bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural Mating and Tadpole Husbandry in the Western Clawed Frog Xenopus tropicalis
Authors: Showell Chris , Conlon Frank L. 
Published: September 2009

INTRODUCTIONThe routine generation and successful husbandry of tadpoles is essential for investigators using the Western clawed frog Xenopus tropicalis for developmental and genetic studies. We describe a method to induce natural mating by injecting a hormone into sexually mature X. tropicalis, and to raise the offspring through the embryonic, tadpole, and metamorphosis stages. X. tropicalis develop at a faster rate than Xenopus laevis, reaching metamorphosis in as little as 4 wk. Moreover, natural mating produces large numbers of offspring and is therefore particularly useful for mutation screening and genetic mapping. The method includes a technique for the anesthesia of frogs, which makes them easier to handle during injection of the hormone, reducing the likelihood of injury to the animals.
RNA Extraction from Arabidopsis for Northern Blots and Reverse Transcriptase-PCR
Authors: Ahn Ji H. 
Published: September 2009

INTRODUCTIONAnalysis of the cellular distribution of gene products (RNA and protein) can provide important clues to the function of genes in vivo. RNA expression can be monitored either after extraction from plants or tissues or in situ. The former procedure is easier to perform and more quantitative, whereas the latter provides much more detailed resolution of spatial and temporal expression patterns but is often more technically challenging. This protocol describes a method for RNA extraction from Arabidopsis thaliana. Frozen plant tissue is homogenized using a hand drill fitted with a plastic micropestle instead of using a conventional mortar and pestle, which can be inefficient and physically demanding. This homogenization method allows samples to be processed quickly (up to 12 samples/hour). Typical yields are 20-40 μg of total RNA from 100 mg of Arabidopsis seedlings. The RNA extracted using this method is suitable for reverse transcriptase-polymerase chain reaction (RT-PCR) and Northern hybridization.
Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by Noncompetitive PCR
Authors: Ahn Ji H. 
Published: September 2009

INTRODUCTIONThis article describes the analysis of Arabidopsis RNA by reverse transcriptase-polymerase chain reaction (RT-PCR). RNA is first reverse-transcribed into cDNA, which is then amplified by PCR. This method is quick and easy. Although RT-PCR can be performed quantitatively, it is often technically challenging to obtain highly accurate results. We recommend the use of an RT-PCR kit; the procedure given here is adapted from a commercial kit protocol. In the PCR step, it is advisable to use oligonucleotide primers that span at least one intron. In this way, amplification of any contaminating genomic DNA is readily detected, because the product derived from genomic DNA will be larger than the cDNA product. Expression levels are determined by comparing against a gene that is expressed fairly uniformly, such as the ubiquitin gene UBQ10.
Semiquantitative Analysis of Arabidopsis RNA by Reverse Transcription Followed by PCR Using Mimics
Authors: Kardailsky Igor 
Published: September 2009

INTRODUCTIONThis article describes the analysis and quantification of Arabidopsis RNA by reverse transcriptase-polymerase chain reaction (RT-PCR). RNA is first reverse-transcribed into cDNA, which is then amplified by competitive PCR using a mimic. Multiple PCRs are performed using a constant amount of unknown cDNA and varying amounts of a mimic; that is, a template of known concentration that is close in size and GC content to the quantified target and that contains the same annealing sites for primers. Mimics are usually designed to produce PCR products ~10%-20% smaller or larger than the endogenous target. A mimic can be used as a DNA standard (as in this protocol), to be included after the reverse transcription reaction, or, even better, as an RNA standard. In the latter case, an RNA molecule must be generated from a vector designed for in vitro transcription, such as pGEM or pBluescript series vectors. The procedure described here is based on commercial kit protocols.
Alignment, clade robustness and fungal phylogenetics— Crepidotaceae and sister families revisited
Authors: Petersen Gitte , Knudsen Henning , Seberg Ole 
Published: September 2009

AbstractThe circumscription and delimitation of the agaric family Crepidotaceae and related families in the Agaricales have been analysed using nLSU sequence data and direct optimization. The influence of alignment parameters on clade robustness has been explored, and many clades are found to have a low robustness. Nevertheless, based on clades with a high or moderately high robustness to increased gap costs, a few taxonomic changes are suggested: Crepidotaceae has been amended to include Crepidotus, Episphaeria, Simocybe, Pleuroflammula and Inocybe, the latter genus adding the homoplasious character mycorrhization to the family, Pellidiscus is included in Crepidotus, a position supported by micromorphology, two other genera formerly included in the family, Chromocyphella and Phaeosolenia, are excluded, and a new family, Chromocyphellaceae fam. nov., is erected for them based on fruit body shape, microcharacters, and sequences. Monophyly of Tubariaceae as recently circumscribed was not recovered, but tentatively we accept the genera Tubaria and Phaeomarasmius as members of the family.© The Willi Hennig Society 2009.
Program note: Cladescan, a program for automated phylogenetic sensitivity analysis
Authors: Sanders Jon G. 
Published: September 2009

AbstractExamination of trees for the presence of particular nodes is a fundamental aspect of systematics, and is the basis of phylogenetic sensitivity analysis, but becomes unwieldy when performed manually for complex nodes or over large numbers of trees. The program Cladescan is presented here as a stand‐alone application to facilitate the detection of nodes in such situations. Cladescan includes features useful for phylogenetic sensitivity analysis, such as automatic generation of “Navajo rug” sensitivity plots. In addition, researchers may find it useful for general comparisons among large data sets.© The Willi Hennig Society 2009.
From bacterial avirulence genes to effector functions via the hrp delivery system: an overview of 25 years of progress in our understanding of plant innate immunity
Authors: MANSFIELD JOHN W. 
Published: September 2009

SUMMARYCloning the first avirulence (avr) gene has led not only to a deeper understanding of gene‐for‐gene interactions in plant disease, but also to fundamental insights into the suppression of basal defences against microbial attack. This article (focusing on Pseudomonas syringae) charts the development of ideas and research progress over the 25 years following the breakthrough achieved by Staskawicz and coworkers. Advances in gene cloning technology underpinned the identification of both avr and hrp genes, the latter being required for the activation of the defensive hypersensitive reaction (HR) and pathogenicity. The delivery of Avr proteins through the type III secretion machinery encoded by hrp gene clusters was demonstrated, and the activity of the proteins inside plant cells as elicitors of the HR was confirmed. Key roles for avr genes in pathogenic fitness have now been established. The rebranding of Avr proteins as effectors, proteins that suppress the HR and cell wall‐based defences, has led to the ongoing search for their targets, and is generating new insights into the co‐ordination of plant resistance against diverse microbes. Bioinformatics‐led analysis of effector gene distribution in genomes has provided a remarkable view of the interchange of effectors and also their functional domains, as the arms race of attack and defence drives the evolution of microbial pathogenicity. The application of our accrued knowledge for the development of disease control strategies is considered.
Expression of pathogenesis‐related protein PR‐10 in sorghum floral tissues in response to inoculation with Fusarium thapsinum and Curvularia lunata
Authors: KATILÉ SERIBA O. , PERUMAL RAMASAMY , ROONEY WILLIAM L. , PROM LOUIS K. , MAGILL CLINT W. 
Published: September 2009

SUMMARYDifferences in grain mould disease levels among different sorghum varieties grown in the same environment imply that host genes play a role in controlling disease severity. The fungi most often recovered from naturally infected sorghum grain, Fusarium thapsinum and Curvularia lunata, were used to inoculate a set of resistant and susceptible cultivars at anthesis in both field and glasshouse trials. In the field, 12 cultivars were inoculated with a mixture of F. thapsinum and C. lunata and, in the glasshouse, individual panicles from four selected cultivars were inoculated with spore suspensions of C. lunata, F. thapsinum, a mixture of the two or water to serve as a control. Based on grain mould severity ratings and germination tests on the seed from the field trial, Tx2911, Sureno, SC719‐11E and SC650‐11E displayed a high level of resistance to grain mould. To determine whether resistant and susceptible lines differed in response to the pathogens, PR‐10 mRNA levels were measured using real‐time reverse transcriptase‐polymerase chain reaction. PR‐10 is a protein with antifungal properties that has been associated with defence responses in sorghum and other plant species. In field tests, most, but not all, cultivars showed significant induction of normalized relative quantities of PR‐10 after dual inoculation with spores of both C. lunata and F. thapsinum. Under glasshouse‐controlled conditions, glumes of inoculated plants showed the clear induction of PR‐10 mRNA, and the response was greater in resistant (Tx2911 and Sureno) than in susceptible (RTx430 and SC170‐6‐17) cultivars. Inoculation with spores from a single mould‐inducing pathogen generally induced greater responses than when spores were combined. For RTx430, SC170‐6‐17 and Sureno, the response to C. lunata was greater, whereas Tx2911 showed a stronger response to F. thapsinum. The results indicate that the induction of PR‐10 in sorghum glumes may be a factor useful in breeding programmes designed to combine multiple factors for resistance.
Escape of farmed tilapiines into the wild and entry of wild forms in fishponds, and the possible interactions between wild and farmed tilapiines from a sample of smallholder farms in Central Uganda
Authors: Mwanja Matthew Tenywa , Mwanja Wilson Waiswa 
Published: September 2009

AbstractSeven smallholder fishponds in central Uganda were studied between 2000 and 2001 to investigate the interaction of farmed tilapiines with their wild conspecifics. Emphasis was on the features that facilitate escape of fish and/or entry of fish into the farms and interactions between the farmed and the wild. These included number of species, source of seed, connection between pond and natural watercourses, purpose of the farm, destination of cultured fish and interaction between farmed and wild fish. Fishponds had no screens against entry of wild fish into the farm or escape of farmed fish into the wild and occurred within wetlands close to natural watercourses. Ponds stocked with one fish species were found to have multispecies with some individuals that were apparently intermediate morphs between the species. Fry produced within the growout fishponds was shared with other farmers within and outside the watersheds. This study showed that smallholder farms with little or no control of escape or entry of fish out and into the fishponds, and little or no management present circumstances that facilitate continued movement of tilapiines within and across watersheds in Ugandan waters. The study also indicated possible genetic interaction between farmed and their wild conspecifics through interactions within fishponds.
Evaluation of the effectiveness of an early peripheral burning strategy in controlling wild fires in north‐western Zimbabwe
Authors: Mapaure Isaac , Campbell Bruce M. , Gambiza James 
Published: September 2009

AbstractA review of the occurrence of wild fires in Sengwa Wildlife Research Area (SWRA), Zimbabwe, is presented for the period 1965–1993. The effectiveness and desirability of early burning of peripheral areas introduced in 1979 are evaluated. More than 75% of wild fires occurred between July and October, 48.6% of which originated from communal lands. Early burning of peripheral areas led to significant reductions in extent of areas burnt, from annual mean areas of 115 km2 (1965–1978) to 11 km2 (1979–1993) because of effective control of fires, which originated from communal lands. Some areas did not burn at all after 1979, and the overall probability of burning dropped from 0.484 to 0.187. Whilst it may be desirable to keep fires out of SWRA in the short term, fuel build‐ups increase the fire hazard resulting in negative consequences on biodiversity in the long term. Consideration should be given to combine peripheral burning with low‐intensity prescribed burning of selected blocks to keep a semblance of natural fire regimes to ensure the maintenance of biodiversity while simultaneously reducing the fire‐hazard. An integrated fire management plan should be put in place for SWRA.
Home ranges and survival of Nahan’s Francolin Francolinus nahani in Budongo Forest, Uganda
Authors: Sande Eric , Dranzoa Christine , Wegge Per , Carroll John P. 
Published: September 2009

AbstractWe studied home ranges, habitat use and survival of radio‐tagged Nahan’s Francolin in Budongo Forest Reserve, Uganda during July 1998–December 1999. We studied Nahan’s Francolin in an unlogged nature reserve, in a compartment logged in 1947–1952 and in a compartment logged twice, in 1963–1964 and 1996–1997. Mean home range was 14.22 ± 1.35 ha (n = 17). The home range was significantly larger in the nature reserve than in the recently logged compartment. Birds spent more time during the day in areas with high understorey vegetation density but preferred to roost and nest between buttresses of large trees. Understorey vegetation density and canopy openness were significantly greater in the logged forest than in the nature reserve. Annual survival of adult Nahan’s Francolins was 20.09 ± 7.33% (n = 23). Our results suggest that the maintenance of large trees and areas with high understorey vegetation density are both important for Nahan’s Francolin.
Natural regeneration and population dynamics of the tree Afzelia quanzensis in woodlands in Southern Africa
Authors: Gerhardt Karin , Todd Colleen 
Published: September 2009

AbstractThe logging of tree species of high commercial value is increasing throughout the African continent, yet the ecology of these species is generally poorly known. We studied the regeneration pattern and size class distribution of Afzelia quanzensis populations in northern South Africa over a 5‐year period. Recruitment was low as the annual seedling mortality was >65%. Seedlings were located under the canopy and were affected by drought and browsing. The adults were scattered or were in a clump‐dispersed pattern, which would result in higher recruitment of offspring near parents. Individuals of 0–10 cm diameter at breast height (DBH) were few, while there were 32 trees ha−1 at >10 cm DBH with an annual mortality of 0.8%. Annual diameter increments varied between 0.06 and 0.28 cm. It appears that the transition from the sapling into the juvenile stage could be a bottleneck in the regeneration of the species. A longer study, including more rainfall cycles, may reveal other patterns as dry and wet years have different impacts on dynamics.
An assessment of the puku (Kobus vardoniiLivingstone 1857) population at Lake Rukwa, Tanzania
Authors: Waltert Matthias , Chuwa Mark , Kiffner Christian 
Published: September 2009

AbstractThe population of puku,Kobus vardonii, at Lake Rukwa, one of only two in Tanzania, is poorly known. A multi‐species dry season game count carried out in Rukwa Game Reserve (RGR) in 2004 estimated a population size of 1729, but was associated with a high margin of error [coefficient of variation (CV) 0.88]. To increase the precision for the local puku population estimate, we conducted a zig‐zag line transect survey restricted only to areas occupied by puku in the dry season of 2006. This survey technique produced an estimate of 776 individuals and the CV was considerably reduced to 0.29. Puku herd size was comparable with the studies carried out in the Kilombero valley, Tanzania and in Kasanka National Park, Zambia, thus broadly confirming the herding ecology of this species. We found that pukus were restricted to the central parts of the floodplains, suggesting an avoidance of habitats used by pastoralists at the edge of RGR. Compared with the estimates of the puku population made in the 1980s, the puku population has declined. We recommend regular monitoring and enforcement of the current management plan to conserve the local puku population.
Rotterdam score predicts early mortality in Budd‐Chiari syndrome, and surgical shunting prolongs transplant‐free survival
Authors: MONTANO‐LOZA A. J. , TANDON P. , KNETEMAN N. , BAILEY R. , BAIN V. G. 
Published: September 2009

SummaryBackground  Budd–Chiari syndrome carries significant mortality, but factors predicting this outcome are uncertain.Aim  To determine factors associated with 3‐month mortality and compare outcomes after surgical shunting or liver transplantation.Methods  From 1985 to 2008, 51 patients with Budd–Chiari syndrome were identified.Results  By logistic regression analysis, features associated with higher risk of 3‐month mortality were Rotterdam class III, Clichy >6.6, model for end‐stage liver disease (MELD) >20 and Child–Pugh C. Rotterdam class III had the best performance to discriminate 3‐month mortality with sensitivity of 0.89 and specificity of 0.63, whereas Clichy >6.60 had sensitivity of 0.78 and specificity of 0.69; MELD >20 had sensitivity of 0.78 and specificity of 0.75 and Child–Pugh C had sensitivity of 0.67 and specificity of 0.72. Eighteen patients underwent surgical shunts and 14 received liver transplantation with no significant differences in survival (median survival 10 ± 3 vs. 8 ± 2 years; log‐rank, P = 0.9).Conclusions  Rotterdam score is the best discrimination index for 3‐month mortality in Budd–Chiari syndrome and should be used preferentially to determine treatment urgency. Surgical shunts constitute an important therapeutic modality that may help save liver grafts and prolong transplantation‐free survival in a selected group of patients with Budd–Chiari syndrome.
Pharmacokinetics, metabolism and bioavailability of the triazole antifungal agent voriconazole in relation to CYP2C19 genotype
Authors: Scholz Ina , Oberwittler Heike , Riedel Klaus‐Dieter , Burhenne Jürgen , Weiss Johanna , Haefeli Walter E. , Mikus Gerd 
Published: September 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Pharmacokinetic variability of voriconazole is largely caused by CYP3A4‐ and CYP2C19‐mediated metabolism.• Oral bioavailability of voriconazole has been claimed to be almost 100%, thus facilitating a change from intravenous to oral application without dose adjustment.WHAT THIS STUDY ADDS• For the first time voriconazole exposure after intravenous and oral administration in relation to CYP2C19 activity is reported.• In addition, the predominant metabolic pathway is the hydroxylation that seems to be influenced by the CYP2C19 genotype.• Enterohepatic circulation of both hydroxylated metabolites must be anticipated.AIMSThe aim was to determine the pharmacokinetics of voriconazole after a single oral dose in comparison with intravenous (i.v.) administration in healthy individuals stratified according to the cytochrome P450 (CYP) 2C19 genotype. In addition, the possible metabolic pathways and their modulation according to CYP2C19 genotype were investigated after oral and i.v. administration of voriconazole.METHODSIn a single‐centre, open‐label, two‐period crossover study 20 participants received single doses of 400 mg voriconazole orally and 400 mg voriconazole intravenously in randomized order. Blood and urine samples were collected up to 96 h post dose and the voriconazole and three major metabolites were quantified by high‐performance liquid chromatography coupled to mass spectroscopy.RESULTSAbsolute oral bioavailability of voriconazole was 82.6% (74.1, 91.0). It ranged from 94.4% (78.8, 109.9) in CYP2C19 poor metabolizers to 75.2% (62.9, 87.4) in extensive metabolizers. In contrast to voriconazole and its N‐oxide, the plasma concentrations of both hydroxylated metabolites showed a large second peak after 24 h. Independent of the route of administration, voriconazole partial metabolic hydroxylation after i.v. administration was eightfold higher compared with N‐oxidation [48.8 ml min−1(30.5, 67.1)vs.6.1 ml min−1(4.1, 8.0)]. The formation of the metabolites was related to CYP2C19 activity.CONCLUSIONSIndependent of the route of administration, voriconazole exposure was three times higher in CYP2C19 poor metabolizers compared with extensive metabolizers. Voriconazole has a high bioavailability with no large differences between the CYP2C19 genotypes. The hydroxylation pathway of voriconazole elimination exceeded the N‐oxidation, both influenced by the CYP2C19 genotype.
Validation and validity of diagnoses in the General Practice Research Database: a systematic review
Authors: Herrett Emily , Thomas Sara L. , Schoonen W. Marieke , Smeeth Liam , Hall Andrew J. 
Published: September 2009

AIMS To investigate the range of methods used to validate diagnoses in the General Practice Research Database (GPRD), to summarize findings and to assess the quality of these validations.METHODS A systematic literature review was performed by searching PubMed and Embase for publications using GPRD data published between 1987 and April 2008. Additional publications were identified from conference proceedings, back issues of relevant journals, bibliographies of retrieved publications and relevant websites. Publications that reported attempts to validate disease diagnoses recorded in the GPRD were included.RESULTS We identified 212 publications, often validating more than one diagnosis. In total, 357 validations investigating 183 different diagnoses met our inclusion criteria. Of these, 303 (85%) utilized data from outside the GPRD to validate diagnoses. The remainder utilized only data recorded in the database. The median proportion of cases with a confirmed diagnosis was 89% (range 24–100%). Details of validation methods and results were often incomplete.CONCLUSIONS A number of methods have been used to assess validity. Overall, estimates of validity were high. However, the quality of reporting of the validations was often inadequate to permit a clear interpretation. Not all methods provided a quantitative estimate of validity and most methods considered only the positive predictive value of a set of diagnostic codes in a highly selected group of cases. We make recommendations for methodology and reporting to strengthen further the use of the GPRD in research.
Radiopacifiers do not induce genetic damage in murine fibroblasts: an in vitro study
Authors: Ribeiro D. A. , Carlin V. , Fracalossi A. C. C. , Oyama L. M. 
Published: September 2009

AbstractAim  To evaluate whether several radiopacifiers are able to induce genetic damage in a laboratory cell culture study.Methodology  Murine fibroblasts were exposed to barium sulphate, bismuth oxide or zirconium oxide, at final concentrations ranging from 10 to 1 000 μg mL−1 for 1 h at 37 °C. The negative control group was treated with a vehicle control [phosphate buffered solution (PBS)] for 1 h at 37 °C and the positive control group was treated with hydrogen peroxide (at 10 μM) for 5 min on ice. Genotoxicity data were assessed by the single‐cell gel (comet) assay.Results  All the tested compounds did not induce DNA breakage as depicted by the mean tail moment in all the concentrations analysed.Conclusion  Exposure to the tested radiopacifiers may not be a factor that increases the level of DNA lesions in mammalian cells as detected by a single‐cell gel (comet) assay.