bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips
Authors: Wang Yonghong , Miao Ze-Hong , Pommier Yves , Kawasaki Ernest S. , Player Audrey 
Published: June 2007

Abstract
Motivation: For Affymetrix microarray platforms, gene expression is determined by computing the difference in signal intensities between perfect match (PM) and mismatch (MM) probesets. Although the use of PM is not controversial, MM probesets have been associated with variance and ultimately inaccurate gene expression calls. A principal focus of this study was to investigate the nature of the MM signal intensities and demonstrate its contribution to the experimental results.
Results: While most MM intensities were likely associated with random noise, a subset of ∼20% (99 485) of the MM probes displayed relatively high signal intensities to the corresponding PM probes (MM &gt; PM) in a non-random fashion; 13 440 of these probes demonstrated exceptionally high ‘outlier’ intensities. About 15 938 PM probes also demonstrated exceptionally high outlier intensities consistently across all hybridizations. About 92% of the MM &gt; PM probes had either a dThymidine (dT) or a dCytidine (dC) at the 13th position of the probe sequence. MM and PM probes displaying extremely high outlier intensities contained high dC rich nucleotides, and low dA contents at other nucleotides positions along the 25mer probe sequence. Differentially expressed genes generated using Genechip Operating System (GCOS) or modified PM-only methods were also examined. Of those candidate genes identified in the PM-only method, 157 of them were designated by GCOS as absent across all datasets and many others contained probes with MM &gt; PM signal intensities. Our data suggests that MM intensity from PM signal can be a major source of error analysis, leading to fewer potentially biologically important candidate genes.
Contact: wangyong@mail.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
Authors: Elo Laura L. , Järvenpää Henna , Orešič Matej , Lahesmaa Riitta , Aittokallio Tero 
Published: June 2007

Abstract
Motivation: Coexpression networks have recently emerged as a novel holistic approach to microarray data analysis and interpretation. Choosing an appropriate cutoff threshold, above which a gene–gene interaction is considered as relevant, is a critical task in most network-centric applications, especially when two or more networks are being compared.
Results: We demonstrate that the performance of traditional approaches, which are based on a pre-defined cutoff or significance level, can vary drastically depending on the type of data and application. Therefore, we introduce a systematic procedure for estimating a cutoff threshold of coexpression networks directly from their topological properties. Both synthetic and real datasets show clear benefits of our data-driven approach under various practical circumstances. In particular, the procedure provides a robust estimate of individual degree distributions, even from multiple microarray studies performed with different array platforms or experimental designs, which can be used to discriminate the corresponding phenotypes. Application to human T helper cell differentiation process provides useful insights into the components and interactions controlling this process, many of which would have remained unidentified on the basis of expression change alone. Moreover, several human–mouse orthologs showed conserved topological changes in both systems, suggesting their potential importance in the differentiation process.
Contact: laliel@utu.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
The tobacco Cel7 gene promoter is auxin‐responsive and locally induced in nematode feeding sites of heterologous plants
Authors: WANG XIAOHONG , REPLOGLE AMY , DAVIS ERIC L. , MITCHUM MELISSA G. 
Published: June 2007

SUMMARYEmerging evidence suggests that plant cell‐wall‐modifying enzymes induced by root‐parasitic nematodes play important roles in feeding cell formation. We previously identified a tobacco endo‐β‐1,4‐glucanase (cellulase) gene, NtCel7, that was strongly induced in both root‐knot and cyst nematode feeding cells. To characterize further the developmental and nematode‐responsive regulation of NtCel7, we isolated the NtCel7 promoter and analysed its expression over a time course of nematode infection and in response to auxin, gibberellin, ethylene and sucrose in soybean and tomato hairy roots and in Arabidopsis containing the NtCel7 promoter fused to the β‐glucuronidase (GUS) reporter gene. Histochemical analyses of transgenic plant materials revealed that the NtCel7 promoter exhibited a unique organ‐specific expression pattern during plant development suggestive of important roles for NtCel7 in both vegetative and reproductive growth. In all plant species tested, strong GUS expression was observed in root tips and lateral root primordia of uninfected roots with weaker expression in the root vasculature. Further analyses of transgenic Arabidopsis plants revealed expression in shoot and root meristems and the vasculature of most organs during plant development. We also determined that the NtCel7 promoter was induced by auxin, but not gibberellin, ethylene or sucrose. Moreover, strong GUS activity was observed in both cyst and root‐knot nematode‐induced feeding sites in transgenic roots of soybean, tomato and Arabidopsis. The conserved developmental and nematode‐responsive expression of the NtCel7 promoter in heterologous plants indicates that motifs of this regulatory element play a fundamental role in regulating NtCel7 gene expression within nematode feeding sites and that this regulation may be mediated by auxin.
Competitive index in mixed infections: a sensitive and accurate assay for the genetic analysis of Pseudomonas syringae–plant interactions
Authors: MACHO ALBERTO P. , ZUMAQUERO ADELA , ORTIZ‐MARTÍN INMACULADA , BEUZÓN CARMEN R. 
Published: June 2007

SUMMARYMixed infections have been broadly applied to the study of bacterial pathogens in animals. However, the application of mixed infection‐based methods in plant pathogens has been very limited. An important factor for this limitation is the different dynamics that mixed infections have been reported to show in the different types of models. Reports in systemic animal infections have shown that any bacterium has the same probability of multiplying within a mixed infection than in a single infection. However, in plant pathogens, bacterial growth in a mixed infection does not seem to reflect growth in a single infection, as growth interference takes place between the co‐inoculated strains. Here we show that growth interference in mixed infection between different Pseudomonas syringae strains is not intrinsic to growth within a plant host, but dependent on the dose of inoculation. We also show that the minimal inoculation dose required to avoid interference depends on the aggressiveness of the pathogen as well as the type of virulence factor that differentiates the co‐inoculated strains. This study establishes the basis for the use of mixed infection‐based applications to the study of phytopathogenic bacteria. Analysis of the virulence of a type III effector mutant and an hrp regulatory mutant illustrate the increased accuracy and sensitivity of competitive index assays vs. regular growth assays. Several applications of this assay are addressed, and potential implications for this and other mixed infection‐based methods are discussed.
The bifunctional effector AvrXccC of Xanthomonas campestris pv. campestris requires plasma membrane‐anchoring for host recognition
Authors: WANG LIFENG , TANG XIAOYAN , HE CHAOZU 
Published: June 2007

SUMMARYBacterial pathogens use type III secretion systems (TTSS) to deliver effector proteins into eukaryotic cells for pathogenesis. In bacterial–plant interactions, one effector may function as an avirulence factor to betray the pathogen to the plant surveillance system and induce the hypersensitive response (HR) in the resistant host carrying a corresponding resistance (R) gene. However, the same effector can also sustain the growth of the pathogen by acting as a virulence factor to modulate plant physiology in the susceptible host lacking the corresponding R gene. Here, we identified and characterized a bifunctional TTSS effector AvrXccC belonging to the AvrB effector family in Xanthomonas campestris pv. campestris 8004. This effector is required for full bacterial virulence in the susceptible host cabbage (Brassica oleracea) and avirulence in the resistant host mustard (Brassica napiformis L.H. Baily). Expressing avrXccC in mustard‐virulent strain Xcc HRI 3849A converts its virulence to avirulence. The effector AvrXccC is anchored to the plant plasma membrane, and the N‐terminal myristoylation site (amino acids 2–7: GLcaSK) is essential for its localization. In addition, the avirulence function of AvrXccC for host recognition depends on its plasma membrane localization. Promoter activity assays showed that the expression of avrXccC is hrpG/hrpX‐dependent. Moreover, the secretion of AvrXccC displayed hrp‐dependency and the core sequence for AvrXccC translocation was defined to the N‐terminal 40 amino acids.
Reactive perivascular T‐cell infiltrate predicts survival in primary central nervous system B‐cell lymphomas
Authors: Ponzoni M. , Berger F. , Chassagne‐Clement C. , Tinguely M. , Jouvet A. , Ferreri A. J. M. , Dell'Oro S. , Terreni M. R. , Doglioni C. , Weis J. , Cerati M. , Milani M. , Iuzzolino P. , Motta T. , Carbone A. , Pedrinis E. , Sanchez J. , Blay J.‐Y. , Reni M. , Conconi A. , Bertoni F. , Zucca E. , Cavalli F. , Borisch B. ,   on Behalf of the International Extranodal Lymphoma Study Group (IELSG)
Published: June 2007

AbstractWell‐established histopathological prognostic factors are lacking in primary central nervous system (CNS) lymphomas (PCNSL). The present study investigated the presence and prognostic role of tumour necrosis (TN) and reactive perivascular T‐cell infiltrate (RPVI), defined as a rim of small reactive T‐lymphocytes occurring alone or located between the vascular wall and large neoplastic cells, in tumour samples from 100 immunocompetent patients with PCNSL. World Health Organization histotypes of the patients were: 96 diffuse large B‐cell lymphomas, two Burkitt‐like lymphomas, one anaplastic large T‐cell lymphoma and one unclassified B‐cell lymphoma. TN was observed in 24 (24%) cases and RPVI in 26 (36%) of 73 assessable cases. Patients with RPVI‐positive lesions exhibited a significantly better overall survival (OS) than patients with RPVI‐negative lymphoma, particularly among patients treated with high‐dose methotrexate‐based chemotherapy (3‐year OS: 59 ± 14% vs. 42 ± 9%, P = 0·02). By contrast, the presence of TN did not demonstrate prognostic significance. Multivariate analysis confirmed an independent association between RPVI and survival. In conclusion, the presence of RPVI is independently associated with survival in PCNSL. This parameter can be easily and routinely assessed at diagnosis on histopathological specimens.
Insulin resistance after precocious pubarche: relation to PAI‐1–675 4G/5G polymorphism, and opposing influences of prenatal and postnatal weight gain
Authors: López‐Bermejo Abel , Casano‐Sancho Paula , Petry Clive J. , Jaramillo Adriana M. , Rodríguez‐González Francesc‐Xavier , Dunger David B. , De Zegher Francis , Ibáñez Lourdes 
Published: June 2007

SummaryObjective   The common promoter –675 4G/5G insertion/deletion polymorphism (indel) in the plasminogen activator inhibitor‐1 (PAI‐1) gene has been associated with quantitative components of the metabolic syndrome. We hypothesized that this polymorphism is associated with precocious pubarche (PP), a population known to be at risk for hyperinsulinaemic hyperandrogenism.Design   A cross‐sectional, hospital‐based study.Patients   A total of 115 control and 182 PP Catalan girls and young women.Measurements   Subjects were genotyped for the –675 4G/5G indel in the PAI‐1 gene. Insulin resistance and insulin secretion were estimated by the homeostasis model assessment.Results   Genotype frequencies for the PAI‐1–675 4G/5G indel (4G4G, 4G5G and 5G5G) were similar in control and PP subjects (24%vs. 27%, 50%vs. 47%, and 26%vs. 26%, respectively; P = 0·85) and these frequencies were in Hardy–Weinberg equilibrium. The 5G allele, however, was associated with insulin resistance in both postmenarcheal control and PP subjects (P < 0·01 for pooled postmenarcheal subjects, N = 122). The coexistence with the at‐risk genotype of both a low birthweight (standard deviation score, SDS < –1·0) and a high body mass index (BMI) at time of the study (SDS > +1·0) resulted in a noteworthy increase (P < 0·001) in insulin resistance.Conclusion   The common promoter –675 4G/5G indel of the PAI‐1 gene is not associated with PP but, in Catalan young women, the 5G allele enhances the risk for insulin resistance imposed by the sequence of a low birth weight (LBW) and a high BMI.
Exon 3‐deleted genotype of growth hormone receptor (GHRd3) positively influences IGF‐1 increase at generation test in children with idiopathic short stature
Authors: Toyoshima Marcos T. K. , Castroneves Luciana A. , Costalonga Everlayny F. , Mendonca Berenice B. , Arnhold Ivo J. P. , Jorge Alexander A. L. 
Published: June 2007

SummaryContext   A GHR‐exon 3 polymorphism has been reported to influence the growth response to hGH therapy in short stature children. None of these studies provided data on IGF‐1 generation test.Objective   To evaluate the influence of the GHR‐exon 3 polymorphism on the generation test in children with idiopathic short stature (ISS).Design and patients   A total of 45 prepubertal ISS children were submitted to IGF‐1 and IGFBP‐3 generation test (4 days of hGH 33 µg/kg/day). Children were genotyped for GHR‐exon 3: full‐length (fl) and exon 3‐deleted (d3) alleles.Measurements   IGF‐1 and IGFBP‐3 increment as absolute values and standard deviation scores (SDS).Results   Basal clinical and laboratory data were similar among patients with different genotypes (fl/fl vs. fl/d3 or d3/d3). All patients presented IGF‐1 increase ≥ 15 µg/l at generation test. Children with GHRd3 allele, as a group, presented a statistically significant higher IGF‐1 SDS increase at generation test than children homozygous for GHRfl allele (1·0 ranging from 0·1 to 3·7 for fl/fl vs. 1·2 ranging from 0·3 to 4·4 for fl/d3 and d3/d3; P = 0·037). Multiple linear regression found a positive association between increase in IGF‐1 SDS with chronological age (P = 0·007) and GHR genotype (P = 0·027), which together explain 24% of the variability of IGF‐1 SDS increment at generation test. There was no difference in IGFBP‐3 generation test between the two genotype groups.Conclusion   This study demonstrates that ISS children carrying the GHRd3 allele, as a group, present a slightly higher GH sensitivity regarding short‐term IGF‐1 generation during hGH stimulus than children homozygous for GHRfl allele.
Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine
Authors: TOON ALICIA , MATHER PETER B. , BAKER ANDREW M. , DURRANT KATE L. , HUGHES JANE M. 
Published: June 2007

AbstractWhile many studies have documented the effect that glacial cycles have had on northern hemisphere species, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. We investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen). One thousand one hundred and sixty‐six samples from across its native range were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. The contemporary distribution of east and west clades is nonoverlapping but in close proximity. Populations were estimated to have diverged in the Pleistocene around 36 000 years ago. The putative Carpentarian and Nullarbor arid barriers appear to be associated with the divergence between east and west mainland populations. Nested clade analysis indicated a signature of range expansion in the eastern region suggesting movement possibly inland and northward subsequent to the last period of aridity. The island population of Tasmania was of very recent origin, possibly since sea levels rose 16 000 years ago. Given the east‐west structure, there was no congruence between morphology and recent history of this species indicating a lack of support for morphological taxa. Overall mitochondrial DNA and microsatellite variation suggest that increasing aridity and Pleistocene refugia played a role in structuring populations of the Australian magpie; however, the dispersal ability and generalist habitat requirements may have facilitated the movement of magpies into an almost contiguous modern distribution across the continent. This study supports the idea that Pleistocene aridification played an important role in structuring intraspecific variation in low latitudinal southern hemisphere avian species.
Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004
Authors: PROSPERO S. , HANSEN E. M. , GRÜNWALD N. J. , WINTON L. M. 
Published: June 2007

Abstract Phytophthora ramorum (Oomycetes) is an emerging plant pathogen in forests in southwestern Oregon (Curry County). Moreover, since 2003 it has been repeatedly isolated from plants in Oregon nurseries. In this study, we analysed the genetic diversity of the P. ramorum population in Oregon from 2001 to 2004 by using microsatellites. A total of 323 isolates (272 from the infested forest; 51 from nurseries) were screened at 10 loci. The overall P. ramorum population in Oregon is characterized by low genetic diversity and has all the hallmarks of an introduced organism. All isolates within the A2 mating type belonged to the same clonal lineage and no recombinant genotypes were found. The forest population (24 genotypes) was dominated by a single multilocus genotype which persisted over years, indicating that eradication efforts in the forest have not completely eliminated inoculum sources. In contrast, genotypic evidence suggests that eradication was effective in nurseries. In 2003 and 2004, a total of 11 genotypes were found in the nurseries (one belonged to the European lineage of P. ramorum) but no genotype was recovered in both sampling years. Significant differentiation and low gene flow were detected between nursery and forest populations. Only two nursery genotypes were also found in the forest, and then at low frequency. Thus, the nursery infestation is not caused by the genotypes observed in Curry County, but likely resulted through introduction of novel genotypes from nurseries out‐of‐state. This highlights the continued importance of sanitation and quarantine in nurseries to prevent further introduction and spread of P. ramorum.
The phylogeographical clade trade: tracing the impact of human‐mediated dispersal on the colonization of northern Europe by the oak gallwasp Andricus kollari
Authors: STONE GRAHAM N. , CHALLIS RICHARD J. , ATKINSON RACHEL J. , CSÓKA GYÖRGY , HAYWARD ALEX , MELIKA GEORGE , MUTUN SERAP , PREUSS SONJA , ROKAS ANTONIS , SADEGHI EBRAHIM , SCHÖNROGGE KARSTEN 
Published: June 2007

AbstractHuman dispersal of organisms is an important process modifying natural patterns of biodiversity. Such dispersal generates new patterns of genetic diversity that overlie natural phylogeographical signatures, allowing discrimination between alternative dispersal mechanisms. Here we use allele frequency and DNA sequence data to distinguish between alternative scenarios (unassisted range expansion and long range introduction) for the colonization of northern Europe by an oak‐feeding gallwasp, Andricus kollari. Native to Mediterranean latitudes from Portugal to Iran, this species became established in northern Europe following human introduction of a host plant, the Turkey oak Quercus cerris. Colonization of northern Europe is possible through three alternative routes: (i) unassisted range expansion from natural populations in the Iberian Peninsula; (ii) unassisted range expansion from natural populations in Italy and Hungary; or (iii) descent from populations imported to the UK as trade goods from the eastern Mediterranean in the 1830s. We show that while populations in France were colonized from sources in Italy and Hungary, populations in the UK and neighbouring parts of coastal northern Europe encompass allozyme and sequence variation absent from the known native range. Further, these populations show demographic signatures expected for large stable populations, rather than signatures of rapid population growth from small numbers of founders. The extent and spatial distribution of genetic diversity in the UK suggests that these A. kollari populations are derived from introductions of large numbers of individuals from each of two genetically divergent centres of diversity in the eastern Mediterranean. The strong spatial patterning in genetic diversity observed between different regions of northern Europe, and between sites in the UK, is compatible with leptokurtic models of population establishment.
Insights on the evolution of a vegetatively propagated crop species
Authors: OLSEN KENNETH M. , SCHAAL BARBARA A. 
Published: June 2007

AbstractThe opportunity for gene flow between a vegetatively propagated crop and its wild relatives is expected to be much lower than for seed‐propagated crops, since sexual reproduction in the crop occurs only infrequently. A study by Duputié and colleagues now demonstrates evidence of sexual reproduction between a vegetatively propagated crop and a closely related wild congener. Working in French Guiana, these workers have documented a hybrid zone arising from introgression between cassava (Manihot esculenta ssp. esculenta, Euphorbiaceae), which is propagated by stem cuttings, and wild Manihot populations growing in close proximity. Patterns of heterozygosity suggest that there are little–to–no barriers to reproduction between the crop and these wild populations. Previous work by these researchers has documented the importance of occasional sexual reproduction for the development of cassava varieties in traditional Amerindian farming systems. Taken together with their previous work, these new findings suggest that gene flow between wild Manihot populations and cassava plants could potentially play a much greater role in the crop's evolution than previously thought.
On the horns of a dilemma: molecular approaches refine ex situ conservation in crisis
Authors: RUSSELLO MICHAEL A. , AMATO GEORGE 
Published: June 2007

AbstractSeven years into this new millennium, species and habitat loss continue at an accelerated rate. While there have been individual examples of conservation success, the trend towards catastrophic loss of biological diversity persists. If we are to be successful in saving even a handful of critically endangered species, it is clear that they will need to be intensively managed using a variety of in situ and ex situ approaches. The highest profile ex situ conservation strategy is captive breeding. Although its relative role in an overall conservation management plan varies, captive breeding may present the only viable option for propagating the future of a species once rendered extinct in the wild. The study of Iyengar et al. in this issue of Molecular Ecology on one such species, the scimitar‐horned oryx (Oryx dammah), represents an important contribution to ex situ conservation, demonstrating how critical insights into demographic history and population genetic structure obtained using molecular approaches may significantly contribute to captive breeding and reintroduction strategies.