1,721,113 research outputs found
Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato- Pseudomonas pathosystem
No full textThe agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in di erent systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identi cation of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves in ltrated with di erent immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Speci cally, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT- qPCR experiments involving this pathosystem.Fil: Pombo, Marina Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; ArgentinaFil: Zheng, Yi. Cornell University; Estados UnidosFil: Fei, Zhangjun. Cornell University; Estados UnidosFil: Martin, Gregory. Cornell University; Estados UnidosFil: Rosli, Hernan Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Fisiología Vegetal. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Fisiología Vegetal; Argentin
EVALUATING TRANSCRIPTOME CHANGES IN SWEET POTATO DURING VIRAL PATHOGEN INFECTION
No full text117 pagesSweet potato (Ipomoea batatas) ranks among the most important crops in the world and provides nutritional and economic sustainability for subsistence farmers in Sub-Saharan Africa. Its production is mainly constrained by Sweet potato virus disease (SPVD) caused by the coinfection by two positive-sense single-stranded RNA viruses, Sweet potato chlorotic stunt virus and Sweet potato feathery mottle virus. Current understanding of sweet potato responses to these viruses at the molecular level remains very limited. In this study, we performed deep transcriptome sequencing in three sweet potato cultivars with varying degrees of viral resistance, coupled with comprehensive and integrated analytical approaches, to identify biological pathways that contribute to both general and specific host responses to these important viral pathogens. We found that much of the antiviral response was effector-triggered immunity (ETI) specific, and that the expression patterns (both timing and magnitude) of this response were dependent on each cultivar’s resistance to SPVD
UNDERSTANDING INSECT MIDGUT RECEPTORS FOR BT PROTEIN CRY1AC AND MECHANISM OF RESISTANCE TO CRY1AC IN THE CABBAGE LOOPER, TRICHOPLUSIA NI
No full text226 pagesThe successful deployment of insecticidal proteins from Bacillus thuringiensis (Bt) via genetically engineered crops has revolutionized pest management practices in agriculture. However, the development of insect resistance to Bt toxins threatens the sustainable application of Bt-biotechnology. Current understanding of Bt resistance has indicated that resistance to Bt in insects is complex, involving multiple midgut proteins that serve as receptors for Bt toxins in the intoxication pathways. In this dissertation, I studied the genetic basis of resistance to Bt protein Cry1Ac in a greenhouse-evolved resistant strain of the cabbage looper, Trichoplusia ni. Using genetic and molecular approaches, I studied the genetic association of altered APN (Aminopeptidase N) expression with the ABCC2 (ABC transporter C2) and the association of Cry1Ac resistance with APNs. The results indicated that the downregulated APN1 expression in resistant T. ni and low expression of APN6 in susceptible T. ni were associated with mutations in APN1 and APN6 genes but were not with ABCC2. The high-level resistance to Cry1Ac in T. ni is associated with both ABCC2 and APN1 mutations and additional factors to be identified. The functional roles of putative Cry1Ac receptors ABCC2, ALP (alkaline phosphatase), APN1, and midgut cadherin (CAD) in larval susceptibility to Cry1Ac were systematically examined, using a series of gene knockout T. ni mutant strains. ABCC2 was confirmed to be a major receptor for Cry1Ac in T. ni, but knockout mutations in the ALP, APN, and CAD receptors resulted in none to low resistance in T. ni. Results also indicated additional resistance genes to be identified. Finally, I studied the role of carbohydrate moieties in the mode of action of Cry1Ac. The interaction of Cry1A with the midgut and Cry1Ac toxicity in larvae were analyzed in vitro and in vivo, using a carbohydrate binding chemical, Calcofluor. The results demonstrated that carbohydrate moieties play critically important roles in the functional specific binding of the toxin to the midgut receptors in the pathway of toxicity. Overall, the findings from this thesis research advanced our understanding of the mode of action of Cry proteins and mechanisms of insect resistance to Cry proteins
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
NEW INSIGHTS INTO THE PHYSIOLOGY, BIOSYNTHESIS, AND MOLECULAR CONTROLS OF ORGANIC ACIDS AND POLYPHENOLS IN CIDER APPLES
No full text196 pagesThe organic acids and polyphenols in apple (Malus ×domestica) juice are responsible for hard cider flavor, aroma, color, and microbial stability. The second chapter of this dissertation describes how the malic acid marker Ma1 was able to categorize 217 cider apple cultivars into low (5.8 g·L-1) acidity groups. Triploid cultivars had a significant 0.36 g·L-1 greater titratable acidity than diploid cultivars (P = 0.0111). The third and fourth chapters focused on the effect of crop density and early tree shading on polyphenol development in cider apples respectively to understand source-sink relationships and explain the year-to-year variation in polyphenol content. There was a significant increase in the concentrations of most polyphenol compounds, including monomeric and oligomeric proanthocyanidin compounds in the low crop density treatment (5 fruit/cm2 trunk cross-sectional area) compared to the unthinned control (P < 0.0100). Transcriptome profiling through RNA sequencing indicated the critical genes involved in hydroxylation, methylation, and glycosylation in the phenylpropanoid pathway were upregulated in the low crop density treatment at 27 DAFB and 81 DAFB, which corresponded with increased concentration of phenylpropanoids. Specifically, there was a significant increase in the expression of the gene encoding anthocyanidin reductase (catalyzes the production of epicatechin) in the low crop density treatment at 27 and 81 days after full bloom (P < 0.0100). In Chapter 4, carbohydrate stress applied through early tree shading (1-5 weeks after full bloom) reduced phenolic acids and quercetin glycoside concentrations at harvest in the 60-tree shade treatment (60% of photosynthetically active radiation blocked) in comparison to the unshaded control, with minimal impact on production of procyanidin monomers and oligomers in cider apples. Fruit shaded trees were not significantly different from the control. This dissertation elucidates a new marker-based acidity classification system allowing for cultivar comparisons across geographical, seasonal, and horticultural considerations; illustrates the differing polyphenol accumulation patterns in the peel and flesh tissue; provides compelling evidence for a positive source-sink relationship with polyphenol development in cider apples; and lists transcription factors that could possibly be involved in the polyphenol production in cider apples
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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