bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic quality influences fertility in Gombe chimpanzees
Authors: Jones James Holland , Wilson Michael L. , Murray Carson , Pusey Anne 
Published: April 2010

Summary 1. Fertility is an important fitness component, but is difficult to measure in slowly reproducing, long‐lived animals such as chimpanzees (Pan troglodytes). 2. We measured fertility and the effect of measured covariates on fertility in a 43‐year sample of birth intervals of chimpanzees from the Gombe National Park, Tanzania using Cox proportional hazards regression with individual‐level random effects. 3. The birth hazard declined with mothers’ age at a rate of 0·84 per year following age at first reproduction. This value is somewhat stronger than previous estimates. 4. Loss of the infant that opened the birth interval increased the birth hazard 134‐fold. 5. Birth intervals following the first complete birth interval were shorter than this first interval, while sex of the previous infant had no significant effect. 6. Maternal dominance rank was significant at the P < 0·1 level when coded as high/middle/low but was highly significant when we simply considered high rank vs. others. 7. Individual heterogeneity had a substantial impact on birth interval duration. We interpret this individual effect as a measure of phenotypic quality, controlling for the measured covariates such as dominance rank. This interpretation is supported by the correlation of individual heterogeneity scores with similar independent measures of body mass.
WRKY72‐type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene‐for‐gene resistance mediated by the tomato R gene Mi‐1
Authors: Bhattarai Kishor K. , Atamian Hagop S. , Kaloshian Isgouhi , Eulgem Thomas 
Published: April 2010

SummaryWRKY transcription factors play a central role in transcriptional reprogramming associated with plant immune responses. However, due to functional redundancy, typically the contribution of individual members of this family to immunity is only subtle. Using microarray analysis, we found that the paralogous tomato WRKY genes SlWRKY72a and b are transcriptionally up‐regulated during disease resistance mediated by the R gene Mi‐1. Virus‐induced gene silencing of these two genes in tomato resulted in a clear reduction of Mi‐1‐mediated resistance as well as basal defense against root‐knot nematodes (RKN) and potato aphids. Using Arabidopsis T‐DNA insertion mutants, we found that their Arabidopsis ortholog, AtWRKY72, is also required for full basal defense against RKN as well as to the oomycete Hyaloperonospora arabidopsidis. Despite their similar roles in basal defense against RKN in both tested plant species, WRKY72‐type transcription factors in tomato, but not in Arabidopsis, clearly contributed to basal defense against the bacterial pathogen Pseudomonas syringae. Of the five R genes that we tested in tomato and Arabidopsis, only Mi‐1 appeared to be dependent on WRKY72‐type transcription factors. Interestingly, AtWRKY72 target genes, identified by microarray analysis of H. arabidopsidis‐triggered transcriptional changes, appear to be largely non‐responsive to analogs of the defense hormone salicylic acid (SA). Thus, similarly to Mi‐1, which in part acts independently of SA, AtWRKY72 appears to utilize SA‐independent defense mechanisms. We propose that WRKY72‐type transcription factors play a partially conserved role in basal defense in tomato and Arabidopsis, a function that has been recruited to serve Mi‐1‐dependent immunity.
A HECT E3 ubiquitin ligase negatively regulates Arabidopsis leaf senescence through degradation of the transcription factor WRKY53
Authors: Miao Ying , Zentgraf Ulrike 
Published: April 2010

SummaryWRKY transcription factors play a central role in controlling leaf senescence in Arabidopsis. One important member, WRKY53, is tightly regulated by various mechanisms, and is a convergence node between senescence and pathogen responses. Using WRKY53 in a yeast two‐hybrid screen, we isolated the HECT domain E3 ubiquitin ligase UPL5. In contrast to mammals, Arabidopsis contains only seven HECT E3 ubiquitin ligases, whose targets and functions are largely unknown. In yeast cells, UPL5 interacts with WRKY53 via its leucine zipper domain, and this interaction was confirmed in the cytoplasm of plant cells by a bimolecular fluorescence complementation assay. UPL5 was able to use the WRKY53 protein as a substrate for polyubiquitination in an in vitro system, and induction of UPL5 expression by an ethanol‐inducible system in upl5 plants led to degradation of the WRKY53 protein. Expression of both genes is regulated antagonistically in response to hydrogen peroxide, jasmonic acid and plant development. Two T‐DNA insertion lines (upl5‐1 and upl5‐2) showed the same senescence phenotype as WRKY53 over‐expressers. Over‐expression of WRKY53 in the upl5 background enhanced the accelerated senescence phenotype of WRKY53 over‐expressers. Therefore, we conclude that UPL5 regulates leaf senescence in Arabidopsis through degradation of WRKY53 and ensures that senescence is executed in the correct time frame.
BROTHER OF FT AND TFL1(BFT) hasTFL1‐like activity and functions redundantly withTFL1in inflorescence meristem development in Arabidopsis
Authors: Yoo Seong Jeon , Chung Kyung Sook , Jung Seung Hye , Yoo So Yeon , Lee Jong Seob , Ahn Ji Hoon 
Published: April 2010

SummaryTheFLOWERING LOCUS T(FT)/TERMINAL FLOWER 1(TFL1) family is a small gene family that encodes important regulators that control flower development in Arabidopsis. Here, we investigated the biological role of the product ofBROTHER OF FT AND TFL1(BFT), a member of this family, whose function remains unknown. Comparison of the critical residues that play a role in distinguishingFT‐ orTFL1‐like activity revealed thatBFTis more similar toFT. Similar toFTexpression,BFTexpression showed a diurnal oscillation pattern, peaking in the evening.In situhybridization revealedBFTexpression in the shoot apical meristem, young leaf and axillary inflorescence meristem. Transgenic plants over‐expressingBFTexhibited delayed flowering and severe floral defects (floral indeterminacy and compact inflorescences surrounded by serrate leaves), similar to35S::TFL1plants.LEAFY(LFY) andAPETALA1(AP1) expression was significantly reduced in35S::BFTplants.BFTover‐expression failed to rescue the terminal flower phenotype oftfl1mutants; however, it delayed both terminal flower formation in the primary inflorescence and axillary inflorescence development in thetfl1mutant background. Consistent with this, the loss‐of‐functionBFTalleles,bft‐2and anBFTRNAi line, accelerated termination of the primary inflorescence and formation of axillary inflorescences in thetfl1mutant background. Taken together, our results suggest that, despite similarities in the critical residues of BFT and FT,BFTpossesses aTFL1‐like activity and functions redundantly withTFL1in inflorescence meristem development, and possibly contributes to the regulation of plant architecture.
Mandibulofacial dysostosis, microtia, and limb anomalies in a newborn: a new form of acrofacial dysostosis syndrome?
Authors: Zhang Y , Dai Y , Liu Y , Ren J 
Published: April 2010

Zhang Y, Dai Y, Liu Y, Ren J. Mandibulofacial dysostosis, microtia, and limb anomalies in a newborn: a new form of acrofacial dysostosis syndrome?The acrofacial dysostoses (AFDs) are a heterogeneous group of disorders involving craniofacial dysostosis and limb anomalies. Depending on the type of limb defects, two major groups have been defined: Nager syndrome with predominant preaxial anomalies and Miller syndrome with postaxial malformations. Genomic copy number variation, a common type of genomic variability, can influence gene expression by disrupting coding sequences, perturbing long‐range gene regulation, or altering gene dosage, and these effects could contribute to phenotypic variations or disease risk. We present a distinct AFD case with mandibulofacial dysostosis, microtia and limb malformations but without limb defects, which may represent a new form of AFD. To investigate the etiology of the phenotype, whole genomic high‐resolution array comparative genomic hybridization analysis was carried out, revealing two cryptic duplications, 1p36.33 and 1q21.3‐q22 duplications. Two genes, VWA1 and PYGO2, contained in the two duplications, respectively, are likely to be the candidate genes for the phenotype of our patient.
The Complete Genome Sequence of Two Isolates of Southern rice black‐streaked dwarf virus, a New Member of the Genus Fijivirus
Authors: Wang Qiang , Yang Jian , Zhou Guo‐Hui , Zhang Heng‐Mu , Chen Jian‐Ping , Adams Michael J. 
Published: April 2010

AbstractThe nucleotide sequences of genomic segments S1–S8 and S1–S6, respectively, of the Hainan (HN) and Guangdong (GD) isolates of a rice‐infecting fijivirus were determined, completing the genome sequences of these isolates. The isolates were most closely related to Rice black‐streaked dwarf virus (RBSDV): S1, S2 and S10 were most conserved with identities of 78.5–79.2% nt (83.4–89.0% aa) while S5 and S6 were the least conserved with 70.6–71.6% nt (63.1–69.9% aa) identity. Whole genome comparisons and phylogenetic analyses supported suggestions that the isolates represent a new species within the genus Fijivirus, family Reoviridae. Of the two names previously suggested for this virus, Southern rice black‐streaked dwarf virus is preferred.
Medical mushrooms used for biochemical failure after radical treatment for prostate cancer: An open‐label study
Authors: Yoshimura Koji , Kamoto Toshiyuki , Ogawa Osamu , Matsui Shigeyuki , Tsuchiya Norihiko , Tada Harue , Murata Keiko , Yoshimura Kenichi , Habuchi Tomonori , Fukushima Masanori 
Published: April 2010

Objective:  The aim of this study was to assess the efficacy and safety of two different types of medical mushrooms in patients with prostate cancer in Japan.Methods:  Patients with biochemical failure after radical treatment for non‐metastasized prostate cancer were enrolled in this open‐label study. For 6 months they ingested one of the two following supplements: Senseiro, containing extracts from the Agaricus blazei Murill mushroom; and Rokkaku Reishi, containing the Ganoderma lucidum mushroom. Levels of serum prostate‐specific antigen (PSA) level and PSA doubling time were examined before and after study entry to assess the impact of these supplements on disease progression. The primary end‐point of this study was partial response rate (50% or more decrease of serum PSA). Hormonal status, represented by serum testosterone levels, and toxicity were also assessed.Results:  A total of 51 patients were enrolled following radical prostatectomy. Forty‐seven completed the protocol and could be assessed. Thirty‐two patients received Senseiro and the remaining 15 received Rokkaku Reishi. No partial response in terms of PSA was observed. Alteration of PSA doubling time did not correlate with that of serum testosterone levels. Serious adverse effects were not observed.Conclusions:  No significant anticancer effects were observed with the intake of these two medical mushrooms.
Evaluating model transferability for a threatened species to adjacent areas: Implications for rock‐wallaby conservation
Authors: MURRAY J. V. , LOW CHOY S. , MCALPINE C. A. , POSSINGHAM H. P. , GOLDIZEN A. W. 
Published: April 2010

AbstractWhen modelling the distribution of a species, it is often not possible to comprehensively sample the whole distribution of the species and managers may have habitat models based on data from one area that they want to apply in other areas. Hence, an important question is: how accurate are models of the distributions of species when applied beyond the areas where they were developed? A first step in measuring model transferability could be testing models in adjacent areas. We predicted the habitat associations of the brush‐tailed rock‐wallaby (Petrogale penicillata) across two spatial scales in two neighbouring study areas in eastern Australia, south‐east Queensland and north‐east New South Wales. We used classification trees for exploratory data analysis of habitat relationships and then applied logistic regression models to predict species occurrence. We assessed the within‐area discriminative ability of the habitat models using cross‐validation and threshold plots, and tested the predictive ability of the models for adjacent areas using the receiver operating characteristic statistic to determine the area under the curve. We found that models performed well within an area and extrapolating them to adjacent areas resulted in good predictive performance at the site scale but substantially poorer predictive performance at the landscape scale. We conclude that distribution models for wildlife species should only be extrapolated to neighbouring areas with caution when using landscape‐scale environmental variables. Alternatively, only key habitat associations predicted by the models at this scale should be transferred across adjacent areas once verified against local knowledge of the ecology of the study species.
Fire refugia: The mechanism governing animal survivorship within a highly flammable plant
Authors: BRENNAN KARL E. C. , MOIR MELINDA L. , WITTKUHN ROY S. 
Published: April 2010

AbstractIdentifying factors that influence the survival of individuals during disturbance is critical to understanding patterns of species reassembly within ecological communities. Although most studies of recovery of populations post‐burning acknowledge the potentially important contribution of animals surviving in situ, few have measured the effectiveness of refugia. This paper tests the hypothesis that some plants with tightly packed leaf‐bases provide a refuge for invertebrates during fire (even when the plants themselves burn) by using the highly flammable grass tree (Xanthorrhoeaceae: Xanthorrhoea). Invertebrates were sampled from four unburnt and five experimentally burnt grass trees (Xanthorrhoea preissii Endl.). Also collected were invertebrates fleeing during burning. The dataset comprises 949 specimens, representing 81 species from 18 orders, of which 749 individuals were from unburned plants. Slaters (Isopoda), silverfish (Thysanura), spiders (Araneae) and bugs (Hemiptera) dominated assemblages of the unburnt grass trees. Despite grass trees burning at temperatures of up to 515°C, some invertebrates survived in situ. Species‐specific microhabitat preferences within the plant appeared to influence survivorship. Species collected in the crown of unburned plants were found more often alive on burnt plants than species typically inhabiting the dead skirt of decaying leaves (thatch). We contend that the mechanism causing differential mortality is fire temperature. In the dead skirt, temperatures reached 225.33 ± 66.57°C. In contrast, a region of mild temperature (25.00 ± 3.54°C) persisted throughout burning near the apical meristem (within the crown). We conclude that grass trees are a potential reservoir from which invertebrates might re‐colonize recently burnt areas. However, owing to species‐specific microhabitat preferences and differential mortality across microhabitats, the invertebrate assemblage remaining in situ will be restricted taxonomically compared with the original grass tree fauna. Moreover, different fire regimes might mediate the effectiveness of grass trees as refugia. Finally, we argue that in situ survival of invertebrates within plants with tightly packed leaf‐bases is an unrecognized global phenomenon applicable to a wide array of plant taxa.
Effects of forest fragment management on vegetation condition and maintenance of canopy composition in a New Zealand pastoral landscape
Authors: BURNS B. R. , FLOYD C. G. , SMALE M. C. , ARNOLD G. C. 
Published: April 2010

AbstractResidual forest fragments in areas dominated by pastoral agriculture can have high value for biodiversity conservation but are still subject to ongoing degradation as (i) processes initiated by fragmentation continue to operate, for example, changes in canopy replacement probabilities; and (ii) deleterious processes impinge upon them from the surrounding matrix, for example, browsing and trampling by vagrant livestock. Responses by management to slow or reverse these processes require evaluation. Stock (mainly cattle and sheep) exclusion by fencing and mammal pest (mainly Trichosurus vulpecula (brushtail possum)) control are currently used as management tools to maintain or improve the vegetation condition of fragments in New Zealand. We examined the effectiveness of these tools by sampling vegetation composition, forest structure and regeneration of woody species in 41 old‐growth fragments dominated by Beilschmiedia tawa, selected to populate a factorial design that included four different fencing classes (unfenced, fenced 2–10, 10–20 and >20 years ago), with and without sustained mammal pest control. Fencing for more than 10 years led to higher abundances of native ground ferns and shrubs, and lower abundances and numbers of mostly adventive herbaceous ground cover species. In contrast, lianes were less abundant with mammal pest control, whereas herbs were more abundant. Fencing led to a high‐density pulse of seedlings and saplings of woody species within 10 years that then thinned. Mammal pest control allowed increases in abundance of some species palatable to T. vulpecula, and increased the ratio of canopy to subcanopy seedlings in the regeneration pulse caused by fencing. Neither treatment, however, led to the restoration of indigenous species richness to reference forest levels, nor allowed densities of juveniles of shade‐tolerant canopy species to establish to levels commensurate with replacement of existing canopy trees. Most woody seedlings that established following fencing were of short‐lived subcanopy species. These management actions will therefore slow but not reverse the long‐term degradation of these forest fragments, which will eventually differ substantially from continuous forest under current management regimes. Additional measures such as replanting may be necessary not only to ensure replacement of some current species but also to restore lost species.
Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture
Authors: Fazzini Roberto A. Bobadilla , Preto Maria J. , Quintas Ana C. Poucas , Bielecka Agata , Timmis Kenneth N. , dos Santos Vitor A. P. Martins 
Published: April 2010

SummaryThe high complexity of naturally occurring microbial communities is the major drawback limiting the study of these important biological systems. In this study, a comparison between pure cultures of Pseudomonas reinekei sp. strain MT1 and stable community cultures composed of MT1 plus the addition of Achromobacter xylosoxidans strain MT3 (in a steady‐state proportion 9:1) was used as a model system to study bacterial interactions that take place under simultaneous chemical and oxidative stress. Both are members of a real community isolated from a polluted sediment by enrichment in 4‐chlorosalicylate (4CS). The analysis of dynamic states was carried out at the proteome, metabolic profile and population dynamic level. Differential protein expression was evaluated under exposure to 4CS and high concentrations of toxic intermediates (4‐chlorocatechol and protoanemonin), including proteins from several functional groups and particularly enzymes of aromatic degradation pathways and outer membrane proteins. Remarkably, 4CS addition generated a strong oxidative stress response in pure strain MT1 culture led by alkyl hydroperoxide reductase, while the community showed an enhanced central metabolism response, where A. xylosoxidans MT3 helped to prevent toxic intermediate accumulation. A significant change in the outer membrane composition of P. reinekei MT1 was observed during the chemical stress caused by 4CS and in the presence of A. xylosoxidans MT3, highlighting the expression of the major outer membrane protein OprF, tightly correlated to 4CC concentration profile and its potential detoxification role.
Effects of temperature, nutrients, organic matter and coral mucus on the survival of the coral pathogen, Serratia marcescens PDL100
Authors: Looney Erin E. , Sutherland Kathryn P. , Lipp Erin K. 
Published: April 2010

Summary Serratia marcescens is an enteric bacterium that causes white pox disease in elkhorn coral, Acropora palmata; however, it remains unclear if the pathogenic strain has adapted to seawater or if it requires a host or reservoir for survival. To begin to address this fundamental issue, the persistence of strain PDL100 was compared among seawater and coral mucus microcosms. Median survival time across all conditions ranged from a low of 15 h in natural seawater [with a first‐order decay constant (k) = −0.173] at 30°C to a maximum of 120 h in glucose‐amended A. palmata mucus (k = −0.029) at 30°C. Among seawater and mucus microcosms, median survival time was significantly greater within Siderastrea siderea mucus compared with seawater or mucus of Montastraea faveolata or A. palmata (P < 0.0001). In seawater, the addition of phosphate and especially glucose resulted in significant improvements in survival (P < 0.001), while only the addition of glucose resulted in significant improvement in survival in A. palmata mucus (P < 0.0001). Increasing the temperature of seawater to 35°C resulted in a significantly slower decay than that observed at 30°C (P < 0.0001). The results of this study indicate that PDL100 is not well‐adapted to marine water; however, survival can be improved by increasing temperature, the availability of coral mucus from S. siderea and most notably the presence of dissolved organic carbon.
BLAME, MORAL STANDING AND THE LEGITIMACY OF THE CRIMINAL TRIAL
Authors: Duff R. A. 
Published: April 2010

AbstractI begin by discussing the ways in which a would‐be blamer's own prior conduct towards the person he seeks to blame can undermine his standing to blame her (to call her to account for her wrongdoing). This provides the basis for an examination of a particular kind of ‘bar to trial’ in the criminal law – of ways in which a state or a polity's right to put a defendant on trial can be undermined by the prior misconduct of the state or its officials. The examination of this often neglected legal phenomenon illuminates some central features of the criminal law and the criminal process, and some of the preconditions for the legitimacy of the criminal law in a liberal republic.
IN DEFENCE OF FICTIONAL INCOMPETENCE
Authors: Cavedon‐Taylor Dan 
Published: April 2010

AbstractThe claim that photographs are fictionally incompetent (i.e. that they can only depict those particulars they are appropriately causally related to) is argued by Noël Carroll, Gregory Currie, and Nigel Warburton to be falsified by cinematic works of fiction. In response I firstly argue that it does not follow from cinema's having a capacity for the representation of ficta that photography has a capacity for the representation of ficta. Secondly, and inspired by the work of Roger Scruton, I develop an account of how it is that cinema represents ficta on which this is fundamentally a matter of dramatic/theatrical representation. I argue that in cinematic fiction photography delivers a pre‐existent representation of ficta rather than creating or generating fictional content. With this being so, the claim that photography is fictionally incompetent is compatible with cinematic fiction.1