bluuebunny/crossref_metadata_2025 huggingface dataset:
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
Authors: Valouev Anton , Ichikawa Jeffrey , Tonthat Thaisan , Stuart Jeremy , Ranade Swati , Peckham Heather , Zeng Kathy , Malek Joel A. , Costa Gina , McKernan Kevin , Sidow Arend , Fire Andrew , Johnson Steven M.
Published: May 2008

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome.
Plant ploidy level influences selection by butterfly seed predators
Authors: Arvanitis Leena , Wiklund Christer , Ehrlén Johan
Published: May 2008

Polyploidization is a common route to plant diversification. Polyploids often differ from their progenitors in size, flower number, flower size and flowering phenology. Such differences may translate into differences in the intensity of interactions with animals. Here we investigated the impact of the ploidy‐related differences in tetraploids and octoploids of the perennial herb Cardamine pratensis on pre‐dispersal seed predation by the butterfly Anthocharis cardamines. The probability of escaping attack was lower for octoploids than for tetraploids, even after accounting for the fact that octoploids were larger and had fewer flowers than tetraploids. Flower shoot size was correlated with probability of attack in tetraploids but not in octoploids. Differences in plant traits associated with polyploidization can alter interactions with animals, and animal‐mediated differences in trait selection between ploidy types can contribute to their further divergence.
Radiation Therapy for Cancer The Fifteenth Anniversary of Hiroshima Cancer Seminar Foundation, the Seventeenth International Symposium of Hiroshima Cancer Seminar, November 2007
Authors: Hirokawa Yutaka , Yasui Wataru , Komaki‐Cox Ritsuko U. , Cox James D. , Itou Katsuhide , Tahara Eiichi
Published: May 2008

This symposium presented what we do to really know about new technology for radiation therapy and what we do to realize our final goal of selective radiation therapy and CRT for cancer. It no doubt provided us for a great deal of information on technological and conceptual advances in radiation therapy and radiation biology. (Cancer Sci 2008; 99: 1287–1291)
The JAK kinase inhibitor CP‐690,550 supresses the growth of human polycythemia vera cells carrying the JAK2V617F mutation
Authors: Manshouri Taghi , Quintás‐Cardama Alfonso , Nussenzveig Roberto H. , Gaikwad Amos , Estrov Zeev , Prchal Josef , Cortes Jorge E. , Kantarjian Hagop M. , Verstovsek Srdan
Published: May 2008

The somatic activating janus kinase 2 mutation (JAK2)V617F is detectable in most patients with polycythemia vera (PV). Here we report that CP‐690,550 exerts greater antiproliferative and pro‐apoptotic activity against cells harboring JAK2V617F compared with JAK2WT. CP‐690,550 treatment of murine factor‐dependent cell Patersen–erythropoietin receptor (FDCP‐EpoR) cells harboring human wild‐type or V617F JAK2 resulted in inhibition of cell proliferation with a 50% inhibitory concentration (IC50) of 2.1 µM and 0.25 µM, respectively. Moreover, CP‐690,550 induced a significant pro‐apoptotic effect on murine FDCP‐EpoR cells carrying JAK2V617F, whereas a lesser effect was observed for cells carrying wild‐type JAK2. This activity was coupled with inhibition of phosphorylation of the key JAK2V617F‐dependent downstream signaling effectors signal transducer and activator of transcription (STAT)3, STAT5, and v‐akt murine thymoma viral oncogene homolog (AKT). Furthermore, CP‐690,550 treatment of ex‐vivo‐expanded erythroid progenitors from JAK2V617F‐positive PV patients resulted in specific, antiproliferative (IC50 = 0.2 µM) and pro‐apoptotic activity. In contrast, expanded progenitors from healthy controls were less sensitive to CP‐690,550 in proliferation (IC50 > 1.0 µM), and apoptosis assays. The antiproliferative effect on expanded patient progenitors was paralleled by a decrease in JAK2V617F mutant allele frequency, particularly in a patient homozygous for JAK2V617F. Flow cytometric analysis of expanded PV progenitor cells treated with CP‐690,550 suggests a possible transition towards a pattern of erythroid differentiation resembling expanded cells from normal healthy controls. (Cancer Sci 2008; 99: 1265–1273)
Bringing alcohol on campus to raise money: impact on student drinking and drinking problems
Authors: Voas Robert B. , Johnson Mark , Turrisi Robert J. , Taylor Dexter , Honts Charles Robert , Nelsen Lisa
Published: May 2008

Aims  Universities are striving to raise funds, often attracting spectators by selling alcohol at campus events. This study evaluates the effect of a policy change on student drinking at a large western university that had historically banned alcohol on campus but transitioned to permitting the sale of alcohol in some of its facilities.

Methods  Surveys of student drinking and perceptions of other students' drinking were conducted before, during and after the policy change at the transition university (TU) and compared to similar data from a control university (CU). Surveys of student drinking at on‐campus and off‐campus venues and observations of alcohol service practices were also conducted.

Results  The policy change at the TU was introduced cautiously, and sales to underage drinkers were relatively well controlled. Despite this, student drinking rose initially, then declined after 1 year. Perceptions of the amount of drinking by other students increased slightly, but there was no overall measurable increase in student drinking during the first 3 years of the new policy.

Conclusions  The conservative TU policy—to sell alcohol only at select events and to control sales to minors—may have limited the impact of on‐campus alcohol sales on student consumption. Although the study results did not find a stable increase in student drinking, they do not necessarily support the liberalization of campus alcohol policy, because the transition is still ‘in progress’ and the final outcome has not been evaluated.
Self‐treatment of opioid withdrawal using kratom (Mitragynia speciosa korth)
Authors: Boyer Edward W. , Babu Kavita M. , Adkins Jessica E. , McCurdy Christopher R. , Halpern John H.
Published: May 2008

Background  Kratom (Mitragynia speciosa korth) is recognized increasingly as a remedy for opioid withdrawal by individuals who self‐treat chronic pain.

Case description  A patient who had abruptly ceased injection hydromorphone abuse self‐managed opioid withdrawal and chronic pain using kratom. After co‐administering the herb with modafinil he experienced a tonic‐clonic seizure, but he reported only modest abstinence once kratom administration stopped. We confirmed the identity of the plant matter he ingested as kratom and identified no contaminants or adulterants. We also conducted high‐throughput molecular screening and the binding affinity at mu, delta and kappa receptors of mitragynine.

Conclusion  We report the self‐treatment of chronic pain and opioid withdrawal with kratom. The predominant alkaloid of kratom, mitragynine, binds mu‐ and kappa‐opioid receptors, but has additional receptor affinities that might augment its effectiveness at mitigating opioid withdrawal. The natural history of kratom use, including its clinical pharmacology and toxicology, are poorly understood.
Relationship of sex steroid hormones with bone mineral density (BMD) in a nationally representative sample of men
Authors: Paller Channing J. , Shiels Meredith S. , Rohrmann Sabine , Basaria Shehzad , Rifai Nader , Nelson William , Platz Elizabeth A. , Dobs Adrian
Published: May 2008

Objective  Sex steroid hormones influence bone mineral density (BMD) in women, but are less well‐studied in men. We evaluated the association of serum total and free sex steroid hormones and SHBG with osteopaenia in a nationally representative sample of men aged 20–90 years.

Design  BMD and sex steroid hormones were measured among participants in NHANES III, a cross‐sectional study of the US population.

Population  A total of 1185 adult men in morning examination session of Phase I of NHANES III (1988–91).

Measurements  Relation of oestradiol (E2), testosterone, and SHBG concentrations with BMD. Osteopaenia was defined as 1–2·5 SD below the mean for white men aged 20–29 years.

Results  Men in the lowest quartile of free E2 had 70% increased odds (OR = 1·69, 95% CI 0·95–2·98) of osteopaenia compared with men in the highest quartile. Men in the lowest quartile of free testosterone had nearly four times the odds of osteopaenia than those in the highest quartile (OR = 3·82, 95% CI 1·87–7·78). Lower concentrations of SHBG appeared protective against osteopaenia (P‐trend = 0·01). Neither total testosterone nor total E2 was associated with BMD, although men with clinically low E2 (< 20 ng/l) had lower BMD (0·930 g/cm2, 95% CI 0·88–0·98) than men with normal‐range E2 (1·024 g/cm2, 95% CI 1·01–1·04; P = 0·004). Findings for free E2 were most pronounced among elderly men, while the findings for free testosterone were most pronounced among younger men.

Conclusions  In this nationally representative study, men with lower free E2, lower free testosterone, and higher SHBG concentrations in circulation were more likely to have low BMD.
Polypoid mucosal prolapse complicating low rectal adenomas: beware the inflammatory cloacogenic polyp!
Authors: Parfitt J R , Shepherd N A
Published: May 2008

Aims:  Polypoid mucosal prolapse near the anorectal junction mimics adenomas endoscopically and histopathologically. The aim was to describe the phenomenon of polypoid mucosal prolapse arising secondary to adenomas at the anorectal junction.

Methods and results:  Four cases of low rectal adenoma with polypoid mucosal prolapse were assessed histopathologically, as well as with p53 and Ki67 antibodies. Two were male and two female; the mean age was 45 years. Available follow‐up has revealed no recurrence in any patient. All cases showed mucosal expansion with ulceration or erosion, crypt architectural irregularity, fibromuscular proliferation between crypts and variable epithelial serration and inflammation. Each case also showed unequivocal dysplasia, often co‐mingled with features of prolapse, highlighted by p53 and Ki67 immunohistochemistry, which demonstrated positivity within dysplastic areas.

Conclusions:  Histopathologists must recognize the potential for adenomatous/dysplastic foci in anorectal lesions to superficially resemble inflammatory cloacogenic polyps. We recommend use of immunomarkers p53 and Ki67 to aid the interpretation of challenging cases. We believe that polypoid mucosal prolapse changes can be a secondary phenomenon, due to adenomas close to or at the anorectal junction.
Induction of cytotoxic T‐lymphocyte and antibody responses against highly pathogenic avian influenza virus infection in mice by inoculation of apathogenic H5N1 influenza virus particles inactivated with formalin
Authors: Sawai Toshihiro , Itoh Yasushi , Ozaki Hiroichi , Isoda Norikazu , Okamoto Kiyoko , Kashima Yoshitaka , Kawaoka Yoshihiro , Takeuchi Yoshihiro , Kida Hiroshi , Ogasawara Kazumasa
Published: May 2008

We investigated whether a vaccine derived from an apathogenic reassortant type A H5N1 influenza strain could induce immune responses in vivo that mediated protection from highly pathogenic avian influenza virus infection in mice. After two subcutaneous immunizations with formalin‐inactivated H5N1 whole virus particles (whole particle vaccine), significant killing specific for cells presenting a nucleoprotein peptide from the vaccine strain of the virus was observed. Similar vaccination with viruses treated with ether and formalin, which are commonly used for humans as ether‐split vaccines, induced little or no cytotoxic T‐cell response. Furthermore, whole particle vaccines of the apathogenic H5N1 strain were more effective than ether‐split vaccines at inducing antibody production able to neutralize a highly pathogenic H5N1 strain. Finally, whole particle vaccines of H5N1 protected mice against infection by an H5N1 highly pathogenic avian influenza virus more effectively than did ether‐split vaccines. These results suggest that formalin‐inactivated virus particles of apathogenic strains are effective for induction of both cytotoxic T‐lymphocyte and antibody responses against highly pathogenic avian influenza viruses in vivo, resulting in protection from infection by a highly pathogenic H5N1 virus.
Translating innate response into long‐lasting antibody response by the intrinsic antigen‐adjuvant properties of papaya mosaic virus
Authors: Acosta‐Ramírez Elizabeth , Pérez‐Flores Rebeca , Majeau Nathalie , Pastelin‐Palacios Rodolfo , Gil‐Cruz Cristina , Ramírez‐Saldaña Maricela , Manjarrez‐Orduño Nataly , Cervantes‐Barragán Luisa , Santos‐Argumedo Leopoldo , Flores‐Romo Leopoldo , Becker Ingeborg , Isibasi Armando , Leclerc Denis , López‐Macías Constantino
Published: May 2008

Identifying the properties of a molecule involved in the efficient activation of the innate and adaptive immune responses that lead to long‐lasting immunity is crucial for vaccine and adjuvant development. Here we show that the papaya mosaic virus (PapMV) is recognized by the immune system as a pathogen‐associated molecular pattern (PAMP) and as an antigen in mice (Pamptigen). A single immunization of PapMV without added adjuvant efficiently induced both cellular and specific long‐lasting antibody responses. PapMV also efficiently activated innate immune responses, as shown by the induction of lipid raft aggregation, secretion of pro‐inflammatory cytokines, up‐regulation of co‐stimulatory molecules on dendritic cells and macrophages, and long‐lasting adjuvant effects upon the specific antibody responses to model antigens. PapMV mixed with Salmonella enterica serovar Typhi (S. typhi) outer membrane protein C increased its protective capacity against challenge with S. typhi, revealing the intrinsic adjuvant properties of PapMV in the induction of immunity. Antigen‐presenting cells loaded with PapMV efficiently induced antibody responses in vivo, which may link the innate and adaptive responses observed. PapMV recognition as a Pamptigen might be translated into long‐lasting antibody responses and protection observed. These properties could be used in the development of new vaccine platforms.
Proteasome inhibition suppresses essential immune functions of human CD4+ T cells
Authors: Berges Carsten , Haberstock Heinrich , Fuchs Dominik , Miltz Marion , Sadeghi Mahmoud , Opelz Gerhard , Daniel Volker , Naujokat Cord
Published: May 2008

The proteasome constitutes the central proteolytic component of the highly conserved ubiquitin–proteasome system, which is required for the maintenance and regulation of basic cellular processes, including differentiation, proliferation, cell cycling, gene transcription and apoptosis. Here we show that inhibition of proteasomal proteolytic activity by the proteasome inhibitors bortezomib and lactacystin suppresses essential immune functions of human CD4+ T cells activated by allogeneic dendritic cells (DCs). In activated CD4+ T cells, proteasome inhibition induces apoptosis accompanied by rapid accumulation and stabilization of the tumour suppressor protein p53. Activated CD4+ T cells surviving proteasome inhibition undergo inhibition of proliferation by induction of G1 phase cell‐cycle arrest. Induction of G1 arrest is accompanied by the accumulation of cyclin‐dependent kinase inhibitors p21WAF1/CIP1 and p27KIP1 and the disappearance of cyclin A, cyclin D2 and proliferating cell nuclear antigen, proteins known to regulate G1 to S phase cell‐cycle transitions. Expression of the activation‐associated cell surface receptors CD25, CD28, CD120b and CD134 as well as production of interferon‐γ (IFN‐γ), tumour necrosis factor‐α (TNF‐α), interleukin‐4 (IL‐4) and IL‐5 is suppressed in response to proteasome inhibition in CD4+ T cells activated by DCs. Expression of CD25, IFN‐γ, TNF‐α, IL‐4 and IL‐5 is known to be mediated by the transcriptional activity of nuclear factor of activated T cells (NFAT), and we show here that proteasome inhibition suppresses activation and nuclear translocation of NFATc2 in activated CD4+ T cells. Thus, the proteasome is required for essential immune functions of activated CD4+ T cells and can be defined as a molecular target for the suppression of deregulated and unwanted T‐cell‐mediated immune responses.
Enhanced immunostimulatory activity of oligodeoxynucleotides by Y‐shape formation
Authors: Nishikawa Makiya , Matono Mitsuhiro , Rattanakiat Sakulrat , Matsuoka Nao , Takakura Yoshinobu
Published: May 2008

DNA containing unmethylated CpG dinucleotides (CpG DNA) is a potent activator of innate and acquired immune responses. Although the sequence‐specific immunostimulatory activity of CpG DNA has been extensively explored, little information is available about the importance of the stereochemical properties of CpG DNA. In this study, Y‐shaped oligodeoxynucleotides (Y‐ODNs) were prepared using three ODNs with the halves of each ODN being partially complementary to a half of the other two ODNs. Y‐ODN induced greater amounts of tumour necrosis factor‐α and interleukin‐6 from RAW264.7 macrophage‐like cells than did conventional single‐stranded ODN (ssODN) or double‐stranded ODN (dsODN). The Y‐ODN was less stable in serum than dsODN, but greater amounts of Y‐ODN were taken up by macrophage‐like cells compared with dsODN. A newly designed Y‐ODN containing three potent CpG motifs generated significantly higher levels of cytokines compared with dsODN containing the identical sequences. These results indicate that the Y‐shaped form of ODN is a novel, reproducible and reliable approach to enhancing the immunostimulatory activity of ODNs.
Covariation between intraspecific genetic diversity and species diversity within a plant functional group
Authors: He Tianhua , Lamont Byron B. , Krauss Siegfried L. , Enright Neal J. , Miller Ben P.
Published: May 2008

Species diversity and genetic diversity are fundamental components of biodiversity. A primary goal of biodiversity studies is to explain the distribution of species and alleles in space and time. A new challenge is to cross discipline boundaries and explore the relationship between these two scales of diversity.

In the biodiverse northern sandplain shrublands of south‐western Australia, the woody shrub Banksia attenuata occurs on patchily distributed sand dunes, and coexists with B. hookeriana, B. menziesii, and two small tree species, Eucalyptus todtiana and Xylomelum angustifolium, which together comprise a plant functional group of large shrubs/small trees.

Genetic variation (alleles per locus and heterozygosity) between 736 B. attenuata individuals on 27 discrete dunes was assessed using 11 polymorphic microsatellite markers. For each dune, the physical properties of area and height, and species diversity (richness and evenness) of the functional group, were measured.

Synthesis. Genetic diversity of B. attenuata covaried positively with species diversity, which in turn covaried strongly with dune height rather than dune area. The positive relationship between species and genetic diversity demonstrated here supports the theory of common environmental, rather than neutral, processes acting directly or indirectly on both scales of diversity, and suggests the possibility of predicting one component of diversity on the basis of the other.
Genetic structure of natural Nasonia vitripennis populations: validating assumptions of sex‐ratio theory
Authors: GRILLENBERGER B. K. , KOEVOETS T. , BURTON‐CHELLEW M. N. , SYKES E. M. , SHUKER D. M. , VAN DE ZANDE L. , BIJLSMA R. , GADAU J. , BEUKEBOOM L. W.
Published: May 2008

The parasitic wasp Nasonia vitripennis has been used extensively in sex allocation research. Although laboratory experiments have largely confirmed predictions of local mate competition (LMC) theory, the underlying assumptions of LMC models have hardly been explored in nature. We genotyped over 3500 individuals from two distant locations (in the Netherlands and Germany) at four polymorphic microsatellite loci to validate key assumptions of LMC theory, in terms of both the original models and more recent extensions to them. We estimated the number of females contributing eggs to patches of hosts and the clutch sizes as well as sex ratios produced by individual foundresses. In addition, we evaluated the level of inbreeding and population differentiation. Foundress numbers ranged from 1 to 7 (average 3.0 ± 0.46 SE). Foundresses were randomly distributed across the patches and across hosts within patches, with few parasitizing more than one patch. Of the hosts, 40% were parasitized by more than one foundress. Clutch sizes of individual foundresses (average 9.99 ± 0.51 SE) varied considerably between hosts. The time period during which offspring continued to emerge from a patch or host correlated strongly with foundress number, indicating that sequential rather than simultaneous parasitism is the more common. Genetic differentiation at the regional level between Germany and the Netherlands, as estimated by Slatkin's private allele method (0.11) and Hedrick's corrected G′LT (0.23), indicates significant substructuring between regions. The level of population inbreeding for the two localities (FIL = 0.168) fitted the expectation based on the average foundress number per patch.
Selection for reproductive ability in Globodera pallida populations in relation to quantitative resistance from Solanum vernei and S. tuberosum ssp. andigena CPC2802
Authors: Phillips M. S. , Blok V. C.
Published: May 2008

Four field populations of the nematode Globodera pallida were subjected to selection pressure for increased reproductive ability by rearing sub‐populations continuously on four partially resistant potato genotypes for 12 generations. The resistance was derived from either Solanum vernei or from S. tuberosum spp. andigena CPC2802. After the 12th generation the original and sub‐populations of nematodes were assessed for their reproductive ability on a susceptible genotype and on each of the partially resistant genotypes. Selection pressure was shown to have increased reproductive ability but the increases were specific to the source of resistance used. The average increase on the ex S. vernei clones was from 11% reproduction by the unselected populations to 35·5% reproduction after selection. On the clones derived from CPC2802, which had higher levels of resistance, the increases were larger with an average of 6·6% reproduction for the unselected but 47·4% reproduction after selection. The response to selection differed amongst the initial field populations with some rates of reproduction increased to as much as 79%. A RAPD based analysis of the original and sub‐populations after selection indicated small but consistent changes in the genetic structure, which could have been a result of the selection pressure per se and/or the bottlenecks that the populations had gone though.
Molecular characterization of the CP gene and 3′UTR of Chilli veinal mottle virus from South and Southeast Asia
Authors: Tsai W. S. , Huang Y. C. , Zhang D. Y. , Reddy K. , Hidayat S. H. , Srithongchai W. , Green S. K. , Jan F. ‐J.
Published: May 2008

Twenty‐four isolates of Chilli veinal mottle virus (ChiVMV) from China, India, Indonesia, Taiwan and Thailand were analysed to determine their genetic relatedness. Pathogenicity of virus isolates was confirmed by induction of systemic mosaic and/or necrotic ringspot symptoms on Capsicum annuum after mechanical inoculation. The 3′ terminal sequences of the viral genomic RNA were determined. The coat protein (CP) coding regions ranged from 858 to 864 nucleotides and the 3′ untranslated regions (3′UTR) from 275 to 289 nucleotides in length. All isolates had the inverted repeat sequence GUGGNNNCCAC in the 3′UTR. The DAG motif, conserved in aphid‐transmitted potyviruses, was observed in all isolates. All 24 isolates were considered as belonging to ChiVMV because of their high CP amino acid and nucleotide identity (more than 94·8 and 89·5%, respectively) with the reported ChiVMV isolates including the pepper vein banding virus (PVBV), the chilli vein‐banding mottle virus (CVbMV) and the CVbMV Chiengmai isolate (CVbMV‐CM1). Based on phylogenetic analysis, ChiVMV isolates including all 24 isolates tested, PVBV, CVbMV and CVbMV‐CM1 can be classified into three groups. In addition, a conserved region of 204 amino acids with more than 90·2% identity was identified in the C terminal of the CP gene of ChiVMV and Pepper veinal mottle virus (PVMV), and may explain the serological cross reaction between these two viruses. The conserved region may also provide useful information for developing transgenic resistance to both ChiVMV and PVMV.
Virulence characteristics of apple scab (Venturia inaequalis) isolates from monoculture and mixed orchards
Authors: Barbara D. J. , Roberts A. L. , Xu X.‐M.
Published: May 2008

Isolates ofVenturia inaequaliswere sampled from monoculture and mixed orchards of three apple cultivars: Bramley, Cox and Worcester. In addition, single‐ascospore progeny isolates were obtained from three crosses between pairs of isolates originating from the three cultivars in monoculture orchards. These field isolates and single‐ascospore progenies were inoculated onto each of the three cultivars in a glasshouse. The patterns of infection showed that all three cultivars, commonly regarded as susceptible to scab, contained some specific resistance factors and that scab isolates from both mixed and monoculture orchards appeared to have co‐evolved with cultivars. A much higher proportion of isolates from cv. Worcester in the mixed orchard were unable to infect any of the three cultivars than isolates from any other combination of cultivar and orchard type, but there was no other difference between isolates from mixed vs. monoculture orchards. Many isolates could infect both Bramley and Cox, or Cox and Worcester; but only a single isolate could infect both Bramley and Worcester. Results from the testing of 61 single‐ascospore progeny isolates suggested that virulence towards Bramley, Cox and Worcester was controlled by at least one, two and three factors, respectively. Moreover, the exact nature of the interactions between these factors in determining virulence depended on the particular pair of isolates concerned.
A family of GHF5 endo‐1,4‐beta‐glucanases in the migratory plant‐parasitic nematodeRadopholus similis
Authors: Haegeman A. , Jacob J. , Vanholme B. , Kyndt T. , Gheysen G.
Published: May 2008

Endo‐1,4‐beta‐glucanases, which can degrade cellulose, have been identified in a number of plant‐parasitic nematodes, mainly sedentary endoparasites. This study reports the discovery of four different endoglucanases of glycosyl hydrolase family 5 (GHF5) in the migratory endoparasitic nematodeRadopholus similis. Spatial expression of the corresponding genes was analysed byin situhybridization, which showed the presence of transcripts in the pharyngeal gland cells. A semi‐quantitative RT‐PCR on different developmental stages was performed to study the temporal expression pattern. Three of the endoglucanase genes showed reduced expression in adult males compared with that in females. This could be explained by the fact that males do not feed and are considered non‐parasitic. Only one of the endoglucanase genes was expressed in juveniles. The four corresponding proteins had a putative signal peptide for secretion and a catalytic domain. Two of the proteins had an additional linker and carbohydrate‐binding module (CBM). Modelling of the catalytic domain resulted in the α/β‐barrel typical for GHF5 endoglucanases. Mapping the conserved amino acids of the four endoglucanases onto the 3D structure revealed that most were positioned near the catalytic centre of the protein, whereas less conserved amino acids occurred more often in the alpha helices, pointing towards the outside of the protein. Analyses of guanine/cytosine (GC) contents and codon adaptation indices indicated that the endoglucanase genes were well adapted to the codon usage ofR. similis. The GC and GC3 (GC content of the third position of the codons) contents of the endoglucanases were significantly higher than the average for allRadopholusESTs (expressed sequence tags).
A novel role for oleosins in freezing tolerance of oilseeds in Arabidopsis thaliana
Authors: Shimada Takashi L. , Shimada Tomoo , Takahashi Hideyuki , Fukao Yoichiro , Hara‐Nishimura Ikuko
Published: May 2008

Oil bodies in seeds of higher plants are surrounded with oleosins. Here we demonstrate a novel role for oleosins in protecting oilseeds against freeze/thaw‐induced damage of their cells. We detected four oleosins in oil bodies isolated from seeds of Arabidopsis thaliana, and designated them OLE1, OLE2, OLE3 and OLE4 in decreasing order of abundance in the seeds. For reverse genetics, we isolated oleosin‐deficient mutants (ole1, ole2, ole3 and ole4) and generated three double mutants (ole1 ole2, ole1 ole3 and ole2 ole3). Electron microscopy showed an inverse relationship between oil body sizes and total oleosin levels. The double mutant ole1 ole2, which had the lowest levels of oleosins, had irregular enlarged oil‐containing structures throughout the seed cells. Germination rates were positively associated with oleosin levels, suggesting that defects in germination are related to the expansion of oil bodies due to oleosin deficiency. We found that freezing followed by imbibition at 4°C abolished seed germination of single mutants (ole1, ole2 and ole3), which germinated normally without freezing treatment. The treatment accelerated the fusion of oil bodies and the abnormal‐positioning and deformation of nuclei in ole1 seeds, which caused seed mortality. In contrast, ole1 seeds that had undergone freezing treatment germinated normally when incubated at 22°C instead of 4°C, because degradation of oils abolished the acceleration of fusion of oil bodies during imbibition. Taken together, our findings suggest that oleosins increase the viability of over‐wintering oilseeds by preventing abnormal fusion of oil bodies during imbibition in the spring.
Advances in the field of cannabinoid–opioid cross‐talk
Authors: Robledo Patricia , Berrendero Fernando , Ozaita Andrés , Maldonado Rafael
Published: May 2008

A remarkable amount of literature has been generated demonstrating the functional similarities between the endogenous opioid and cannabinoid systems. Anatomical, biochemical and molecular data support the existence of reciprocal interactions between these two systems related to several pharmacological responses including reward, cognitive effects, and the development of tolerance and dependence. However, the assessment of the bidirectionality of these effects has been difficult due to their variety and complexity. Reciprocal interactions have been well established for the development of physical dependence. Cross‐tolerance and cross‐sensitization, although not always bidirectional, are also supported by a number of evidence, while less data have been gathered regarding the relationship of these systems in cognition and emotion. Nevertheless, the most recent advances in cannabinoid–opioid cross‐modulation have been made in the area of drug craving and relapse processes. The present review is focused on the latest developments in the cannabinoid–opioid cross‐modulation of their behavioural effects and the possible neurobiological substrates involved.
Discrimination of Variation in a Male Signaling Trait Affects Detection Time in Visual Predators
Authors: Roberts J. Andrew , Uetz George W.
Published: May 2008

In many species, expression of elaborate male characteristics likely represents a balance between sexual selection and natural selection via predation, as male traits selected to elicit rapid detection or response on the part of females also increase detection by predators. Predation costs are frequently inferred, but the underlying mechanisms associated with specific traits have rarely been directly explored. Males of the wolf spiderSchizocosa ocreata(Araneae: Lycosidae) exhibit a sexually selected signaling trait (dark tufts of bristles) on their forelegs, and are sympatric with a number of visually hunting generalist predators, including cannibalistic conspecifics, that may impact spider survival. Here we use latency of orientation response of the American toad,Bufo americanus(Anura: Bufonidae), to video, ‘virtual’ courtingS. ocreatamale stimuli as an index of predator detection, and latency of orientation response of femaleS. ocreatato the same stimuli as an index of conspecific detection. When compared with stimuli representing the population average, elimination of the signal trait had no significant effect on predator detection but did increase latency to orient in conspecifics. Increasing the size of the signal trait had no effect on conspecific detection but did significantly reduce latency to orient for predatory toads. Results clearly indicate that for a courting male spider of a given size and vigor level, variation in the expression of a secondary sexual characteristic alone can incur differential direct costs and benefits by influencing latency of orientation to visual signals by predators and conspecifics.
Do Hosts Discriminate between Sexually Dichromatic Male and Female Brown‐headed Cowbirds?
Authors: Gill Sharon A. , Neudorf Diane L. H. , Sealy Spencer G.
Published: May 2008

Female brood parasites are recognized as threats to reproductive success by many host species. Male brood parasites may accompany females while they search for nests to parasitize and males depredate nests throughout the nesting cycle. Hence, selection may also favour recognition of males. We examined whether two common host species perceive male brown‐headed cowbirds (Molothrus ater) as brood parasites, as nest predators, or neither. We quantified visits of male cowbirds to nests of yellow warblers (Dendroica petechia) and red‐winged blackbirds (Ageliaus phoeniceus) to assess the frequency with which these host species interact with male cowbirds. Males were observed near nests during hosts’ laying and incubating stages, although less frequently than female cowbirds. No visits by cowbirds occurred while parents cared for nestlings. We then presented models of male and female cowbirds plus a non‐threatening control to yellow warblers and red‐winged blackbirds during laying and nestling periods. If hosts perceive males and females similarly, they should respond more intensely to the cowbird models during the laying period, when nests are most likely to be parasitized. Both species responded similarly to male and female cowbird models during laying, which suggests that hosts view cowbirds of both sexes as threats. The responses of yellow warblers with nestlings to male cowbirds were strongly influenced by the order of model presentation. Warblers first presented with the male cowbird gave much reduced anti‐parasite responses than those that first interacted with the female then the male cowbird. These results suggest that yellow warblers recognized male vs. female cowbirds, but that discrimination was not expressed during laying. By contrast, red‐winged blackbirds did not discriminate between male and female cowbirds at either nesting stage.
Inter‐Mount Social Interactions During Heterosexual and Homosexual Consortships in Japanese Macaques
Authors: Vasey Paul L. , VanderLaan Doug P. , Rains Derek , Duckworth Nadine , Kovacovsky Stefani D.
Published: May 2008

In this study, we examined whether female Japanese macaques (Macaca fuscata) exhibited male‐typical patterns of inter‐mountsocialbehaviour during homosexual consortships. Data were collected on heterosexual and homosexual consortships from a population of free‐ranging Japanese macaques in Arashiyama, Japan. Inter‐mount intervals were defined as the period between two consecutive mounts. A total of 3374 heterosexual inter‐mount intervals and 1412 homosexual inter‐mount intervals were analysed. We examined nine different categories of inter‐mount behaviour. Sex differences between heterosexually consorting males and females existed for three of the inter‐mount behaviours we examined (i.e. ventral‐to‐dorsal orientation, aggression directed toward third party individuals, tree‐shaking displays). The subordinate female partners in homosexually consorting pairs exhibited some sex‐atypical inter‐mount behaviours. This sex‐atypicality did not appear to reflect generalized developmental canalization in the direction of a male‐typical suite of behaviours. Rather, the observed behavioural sex‐atypicality could be best explained in terms of the unique alliance‐related dynamics that characterized homosexual consortships in Japanese macaques.
Does Competition for Clients Increase Service Quality in Cleaning Gobies?
Authors: Soares Marta C. , Bshary Redouan , Cardoso Sónia C. , Côté Isabelle M.
Published: May 2008

In a biological market, members of one trading class try to outbid each other to gain access to the most valuable partners. Competition within class can thus force individuals to trade goods or services more cheaply, ultimately resulting in conflict (e.g. cheating) over the value of commodities. Cleaning symbioses among fish appear to be good examples of biological markets. However, the existence and effect of outbidding competition among either types of traders (cleaners or clients) have never been tested. We examined whether increasing competition among cleaning gobies (Elacatinusspp.) for access to clients results in outbidding in the form of provision of a better cleaning service. On reefs where fish clients visited cleaning stations less frequently, and thus competition among cleaners was higher, cleaning gobies ingested fewer scales relative to the number of ingested parasites, i.e. they cleaned more honestly. This shift in cleaner behaviour towards greater honesty is consistent with a greater market value of access to clients in the face of competition among cleaners. However, this pattern could have also arisen as a result of differences in ectoparasite availability across reefs and therefore in value of the commodity offered by clients. Experimental manipulations will be required to determine whether cleaning service quality by cleaning gobies was enhanced solely because of competitive outbidding.
Innate and Learned Colour Preference in the Zebrafish,Danio rerio
Authors: Spence Rowena , Smith Carl
Published: May 2008

Receiver biases towards specific sensory signals have been demonstrated in insects, birds and fish, both in the context of foraging and mate choice. In some cases, signals important in sexual selection appear to have evolved by exploiting a pre‐existing bias in the sensory system. For instance, female preferences for male nuptial colouration may have arisen from selection on foraging practices. Using the zebrafish (Danio rerio), a species in which red is not a factor in mate choice, we tested for a foraging bias towards the colour red. We further investigated the plasticity of foraging biases by raising groups of fish on diets consisting solely of red, blue, green or white food. When we subsequently tested their colour preferences in a foraging context, each group responded most strongly to red, irrespective of the colour of food with which they had been conditioned. We also detected a significant effect of conditioning on colour preferences; fish responded more strongly to the colour that matched diet colour than to other colours. The observed receiver bias towards red may have evolved as an adaptive preference for carotenoid compounds in their diet. While the bias to red appears to be innate, our results indicate that learning is also important in shaping foraging biases.
Efficiency of alternative MCMC strategies illustrated using the reaction norm model
Authors: Shariati M. , Sorensen D.
Published: May 2008

The Markov chain Monte Carlo (MCMC) strategy provides remarkable flexibility for fitting complex hierarchical models. However, when parameters are highly correlated in their posterior distributions and their number is large, a particular MCMC algorithm may perform poorly and the resulting inferences may be affected. The objective of this study was to compare the efficiency (in terms of the asymptotic variance of features of posterior distributions of chosen parameters, and in terms of computing cost) of six MCMC strategies to sample parameters using simulated data generated with a reaction norm model with unknown covariates as an example. The six strategies are single‐site Gibbs updates (SG), single‐site Gibbs sampler for updating transformed (a prioriindependent) additive genetic values (TSG), pairwise Gibbs updates (PG), blocked (all location parameters are updated jointly) Gibbs updates (BG), Langevin‐Hastings (LH) proposals, and finally Langevin‐Hastings proposals for updating transformed additive genetic values (TLH). The ranking of the methods in terms of asymptotic variance is affected by the degree of the correlation structure of the data and by the true values of the parameters, and no method comes out as an overall winner across all parameters. TSG and BG show very good performance in terms of asymptotic variance especially when the posterior correlation between genetic effects is high. In terms of computing cost, TSG performs best except for dispersion parameters in the low correlation scenario where SG was the best strategy. The two LH proposals could not compete with any of the Gibbs sampling algorithms. In this study it was not possible to find an MCMC strategy that performs optimally across the range of target distributions and across all possible values of parameters. However, when the posterior correlation between parameters is high, TSG, BG and even PG show better mixing than SG.
Development of multiplex PCR markers to distinguish evergreen and deciduous azaleas
Authors: Mizuta D. , Nakatsuka A. , Kobayashi N.
Published: May 2008

We successfully developed new PCR‐based markers for analysing the DNA inheritance patterns of vigorous inter‐subgeneric hybrids of azalea. The hybrids were between evergreen azaleas (Rhododendron nakaharae and its hybrids) and fragrant deciduous azaleas (Rhododendron arborescens and Rhododendron viscosum). We determined the sequence of the nuclear internal transcribed spacer (ITS) region in evergreen and deciduous azaleas, and found a deletion of five base pairs (bp) in evergreen azaleas compared with deciduous azaleas. Sequences for the chloroplast matK‐trnK region were obtained from GenBank. Primers for the multiplex PCRs were designed using these sequence data. In the multiplex PCR of the ITS region, evergreen azaleas showed a specific band of 140 bp and deciduous azaleas showed a specific band of 800 bp. In the multiplex PCR of the matK‐trnK region, evergreen azaleas showed a specific band of 560 bp and deciduous azaleas showed a specific band of 300 bp. These results indicate that multiplex PCR methods are useful to distinguish evergreen and deciduous azaleas easily and rapidly.
Top‐cross vs. poly‐cross as alternative to test‐cross for estimating the general combining ability in potato
Authors: Gopal J. , Kumar V. , Luthra S. K.
Published: May 2008

Test‐crosses for estimating combining ability in potato although useful are difficult to make being labour intensive and time consuming, and due to the problem of sterility. The objective of the present study was to test methods for estimating general combining ability (GCA) of parents based on fewer matings. The GCA of 12 females estimated based on matings with specific single testers (top‐cross) and three types of bulk pollen (poly‐cross) were compared with those estimated by 72 (12 × 6) test‐crosses, using common testers in three types of matings. The study was conducted for 2 years at each of the two locations representing short‐days subtropical conditions in plains and long‐days temperate conditions in hills of India. Analysis of variance of test‐crosses showed that both general and specific combining ability effects were important for tuber yield, late blight resistance as well as general impression, the characters studied. Correlation coefficients among three types of matings showed that bulk pollen matings had poor effectiveness in predicting the GCA of the females, whereas matings with selected individual testers resulted in GCA estimates similar to those based on six testers. Thus use of top‐cross involving selected tester could substantially reduce the number of matings required for estimating the GCA. Among the six testers used, the tester CFK69.1 could estimate the GCA of the females with reasonably high accuracy both for tuber yield and general impression, and ‘Tobique’ for reaction to late blight.
Microspore mutagenesis of Brassica species for fatty acid modifications: a preliminary evaluation
Authors: Ferrie A. M. R. , Taylor D. C. , MacKenzie S. L. , Rakow G. , Raney J. P. , Keller W. A.
Published: May 2008

A microspore mutagenesis protocol was developed for Brassica rapa, Brassica napus and Brassica juncea for the production of double haploid lines with novel fatty acid profiles in the seed oil. Freshly isolated Brassica microspores were first cultured with ethyl methane sulphonate (EMS) for 1.5 h. The EMS was removed and the microspores were then cultured according to the standard Brassica microspore culture protocol. This protocol was used to generate over 80 000 Brassica haploid/double haploid plants. Field evaluation of B. napus and B. juncea double haploids was conducted between 2000 and 2003. Fatty acid analysis of the B. napus double haploid lines showed that saturated fatty acid proportions ranged from 5.0% to 7.7%. For B. juncea, saturate proportions ranged from 5.4% to 9.5%. Of the 7000 B. rapa lines that were analysed, 197 lines had elevated oleic acid (>55%), 69 lines had reduced α‐linolenic acid (<8%) and 157 lines had low saturated fatty acid proportions (<5%), when compared with the parental lines.