives and needs of children who are affected by parental impairment that is congruent with the thrust of current UK policy, Every Child Matters and the 2004 Children Act.
Risky Experiences for Children Online: Charting European Research on Children and the Internet
Authors: Livingstone Sonia , Haddon Leslie
Published: June 2008

Children’s online experience, especially the risks to which they might be exposed, is an increasingly important policy and research concern. This article reports an analysis of the amount, nature and range of empirical research concerning children’s online experiences across 18 European countries. Research teams in each country have collaborated, as part of the ‘EU Kids Online’ network, to identify, code and compare studies. In all, 235 studies were identified and coded in a publicly accessible data repository. All countries had some available evidence regarding children’s online risky experiences, with strengths mainly in relation to research into access and use; several countries were found to have a richer evidence base encompassing research into online learning, literacy, participation, parental mediation and so forth. Regarding risks, more research focused on potentially harmful content than on risky forms of contact. Key research gaps included research on younger children, into mobile online platforms, and into certain types of online risk. The article concludes by observing the challenges facing researchers in this field, including the time‐sensitivity of research that quickly dates, the difficulty of tailoring research to meet the needs of a demanding policy agenda, the complexity of designing projects that recognise the contextual and contingent factors that mediate children’s online activities, and the ethical considerations that apply when asking children about private, transgressive or upsetting experiences.
Prevalence and relevance of the positivity of skin prick testing in patients with chronic urticaria
Authors: KULTHANAN Kanokvalai , JIAMTON Sukhum , RUTNIN Ni‐on , INSAWANG Metavee , PINKAEW Sumrauy
Published: June 2008

Many patients with chronic urticaria (CU) worry that foods or other allergens are responsible for their urticaria. Skin prick testing (SPT) may be one of the investigations used to provide a clear illustration. The purpose of our study was to assess the prevalence of positivity of SPT to food allergens and aeroallergens and their relevance in patients with CU, in order to demonstrate the diagnostic value of SPT in CU. We retrospectively reviewed case record forms of patients with chronic ordinary urticaria who underwent SPT in the Urticaria Clinic, Siriraj Hospital, during the period 2000–2004. The studied allergens included 16 food allergens and 12 aeroallergens. Eighty‐eight patients were enrolled. The prevalence of positive SPT among patients with CU was 47.7%. Patients who had personal histories of atopy had statistically significant positive SPT results compared with patients who had negative SPT. Of 88 patients, 26 patients (30%) gave positive results to food allergens, 36 patients (41%) gave positive results to aeroallergens and 20 patients (22.7%) gave positive results to both food and aeroallergens. One‐third of the subjects (34.6%) who had positive SPT results to food allergens had clinical relevance of food allergy in some systems but only one patient had clinical relevance of food‐induced urticaria. Half of the patients who had a history of aeroallergen sensitivity gave a positive SPT response for aeroallergens; however, there was no clinical relevance to their CU. Our study showed that the prevalence of positive SPT to food allergens and aeroallergens in patients with CU was common but had little clinical relevance to CU.
Case of chromoblastomycosis appearing in an Okinawa patient with a medical history of Hansen's disease
Authors: MIYAGI Hideki , YAMAMOTO Yu‐ichi , KANAMORI Shinako , TAIRA Kiyohito , ASATO Yutaka , MYINT Chomar Kaung , KAYO Susumu , HOSOKAWA Atsushi , HAGIWARA Keisuke , UEZATO Hiroshi
Published: June 2008

Chromoblastomycosis is one of several chronic infectious skin diseases caused by various species of dematiaceous fungi. It is clinically characterized by verrucous skin eruptions and occurs most commonly in tropical and subtropical regions. In Okinawa, a subtropical area, there have been only three reported cases of chromoblastomycosis including the present one. Direct microscopic examination of crust specimens and findings of sclerotic cells in histopathology can confirm the diagnosis, and cultures of crust and/or tissue specimens can identify the causative fungi. We herein report the third case of chromoblastomycosis in Okinawa; it arose in an 87‐year‐old Japanese woman with a history of Hansen's disease, who lived in a leprosarium in Miyako Island. To identify the causative agent as Fonsecaea pedrosoi, we used the polymerase chain reaction and direct sequencing analysis in addition to the usual methods, which include 20% potassium hydroxide microscopy, histopathological confirmation of sclerotic cells by periodic acid‐Schiff stain, culture by Sabouraud's glucose agar, slide culture method, and observation of conidia by scanning electron microscopic examination.
Case of acute generalized exanthematous pustulosis caused by ampicillin/cloxacillin sodium in a pregnant woman
Authors: MATSUMOTO Yuka , OKUBO Yukari , YAMAMOTO Toshiyuki , ITO Tomonobu , TSUBOI Ryoji
Published: June 2008

We report a case of acute generalized exanthematous pustulosis (AGEP) induced by ampicillin/cloxacillin sodium (ABPC/MCIPC) in a pregnant woman. AGEP is caused mostly by drugs. Among them, β‐lactam antibiotics account for a high proportion of the cases, predominantly by amoxicillin. To our knowledge, this is only the second case ever reported in the Japanese language published work of AGEP induced by ABPC/MCIPC.
Guideline for the diagnosis and treatment of scabies in Japan (second edition)
Authors:   Executive Committee of Guideline for the Diagnosis,   Treatment of Scabies
Published: June 2008

The guideline has been prepared by the Japanese Dermatological Association to ensure proper diagnosis and treatment of scabies, as oral therapy became available on August 2006 under health insurance and its clinical use was expected to increase. For making a proper diagnosis, the following three points should be taken into consideration: (i) clinical symptoms; (ii) detection of the mite (Sarcoptes scabiei); and (iii) epidemiological symptoms. The diagnosis is confirmed if the mites or eggs are identified by microscopy or dermoscopy and so forth. Topical sulfur preparations, with only limited usefulness, are the only available topical drugs approved by health insurance coverage for treating scabies. Currently, crotamiton, benzyl benzoate and γ‐benzene hexachloride are also used clinically. It is important to apply these to the whole‐body, including hands, fingers and genitals. The dose for ivermectin is a single administration p.o. of approximately 200 µg/kg bodyweight with water before a meal. Administration of a second dose is considered, if new specific lesions develop or the mites are detected. For treating crusted scabies, concomitant administration of oral ivermectin and the topical preparation is necessary. Some safe and useful topical drug preparations are needed to be approved by health insurance.
Evaluating the validities of different DSM‐IV‐based conceptual constructs of tobacco dependence*
Authors: Hendricks Peter S. , Prochaska Judith J. , Humfleet Gary L. , Hall Sharon M.
Published: June 2008

Aim  To compare the concurrent and predictive validities of two subsets of DSM‐IV criteria for nicotine dependence (tolerance and withdrawal; withdrawal; difficulty controlling use; and use despite harm) to the concurrent and predictive validity of the full DSM‐IV criteria.

Design  Analysis of baseline and outcome data from three randomized clinical trials of cigarette smoking treatment.

Setting  San Francisco, California.

Participants  Two samples of cigarette smokers (n = 810 and 322), differing with regard to baseline characteristics and treatment received, derived from three randomized clinical trials.

Measurements  DSM‐IV nicotine dependence criteria were measured at baseline with a computerized version of the Diagnostic Interview Schedule for DSM‐IV (DIS‐IV). Additional baseline measures included the Fagerström Test of Nicotine Dependence (FTND), number of cigarettes smoked per day, breath carbon monoxide (CO) level, the Minnesota Nicotine Withdrawal Scale (MNWS), the Michigan Nicotine Reinforcement Questionnaire (M‐NRQ) and the Profile of Mood States (POMS). Seven‐day point‐prevalence abstinence was assessed at week 12.

Findings  Full DSM‐IV criteria displayed greater concurrent validity than either of the two subsets of criteria. However, DSM‐IV symptoms accounted for only a nominal amount of the variance in baseline smoking‐related characteristics and were unrelated to smoking abstinence at week 12. Cigarettes smoked per day was the only significant predictor of abstinence at week 12.

Conclusions  Although the findings do not provide a compelling alternative to the full set of DSM‐IV nicotine dependence criteria, its poor psychometric properties and low predictive power limit its clinical and research utility.
Development and psychometric evaluation of a three‐dimensional Gambling Motives Questionnaire
Authors: Stewart Sherry H. , Zack Martin
Published: June 2008

Aims  This study was designed to develop and evaluate a self‐report measure of gambling motives.

Participants  A community‐recruited sample of 193 gamblers (70% male; mean age = 35.5 years) were selected to fill two groups according to scores on the South Oaks Gambling Screen: probable pathological gamblers (PPG; n = 154) and non‐pathological gamblers (NPG; n = 39).

Measures  Participants completed a novel 15‐item measure of gambling motives called the Gambling Motives Questionnaire (GMQ), which was modeled after the original Drinking Motives Questionnaire, as well as a variety of gambling behavior and problem criterion measures.

Results  An exploratory principal components analysis revealed three intercorrelated factors tapping enhancement (ENH), coping (COP), and social (SOC) motives, respectively. Each GMQ subscale showed good internal consistency (alphas > 0.80). The PPG group scored higher on all three scales than the NPG group, with larger differences for ENH and COP. In line with the clinical literature, PPG women scored higher than PPG men on the COP subscale but also, unexpectedly, on the SOC subscale. In concurrent validity analyses, ENH consistently predicted greater gambling behavior, and COP and ENH consistently predicted more severe gambling problems. With gambling behavior levels controlled, only COP remained a significant predictor of gambling problem severity. Finally, gender interacted with gambling motives in predicting gambling problem severity: COP predicted gambling problems more strongly in women, whereas ENH predicted gambling problems more strongly in men.

Conclusions  The GMQ appears to be a promising tool for both research and clinical applications with problem gamblers.
Alcohol outlet density and university student drinking: a national study
Authors: Kypri Kypros , Bell Melanie L. , Hay Geoff C. , Baxter Joanne
Published: June 2008

Aims  To examine the geographic density of alcohol outlets and associations with drinking levels and related problems among university students.

Design  Cross‐sectional survey study using geospatial data, with campus‐level and individual‐level analyses.

Participants  A total of 2550 students (mean age 20.2, 60% women) at six university campuses in New Zealand (63% response).

Measurements  Counts of alcohol outlets within 3 km of each campus were tested for their non‐parametric correlation with aggregated campus drinking levels and related problems. Generalized estimating equations were used to model the relation between outlet counts within 1 km and 3 km of student residences and individual drinking levels/problems, with control for gender, age, ethnicity and high school binge drinking frequency, and adjustment for campus‐level clustering.

Findings  Correlations for campus‐level data were 0.77 (P = 0.07) for drinking and personal problems, and 0.31 (P = 0.54) for second‐hand effects. There were consistent significant associations of both on‐ and off‐licence outlet densities with all outcomes in student‐level adjusted models. Effects were largest for 1 km densities and off‐licence outlets.

Conclusions  There are positive associations between alcohol outlet density and individual drinking and related problems. Associations remain after controlling for demographic variables and pre‐university drinking, i.e. the associations are unlikely to be due to self‐selection effects. Increasing alcohol outlet density, and particularly off‐licences, may increase alcohol‐related harm among university students.
A case of heroin overdose reversed by sublingually administered buprenorphine/naloxone (Suboxone®)
Authors: Welsh Christopher , Sherman Susan G. , Tobin Karin E.
Published: June 2008

Background  Opioid overdose is a major source of morbidity and mortality in injection drug users in the United States and many other countries.

Case description  A case is described in which buprenorphine/naloxone (Suboxone®) was administered sublingually to reverse a heroin overdose.

Conclusions  Sublingually administered buprenorphine/naloxone might be used as a means to reverse opioid overdose.
Chromosome 14q32 translocations involving the immunoglobulin heavy chain locus in chronic lymphocytic leukaemia identify a disease subset with poor prognosis
Authors: Cavazzini Francesco , Hernandez Jose Angel , Gozzetti Alessandro , Russo Rossi Antonella , De Angeli Cristiano , Tiseo Ruana , Bardi Antonella , Tammiso Elisa , Crupi Rosaria , Lenoci Maria Pia , Forconi Francesco , Lauria Francesco , Marasca Roberto , Maffei Rossana , Torelli Giuseppe , Gonzalez Marcos , Martin‐Jimenez Patricia , Maria Hernandez Jesus , Rigolin Gian Matteo , Cuneo Antonio
Published: June 2008

Immunophenotypic studies, fluorescence in situ hybridization (FISH) and conventional karyotyping were used to define the clinicobiological significance of 14q32 translocations involving the immunoglobulin gene locus (14q32/IGH) in 252 chronic lymphocytic leukaemia (CLL) patients. The following regions were studied: 13q14, centromere 12, 6q21; 11q22/ATM; 17p13/TP53, 14q32/IGH. Patients were classified as group 1 (favourable, i.e. 13q‐single or normal), group 2 (intermediate risk, i.e. +12, 6q‐, 1–2 anomalies), group 3 (unfavourable, i.e. 17p‐, 11q‐, complex karyotype), or group 4 (14q32/IGH translocation). Endpoints were treatment‐free survival (TFS) and overall survival (OS). One hundred and ten patients were included in group 1, 99 in group 2, 25 in group 3 and 18 in group 4. 14q32/IGH translocation partners were identified in eight cases (BCL2 in five cases, BCL11A, CCND3 and CDK6 in one case each). group 4 showed shorter TFS versus groups 2 and 1 (25% patients treated at 2 months vs. 12 (P = 0·02) and 20 months (P = 0·002), respectively) and shorter OS (25% patients dead at 18 months versus 50 (P = 0·0003) and >60 months (P < 0·0001) respectively. The 14q32/IGH translocation maintained prognostic significance at multivariate analysis on TFS (P = 0·025) and OS (P < 0·001), along with advanced stage and CD38+. These findings show that the 14q32/IGH translocation predicts for an unfavourable outcome in CLL and that this cytogenetic subset might be included as a separate entity in a hierarchical cytogenetic classification of CLL.
Early infection with Trichuris trichiura and allergen skin test reactivity in later childhood
Authors: Rodrigues L. C. , Newcombe P. J. , Cunha S. S. , Alcantara‐Neves N. M. , Genser B. , Cruz A. A. , Simoes S. M. , Fiaccone R. , Amorim L. , Cooper P. J. , Barreto M. L. ,   SCAALA (Social Change, Asthma and Allergy in Latin America)
Published: June 2008

Background
Allergic diseases cause a large and increasing burden in developed countries and in urban centres in middle‐income countries. The causes of this increase are unknown and, currently, there are no interventions to prevent the development of allergic diseases. The ‘hygiene hypothesis’ has tried to explain the increase through a reduction in the frequency of childhood infections causing a failure to program the immune system for adequate immune regulation. Intestinal helminth parasites are prevalent in childhood in developing countries and are associated with a lower prevalence of allergen skin test reactivity and asthma.

Objectives
To investigate whether children who had intestinal helminth infections during early childhood have a lower prevalence of allergen skin test reactivity later in childhood.

Methods
We re‐visited a population of 1055 children from whom stool samples had been collected for detection of intestinal helminth infections for another study, and collected new stool samples and performed allergen skin prick testing. Information on potential confounding variables was collected.

Results
Children with heavy infections with Trichuris trichiura in early childhood had a significantly reduced prevalence of allergen skin test reactivity in later childhood, even in the absence of T. trichiura infection at the time of skin testing in later childhood.

Conclusion
Early heavy infections with T. trichiura may protect against the development of allergen skin test reactivity in later childhood. Novel treatments to program immune‐regulation in early childhood in a way that mimics the effects of early infections with T. trichiura may offer new strategies for the prevention of allergic disease.
A field experiment on the effect of Nosema bombi in colonies of the bumblebee Bombus terrestris
Authors: OTTI OLIVER , SCHMID‐HEMPEL PAUL
Published: June 2008

Abstract 1. Nosema bombi is a microsporidian parasite of bumblebees that is of potentially great ecological and economic importance. Nosema bombi has been shown to have detrimental fitness effects on the bumblebee Bombus terrestris under laboratory conditions. The present study investigates whether N. bombi also has negative fitness effects under natural conditions.

2. A field experiment was conducted with B. terrestris spring queens caught from the wild. In the laboratory these queens were assigned to either infected or control treatment groups. On the emergence of workers, colonies were placed in the field and a number of fitness and life‐history traits were measured.

3. The size of colonies produced by infected queens was significantly smaller than those of control queens. None of the 14 infected colonies produced sexual offspring, whereas four of the 14 control colonies reached the male production stage. Results of the field experiment are in agreement with prior laboratory‐based results, and even imply that such effects are amplified under natural conditions.

4. The evidence suggests that, on entering the colony early, N. bombi has a highly detrimental effect on the fitness of its host. It would seem that this parasite reduces its opportunities to transmit into the next host generation.