bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil structure and soil‐borne diseases: using epidemiological concepts to scale from fungal spread to plant epidemics
Authors: Otten W. , Gilligan C. A. 
Published: January 2006

SummaryMany epidemics of root diseases involving soil fungi depend on the interplay between fungal growth and the spatial and temporal heterogeneity of the soil environment. Colonization or infection of a root occurs at fine scales with growth and movement of fungal mycelia through soil. However, epidemics are observed at coarser scales, and depend on a cascading spread through populations of roots. We briefly review conventional analyses of soil‐borne epidemics and argue that these treat soil physical conditions at scales too coarse to be meaningful for interactions between soil, plants and fungi, and fail to consider the effect of soil physical conditions on the underlying epidemiological processes. Instead, we propose a conceptual epidemiological framework that integrates spatial scales and use this to review the effect of soil structure on the dynamics of soil‐borne pathogenic fungi. Using the soil‐borne fungal plant pathogenRhizoctonia solanias an example, we demonstrate that invasion of fungi into host populations is critically affected by environmental conditions operating at each of two scales: (i) at the microscopic scale (μm − cm) the fungus preferentially explores certain pathways in soil, and small changes in soil physical conditions make the fungus switch from small, dense colonies to large, sparse and rapidly expanding ones; (ii) at the larger scale (cm − dm) a critical density of susceptible hosts is required, in excess of which fungi switch from non‐invasive to invasive spread. Finally, we suggest that the approach will increase the applicability of research dealing with microscopic soil–plant–microbe interactions towards the solution of large‐scale epidemiological problems.
Depletion of organic phosphorus from Oxisols in relation to phosphatase activities in the rhizosphere
Authors: George T. S. , Turner B. L. , Gregory P. J. , Cade‐Menun B. J. , Richardson A. E. 
Published: January 2006

SummaryPhosphorus (P) deficiency is a major limitation to agricultural production in many parts of the world. It is therefore desirable to identify plants with enhanced abilities to utilize P more efficiently. Exudation of phosphatase from roots may improve P availability, yet there is little direct evidence for this. Here we report the dynamics of organic P in the rhizosphere of plants that have enhanced rhizosphere phosphatase activity. Agroforestry species and transgenic subterranean clover (engineered to produce phytase) were compared with crop and wild‐type plant controls, respectively. Depletion of organic P was measured in pools defined by chemical extraction, solution 31P NMR spectroscopy, and microbial immobilization of radio‐isotopic P. Plants that had greater extracellular phosphatase activity depleted more organic P from P‐deficient Oxisols than control plants. Depleted organic P forms were primarily phosphate monoesters. Plants with enhanced extracellular phosphatase activity also had access to a pool of soil P that was less isotopically exchangeable. Transgenic subterranean clover that expresses a microbial phytase gene appeared to have greater access to recently immobilized P, whereas plants expressing endogenous phosphatases utilized the unlabelled portion of soil organic P to a greater extent. Collectively, these results indicate that the enhancement of phosphatase activity in the rhizosphere of plants is implicated in the depletion of organic P forms from soils, most notably orthophosphate monoesters, whilst also suggesting that there is some exclusivity to the pools of organic P utilized by plants and microorganisms.
Comparison of methods for measuring metal desorption from soils for parameterizing rhizosphere models
Authors: Molina Millán I. , Fitz W. J. , Unterbrunner R. , Wenzel W. W. 
Published: January 2006

SummarySorption curves are commonly used to predict the partitioning of ions between the soil solid and solution in ion transport and rhizosphere models. We review methods for measuring metal desorption for such purposes, and we illustrate the problems involved by means of measurements of Ni desorption from a contaminated soil as an example. We find that measurements of metal concentration in shaken soil suspensions at a range of solution:soil ratios give similar desorption curves to the more tedious method of repeated extraction at a constant, smaller and therefore more realistic solution:soil ratio. We also find that desorption is sensitive to the nature and concentration of the background electrolyte used, and to interactions between these and additions of organic chelating agents of the sort excreted by roots and rhizosphere microbes.
Distributional patterns of freshwater taxa (fishes, crustaceans and plants) from the Mexican Transition Zone
Authors: Huidobro Leticia , Morrone Juan J. , Villalobos José Luis , Álvarez Fernando 
Published: January 2006

AbstractAim To test whether distributional patterns of Neotropical freshwater taxa fit the generalized tracks already postulated for terrestrial groups occurring in the Mexican Transition Zone.Location The study units comprised 17 hydrological basins located along the Pacific coast of the Americas from Mexico to Panama, and in the Gulf of Mexico from the Papaloapan to the Grijalva–Usumacinta basin.Methods Distributional data for 22 fish species, 34 crab species of the tribe Pseudothelphusini, and 22 strictly freshwater species of angiosperms were analysed. Parsimony analysis of endemicity is based on presence/absence data of these taxa and uses the computer programs Winclada and NONA.Results Three generalized tracks were obtained: (1) Mexican North Pacific, (2) Mexican Central Pacific, and (3) Southern Mexico–Guatemala. A node resulted at the intersection of the first two tracks, coinciding with the Neovolcanic Axis in central Mexico.Main conclusions Freshwater generalized tracks with an altitudinal distribution below 1000 m, mainly including fishes and angiosperms, are close to the Tropical Mesoamerican generalized track. Generalized tracks above 1000 m, including freshwater crabs, have a stronger affinity with the Mountain Mesoamerican track. The Isthmus of Tehuantepec represents a node for the Neotropical freshwater and terrestrial biota. These results seem to indicate that common geobiotic processes have induced these patterns.
Three‐dimensional volume reconstruction of extracellular matrix proteins in uveal melanoma from fluorescent confocal laser scanning microscope images
Authors: BAJCSY P. , LEE S‐C. , LIN A. , FOLBERG R. 
Published: January 2006

SummaryThe distribution of looping patterns of laminin in uveal melanomas and other tumours has been associated with adverse outcome. Moreover, these patterns are generated by highly invasive tumour cells through the process of vasculogenic mimicry and are not therefore blood vessels. Nevertheless, these extravascular matrix patterns conduct plasma. The three‐dimensional (3D) configuration of these laminin‐rich patterns compared with blood vessels has been the subject of speculation and intensive investigation. We have developed a method for the 3D reconstruction of volume for these extravascular matrix proteins from serial paraffin sections cut at 4 µm thicknesses and stained with a fluorescently labelled antibody to laminin (Maniotis et al., 2002). Each section was examined via confocal laser‐scanning focal microscopy (CLSM) and 13 images were recorded in the Z‐dimension for each slide. The input CLSM imagery is composed of a set of 3D subvolumes (stacks of 2D images) acquired at multiple confocal depths, from a sequence of consecutive slides. Steps for automated reconstruction included (1) unsupervised methods for selecting an image frame from a subvolume based on entropy and contrast criteria, (2) a fully automated registration technique for image alignment and (3) an improved histogram equalization method that compensates for spatially varying image intensities in CLSM imagery due to photo‐bleaching. We compared image alignment accuracy of a fully automated method with registration accuracy achieved by human subjects using a manual method. Automated 3D volume reconstruction was found to provide significant improvement in accuracy, consistency of results and performance time for CLSM images acquired from serial paraffin sections.
A step by step guide to phylogeny reconstruction
Authors: Jill Harrison C. , Langdale Jane A. 
Published: January 2006

SummaryThe aim of this paper is to enable those who have never reconstructed a phylogeny to do so from scratch. The paper does not attempt to be a comprehensive theoretical guide, but describes one rigorous way of obtaining phylogenetic trees. Those who follow the methods outlined should be able to understand the basic ideas behind the steps taken, the meaning of the phylogenetic trees obtained and the scope of questions that can be answered with phylogenetic methods. The protocols have been successfully tested by volunteers with no phylogenetic experience.
Oxylipin analysis methods
Authors: Mueller Martin J. , Mène‐Saffrané Laurent , Grun Christoph , Karg Kathrin , Farmer Edward E. 
Published: January 2006

SummaryPractical guidelines for monitoring and measuring compounds such as jasmonates, ketols, ketodi(tri)enes and hydroxy‐fatty acids as well as detecting the presence of novel oxylipins are presented. Additionally, a protocol for the penetrant analysis of non‐enzymatic lipid oxidation is described. Each of the methods, which employ gas chromatography/mass spectrometry, can be applied without specialist knowledge or recourse to the latest analytical instrumentation. Additional information on oxylipin quantification and novel protocols for preparing oxygen isotope‐labelled internal standards are provided. Four developing areas of research are identified: (i) profiling of the unbound cellular pools of oxylipins; (ii) profiling of esterified oxylipins and/or monitoring of their release from parent lipids; (iii) monitoring of non‐enzymatic lipid oxidation; (iv) analysis of unstable and reactive oxylipins. The methods and protocols presented herein are designed to give technical insights into the first three areas and to provide a platform from which to enter the fourth area.
Gateway‐compatible vectors for plant functional genomics and proteomics
Authors: Earley Keith W. , Haag Jeremy R. , Pontes Olga , Opper Kristen , Juehne Tom , Song Keming , Pikaard Craig S. 
Published: January 2006

SummaryGateway cloning technology facilitates high‐throughput cloning of target sequences by making use of the bacteriophage lambda site‐specific recombination system. Target sequences are first captured in a commercially available ‘entry vector’ and are then recombined into various ‘destination vectors’ for expression in different experimental organisms. Gateway technology has been embraced by a number of plant laboratories that have engineered destination vectors for promoter specificity analyses, protein localization studies, protein/protein interaction studies, constitutive or inducible protein expression studies, gene knockdown by RNA interference, or affinity purification experiments. We review the various types of Gateway destination vectors that are currently available to the plant research community and provide links and references to enable additional information to be obtained concerning these vectors. We also describe a set of ‘pEarleyGate’ plasmid vectors for Agrobacterium‐mediated plant transformation that translationally fuse FLAG, HA, cMyc, AcV5 or tandem affinity purification epitope tags onto target proteins, with or without an adjacent fluorescent protein. The oligopeptide epitope tags allow the affinity purification, immunolocalization or immunoprecipitation of recombinant proteins expressed in vivo. We demonstrate the utility of pEarleyGate destination vectors for the expression of epitope‐tagged proteins that can be affinity captured or localized by immunofluorescence microscopy. Antibodies detecting the FLAG, HA, cMyc and AcV5 tags show relatively little cross‐reaction with endogenous proteins in a variety of monocotyledonous and dicotyledonous plants, suggesting broad utility for the tags and vectors.
Imaging the live plant cell
Authors: Shaw Sidney L. 
Published: January 2006

SummaryObserving a biological event as it unfolds in the living cell provides unique insight into the nature of the phenomenon under study. Capturing live cell data differs from imaging fixed preparations because living plants respond to the intense light used in the imaging process. In addition, live plant cells are inherently thick specimens containing colored and fluorescent molecules often removed when the plant is fixed and sectioned. For fixed cells, the straightforward goal is to maximize contrast and resolution. For live cell imaging, maximizing contrast and resolution will probably damage the specimen or rapidly bleach the probe. Therefore, the goals are different. Live cell imaging seeks a balance between image quality and the information content that comes with increasing contrast and resolution. That ‘lousy’ live cell image may contain all the information needed to answer the question being posed –provided the investigator properly framed the question and imaged the cells appropriately. Successful data collection from live cells requires developing a specimen‐mounting protocol, careful selection and alignment of microscope components, and a clear understanding of how the microscope system generates contrast and resolution. This paper discusses general aspects of modern live cell imaging and the special considerations for imaging live plant specimens.
TILLING: practical single‐nucleotide mutation discovery
Authors: Comai Luca , Henikoff Steven 
Published: January 2006

SummaryIn the post‐genomic sequencing era, an expanding portfolio of genomic technologies has been applied to the study of gene function. Reverse genetics approaches that provide targeted inactivation of genes identified by sequence analysis include TILLING (for Targeting Local Lesions IN Genomes). TILLING searches the genomes of mutagenized organisms for mutations in a chosen gene, typically single base‐pair substitutions. This review covers practical aspects of the technology, ranging from building the mutagenized population to mutation discovery, and discusses possible improvements to current protocols and the impact of new genomic methods for mutation discovery in relation to the future of the TILLING approach.
Sequence‐based typing reveals a novel DLA‐88 allele, DLA‐88*04501, in a beagle family
Authors: Hardt C. , Ferencik S. , Tak R. , Hoogerbrugge P. M. , Wagner V. , Grosse‐Wilde H. 
Published: January 2006

AbstractThe dog is an important animal model for solid organ as well as stem cell allo transplantation. Methods such as cellular and serological typing and more recently sequence‐based typing (SBT) have been used to discriminate tissue antigen disparity of donor and recipient. We applied SBT for the canine class I (DLA‐88) and class II (DLA‐DRB1) genes in beagle families prior stem cell transplantation. A novel DLA‐88 (DLA‐88*04501) allele in combination with a DLA‐DRB1*01901 allele was found. Sequence comparison of exons 2 and 3 of the novel allele revealed most sequence identity to the DLA‐88*01301 allele (96.15% identity at the nucleotide and 90.65% identity at the protein level).
Identification of a novel HLA‐A allele (A*1115) in the UK National External Quality Assessment Schemes for Histocompatibility and Immunogenetics' Educational Cell Exchange
Authors: Bendukidze N. , Day S. , Street J. , Hammond L. , Downing J. , Corbin S. , Dunn P. P. J. , Darke C. 
Published: January 2006

AbstractThe novel allele, HLA‐A*1115, was identified in an ‘Educational Scheme’ sample (ED03/03 – from a north‐western European Caucasoid blood donor) distributed by the UK National External Quality Assessment Schemes for Histocompatibility and Immunogenetics. ED03/03 was typed by serology, the polymerase chain reaction using sequence‐specific primers and sequence‐based typing. A*1115 is most similar to A*110101 with a single mismatch (G to C) at constant position 565, leading to a conservative amino acid change from valine (GTG) to leucine (CTG) at codon 165 in the α2 domain. This substitution has not been reported for any other HLA class I allele so far. The HLA‐A*1115‐bearing haplotype was B*350101; Cw*040101; DRB1*140101; DRB3*020201; DQA1*010401; DQB1*0503; DPA1*0103/07; DPB1*030101. Extensive serological typing indicated that this allele essentially encodes a ‘normal’ HLA‐A11 specificity.
HLA‐DRB1*0826 and HLA‐DQB1*0627, two novel class II alleles identified in blood stem cell donors of Caucasian origin
Authors: Brixner V. , Mosebach M. , Schmidt M. , Hermann S. , Seifried E. , Martin H. , Seidl C. 
Published: January 2006

AbstractThis report describes two novel HLA class II alleles, HLA‐DRB1*0826 and HLA‐DQB1*0627, that have been identified in two unrelated voluntary blood stem cell donors of Caucasian origin. HLA‐DRB1*0826 is characterized by a nucleotide substitution (G to T) in exon 2 at position 163, leading to an amino acid exchange from argenine to leucine. The donor phenotype is HLA‐A*0301,*2902; B*3501,*4403; Cw*0401,*1601; DRB1*0101,*0826; DQB1*0402, *0501. The HLA‐DQB1*0627 alleles contain a nucleotide substitution at position 184 (T to C) resulting in an amino acid exchange from tyrosine to histidine. Family segregation analysis revealed that the HLA‐DQB1*0627 allele belongs to the haplotype A*0101, B*1517, Cw*0701, DRB1*1302, DQB1*0627. The donor phenotype is HLA‐A*0101; B*0801,*1517; Cw*0701; DRB1*1302,*1501; DQB1*0602,*0627.
HLA‐A, ‐B, and ‐DRB1 polymorphism defined by sequence‐based typing of the Han population in Northern China
Authors: Yang G. , Deng Y.‐J. , Hu S.‐N. , Wu D.‐Y. , Li S.‐B. , Zhu J. , Zhu B.‐F. , Liu Y. 
Published: January 2006

AbstractDNA typing for human leukocyte antigen (HLA)‐A, ‐B and ‐DRB1 was performed using polymerase chain reaction–sequence‐based typing method on 618 randomly selected healthy individuals of the Han population in Northern China. Allele frequencies and haplotypes were statistically analyzed. A total of 84 HLA‐A alleles, 143 B alleles, and 122 DRB1 alleles were detected, and 853 A‐B‐DRB1 haplotypes, 473 A‐B haplotypes, and 551 B‐DRB1 haplotypes were statistically inferred. Statistical analysis of three‐locus haplotypes showed that A*0207‐B*4601‐DRB1*0901 (3.06%) was the most predominant. Gene frequencies and haplotypic associations within HLA‐A, ‐B, and ‐DRB1 loci were determined at a high‐resolution (four digit) allelic level and should provide useful information in anthropology, bone marrow donor registry, legal medicine, and disease association studies.
Correlation of interleukin‐10 gene haplotype with hepatocellular carcinoma in Taiwan
Authors: Tseng L.‐H. , Lin M.‐T. , Shau W.‐Y. , Lin W.‐C. , Chang F.‐Y. , Chien K.‐L. , Hansen J. A. , Chen D.‐S. , Chen P.‐J. 
Published: January 2006

AbstractPolymorphisms in cytokine genes can influence immune responses, inflammation and tissue injury, and may affect the outcome of hepatitis B virus (HBV) infection. We analyzed single nucleotide polymorphisms (SNP) in the interleukin (IL)‐10 gene among 344 HBV carriers and 208 patients with hepatocellular carcinoma (HCC). Genotypes and haplotypes were tested for association with HCC. IL‐10/−592 C/C genotype was associated with a higher risk for HCC compared with IL‐10/−592 A/C and A/A genotypes [odds ratio (OR): 2.1, 95% confidence interval (CI): 1.2–3.6]. IL‐10/1927 A/A genotype was also associated with a higher risk for HCC compared with IL‐10/1927 A/C and C/C genotypes (OR: 1.5, 95% CI: 1.0–2.2). Haplotype analysis revealed that the homozygosity of the C‐A haplotype (defined by SNPs at positions −592 and 1927) of IL‐10 gene conveys the highest risk for HCC among HBV carriers compared with the homozygosity for the A‐C haplotype (OR: 2.6, 95% CI: 1.3–4.9). The results demonstrate that IL‐10 gene polymorphism can affect the outcome of chronic HBV infection. Further studies are necessary to clarify how variation in the IL‐10 gene affects IL‐10 function and risk of HCC.
First Record of Bremia lactucae Infecting Sonchus oleraceus and Sonchus asper in Brazil and its Infectivity to Lettuce
Authors: Vieira B. S. , Barreto R. W. 
Published: January 2006

Abstract Bremia lactucae is recorded for the first time causing downy mildew on common sowthistle (Sonchus oleraceus) and spiny sowthistle (Sonchus asper) in Brazil. The disease and etiological agent are described. Pathogencity of sporangia obtained from S. oleraceus was tested on 12 species belonging to the Asteraceae, already recorded in the literature as hosts of B. lactucae, and four commonly cultivated varieties of lettuce. All four cultivars of lettuce, S. oleraceus and S. asper showed symptoms of the disease and sporulation of the pathogen 5 days after inoculation. It has been observed that the disease occurs on Sonchus spp. throughout the year in Viçosa (state of Minas Gerais), being more common on these two hosts than on lettuce. Both weeds are very common invaders of vegetable growing areas in Brazil. This indicates that those two hosts for the fungus may be important inoculum reservoirs for disease occurring in lettuce, highlighting the need for control of these weeds as part of the procedures aimed at controlling this disease. These results are also in agreement with the views that B. lactucae is split into host‐specific infra‐specific taxa. Lettuce and sowthistles are regarded as closely related, belonging to the same subfamily and tribe in the Asteraceae (Subfamily Cichorioideae: Tribe Lactuceae).
Characteristics of Pustula tragopogonis (syn. Albugo tragopogonis) Newly Occurring on Cultivated Sunflower in Germany
Authors: Thines M. , Zipper R. , Schäuffele D. , Spring O. 
Published: January 2006

AbstractIn temperate climates, Pustula tragopogonis is rarely found on cultivated sunflower. In Europe, it was so far of little economic impact on other Asteraceae, except for some regions in the Mediterranean. In 2003, P. tragopogonis was found for the first time in sunflower fields in southern Germany. The pathogen has a widespread occurrence there, especially in the region around Stuttgart, BW. Fatty acid profiling, ultrastructural investigation and ITS sequencing revealed a high similarity to an 2002 isolate from southern Africa and an 2005 isolate from Australia, but revealed significant differences to P. tragopogonis s.l. on Cirsium arvense, a common weed, growing on or in the vicinity of sunflower fields in Germany. P. tragopogonis from this host can therefore be excluded from being the source of the reported infection.
Yellow Death: A Disease of Date Palm in Iran Caused by Fusarium solani
Authors: Mansoori B. , Kord M. H. 
Published: January 2006

AbstractIn December 2003, a severe general yellowing and death of the fronds of date palm (Phoenix dactylifera) occurred in a grove in the vicinity of Kazeron district, west of Fars province, Iran. Fusarium solani was isolated from the crown, and xylem rays sampled from the trunk 1.5 m above soil level. In pathogenicity tests using artificially infested soil and 1‐year‐old date palm seedlings, an isolate from the trunk (FST) induced general chlorosis and death of seedlings 25–28 days after inoculation. Similar results were obtained when seedlings were planted in naturally infested soil. In both procedures, distal portions of the roots and crown were affected. The fungus was re‐isolated from the crown and leaf bases of the inoculated seedlings. This is the first report of a serious disease of date palm, which we call yellow death, incited by F. solani in Iran.