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Search Results: 1 - 10 of 300657 matches for " Lisa J Rowland "
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Superior Cross-Species Reference Genes: A Blueberry Case Study
Jose V. Die, Lisa J. Rowland
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073354
Abstract: The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well.
BBGD: an online database for blueberry genomic data
Nadim W Alkharouf, Anik L Dhanaraj, Dhananjay Naik, Chris Overall, Benjamin F Matthews, Lisa J Rowland
BMC Plant Biology , 2007, DOI: 10.1186/1471-2229-7-5
Abstract: BBGD is the world's first database for blueberry genomics. BBGD is both a sequence and gene expression database. It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function. BBGD is a public online database. Presently, the main focus of the database is the identification of genes in blueberry that are significantly induced or suppressed after low temperature exposure.By using the database, researchers have developed EST-based markers for mapping and have identified a number of "candidate" cold tolerance genes that are highly expressed in blueberry flower buds after exposure to low temperatures.Blueberry (Vaccinium corymbosum) is one of the major berry crops grown in the United States [1]. North America, in fact, is the world's leading blueberry producer, accounting for nearly 90% of world production at the present time. Total area devoted to growing commercial blueberries in North America is approximately 74,000 hectares. Blueberry is a high value crop, often times grown in acidic and imperfectly drained soils that would otherwise be considered unfit for agricultural production [2]. Blueberry is also an important fruit crop because of its nutritional value. Of all fresh fruits and vegetables, blueberries are one of the richest sources of antioxidants [3]. Blueberry is a model organism for the heath family Ericaceae, which also includes the economically important, closely related cranberry as well as the economically important, more distantly related ornamentals, rhododendron, azalea, and mountain laurel. For all these related species, genomic studies, including EST generation and microarray analyses, are lacking or completely absent. Functional genomic studies on berry crops are lacking, especially studies dealing with the molecular impacts of low temperature on berry crop yield. Low temperature extremes reduce blueberry yields and impact the profitability and competitiveness of U.S. producers. Enhanced cold toler
Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation
Lisa J Rowland, Nadim Alkharouf, Omar Darwish, Elizabeth L Ogden, James J Polashock, Nahla V Bassil, Dorrie Main
BMC Plant Biology , 2012, DOI: 10.1186/1471-2229-12-46
Abstract: Efforts to sequence the transcriptome of the commercial highbush blueberry (Vaccinium corymbosum) cultivar Bluecrop and use the sequences to identify genes associated with cold acclimation and fruit development and develop SSR markers for mapping studies are presented here. Transcriptome sequences were generated from blueberry fruit at different stages of development, flower buds at different stages of cold acclimation, and leaves by next-generation Roche 454 sequencing. Over 600,000 reads were assembled into approximately 15,000 contigs and 124,000 singletons. The assembled sequences were annotated and functionally mapped to Gene Ontology (GO) terms. Frequency of the most abundant sequences in each of the libraries was compared across all libraries to identify genes that are potentially differentially expressed during cold acclimation and fruit development. Real-time PCR was performed to confirm their differential expression patterns. Overall, 14 out of 17 of the genes examined had differential expression patterns similar to what was predicted from their reads alone. The assembled sequences were also mined for SSRs. From these sequences, 15,886 blueberry EST-SSR loci were identified. Primers were designed from 7,705 of the SSR-containing sequences with adequate flanking sequence. One hundred primer pairs were tested for amplification and polymorphism among parents of two blueberry populations currently being used for genetic linkage map construction. The tetraploid mapping population was based on a cross between the highbush cultivars Draper and Jewel (V. darrowii is also in the background of 'Jewel'). The diploid mapping population was based on a cross between an F1 hybrid of V. darrowii and diploid V. corymbosum and another diploid V. corymbosum. The overall amplification rate of the SSR primers was 68% and the polymorphism rate was 43%.These results indicate that this large collection of 454 ESTs will be a valuable resource for identifying genes that are potenti
A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers
Kim S Lewers, Chris A Saski, Brandon J Cuthbertson, David C Henry, Meg E Staton, Dorrie S Main, Anik L Dhanaraj, Lisa J Rowland, Jeff P Tomkins
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-69
Abstract: A cDNA library of 18,432 clones was generated from expanding leaf tissue of the cultivar Merton Thornless, a progenitor of many thornless commercial cultivars. Among the most abundantly expressed of the 3,000 genes annotated were those involved with energy, cell structure, and defense. From individual sequences containing SSRs, 673 primer pairs were designed. Of a randomly chosen set of 33 primer pairs tested with two blackberry cultivars, 10 detected an average of 1.9 polymorphic PCR products.This rate predicts that this library may yield as many as 940 SSR primer pairs detecting 1,786 polymorphisms. This may be sufficient to generate a genetic map that can be used to associate molecular markers with phenotypic traits, making possible molecular marker-assisted breeding to compliment existing morphological marker-assisted breeding in blackberry.The recent release of two blackberry (Rubus L.) cultivars with the novel trait, primocane fruiting [1], has the potential to significantly expand the blackberry industry. All other blackberry cultivars produce fruit in the summer on canes called floricanes, canes that grew the year before. Primocane-fruiting cultivars produce fruit on floricanes and then produce a smaller second crop in late summer and early fall on canes that emerged in spring and are just a few months old, thereby extending the potential fruit production period for growers, marketers, and consumers. Alternatively, canes can be mown to the ground in late fall, and the year's entire crop can be produced on canes that emerge the following spring. Because the canes escape winter injury, blackberry production of this type could expand into areas previously thought to be too cold for growing blackberries. The potential effect on the industry of expanding blackberry production both seasonally and geographically has led to a desire to develop new cultivars combining primocane fruiting with other important traits like thornlessness.The allele conferring primocane fr
Bounds on the frequency of 1 in the Kolakoski word
Elizabeth J. Kupin,Eric S. Rowland
Mathematics , 2008,
Abstract: We use a method of Goulden and Jackson to bound freq_1(K), the limiting frequency of 1 in the Kolakoski word K. We prove that |freq_1(K) - 1/2| <= 17/762, assuming the limit exists, and establish the semi-rigorous bound |freq_1(K) - 1/2| <= 1/46.
An Economic Evaluation of Preclinical Testing Strategies Compared to the Compulsory Scrapie Flock Scheme in the Control of Classical Scrapie
Lisa Boden, Ian Handel, Neil Hawkins, Fiona Houston, Helen Fryer, Rowland Kao
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032884
Abstract: Cost-benefit is rarely combined with nonlinear dynamic models when evaluating control options for infectious diseases. The current strategy for scrapie in Great Britain requires that all genetically susceptible livestock in affected flocks be culled (Compulsory Scrapie Flock Scheme or CSFS). However, this results in the removal of many healthy sheep, and a recently developed pre-clinical test for scrapie now offers a strategy based on disease detection. We explore the flock level cost-effectiveness of scrapie control using a deterministic transmission model and industry estimates of costs associated with genotype testing, pre-clinical tests and the value of a sheep culled. Benefit was measured in terms of the reduction in the number of infected sheep sold on, compared to a baseline strategy of doing nothing, using Incremental Cost Effectiveness analysis to compare across strategies. As market data was not available for pre-clinical testing, a threshold analysis was used to set a unit-cost giving equal costs for CSFS and multiple pre-clinical testing (MT, one test each year for three consecutive years). Assuming a 40% within-flock proportion of susceptible genotypes and a test sensitivity of 90%, a single test (ST) was cheaper but less effective than either the CSFS or MT strategies (30 infected-sales-averted over the lifetime of the average epidemic). The MT strategy was slightly less effective than the CSFS and would be a dominated strategy unless preclinical testing was cheaper than the threshold price of £6.28, but may be appropriate for flocks with particularly valuable livestock. Though the ST is not currently recommended, the proportion of susceptible genotypes in the national flock is likely to continue to decrease; this may eventually make it a cost-effective alternative to the MT or CSFS.
Summary of current knowledge of the size and spatial distribution of the horse population within Great Britain
Lisa A Boden, Tim DH Parkin, Julia Yates, Dominic Mellor, Rowland R Kao
BMC Veterinary Research , 2012, DOI: 10.1186/1746-6148-8-43
Abstract: A conservative estimate for the accurately geo-located NED horse population within GB is approximately 840,000 horses. This is likely to be an underestimate because of the exclusion of horses due to age or location criteria. In both datasets, horse density was higher in England and Wales than in Scotland. The high density of horses located in urban areas as indicated in the NED is consistent with previous reports indicating that owner location cannot always be viewed as a direct substitute for horse location. Otherwise, at a regional resolution, there are few differences between the datasets. There are inevitable biases in the stakeholder data, and leisure horses that are unaffiliated to major stakeholders are not included in these data. Despite this, the similarity in distributions of these datasets is re-assuring, suggesting that there are few regional biases in the NED.Our analyses suggest that stakeholder data could be used to monitor possible changes in horse demographics. Given such changes in horse demographics and the advantages of stakeholder data (which include annual updates and accurate horse location), it may be appropriate to use these data for future disease modelling in conjunction with, if not in place of the NED.Understanding how an infectious disease might spread through a population and how then to control that spread requires knowing both the size of the susceptible population at risk and, and how frequently individuals in a population come into contact with one another. In the case of disease spread at a national scale, this requires knowledge of the spatial distribution of the susceptible population, as this will inform 'local' spread that transmits simply as a result of geographical proximity, and can be used to parameterise 'network-based' spread, such as can occur via livestock movements. Great Britain (GB) needs to prepare for a potential equine infectious disease epidemic due to the recent incursion of Bluetongue virus (BTV) from North Af
Differential passage rates of prey components through the gut of serval Felis serval and black-backed jackal Canis mesomelas
J.M Bowland,A.E Rowland
Koedoe : African Protected Area Conservation and Science , 1991, DOI: 10.4102/koedoe.v34i1.412
Abstract: Feeding trials conducted on Felis serval and Canis mesomelas showed that the same prey item may appear in up to seven scats (mean=2.8, n=7). The basic assumption that prey remains of the same species in different scats represent different individuals is invalid. Therefore over-estimation of some prey species relative to others in the diet of carnivores studied can occur.
Form and Function in Grammar Teaching
J. E. Lisa Meyer
TEFLIN Journal , 1998,
Abstract: :In this paper we promote the integration of form-focused grammar teaching with a communicative approach to language learn -ing. After discussion of several principles of L2 acquisition and their pedagogic implications, we recommend a four-stage lesson plan which helps the teacher to focus on a communicative function while presenting a specific grammatical structure. In the proposed lesson structure, teachers are encouraged to guide student. Exploration, dis -covery, and application of grammatical information during specific lesson stages. This type of lesson should pave the way for students to do more than master practice worksheets. One of the greatest ben -efits of this type of lesson is that it gives teachers the confidence to integrate a grammatical focus into their language lessons without violating the essence of communicative approach.
Collaborative Event Ethnography: Conservation and development trade-offs at the fourth world conservation congress
Brosius J,Campbell Lisa
Conservation & Society , 2010,
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