1,720,983 research outputs found
A matter of time: assessing the biological functions of oscillating natural antisense long non-coding RNA transcripts
No full textCircadian rhythms allow organisms to coordinate their metabolic and physiological responsesin accordance with Earth’s predictable daily, and yearly fluctuations in environmentalconditions. The roles of oscillating protein-coding transcripts have been well studied in theplant circadian clock, however recent research has identified that the transcription of long nonprotein coding RNAs can also oscillate in a diurnal manner. Here we document two circadianregulated lncRNAs that are natural antisense transcripts of two CDFs in the model plantArabidopsis thaliana.
The first lncRNA “FLORE” forms a natural antisense transcript pair with CDF5, and these
transcripts were shown to display antiphasic expression, reflecting a mutual inhibitory
relationship. By resorting to ChIRP-seq, a multitude of putative FLORE genomic targets were identified, and through the implementation of molecular and bioinformatics techniques, four genes of interested were selected. Three of these genes; CCL, XPB1, and SR45A, exhibited upregulated transcription in a FLORE over-expressor under LD conditions. The fourth gene, RH27, displayed altered expression patterns between biological replicates. Finally, SR45A and RH27 were shortlisted for in-depth analysis. Histochemical GUS staining revealed that RH27 is transcriptionally active in newly developing tissues, as well as root tips and reproductivetissues. Finally, we found that a depletion in a gene related to SR45A (SR45) was associatedwith marginal changes in FLORE alternative splicing patterns.
The second lncRNA “lncCDF1” is a natural antisense transcript of CDF1. Recent data have
identified the CDFs as regulators of abiotic stress responses, and previous unpublished
experiments have shown both CDF1 and lncCDF1 to be induced by drought. Here, we
recorded a decrease in ABA sensitivity during seed germination, in a lnccdf1 promoter TDNA insertion mutant. Additionally lncCDF1 promoter activity appeared to be induced by ABA in two day old seedlings. Contrastingly, modulation of lncCDF1 transcript levels was not associated with altered ABA-mediated responses in older seedlings. Finally, we observed that CDF1 transcription is reduced in response to lncCDF1 over-expression, suggesting lncCDF1 may act in cis to repress lncCDF1. Taken together, these findings highlight the diverse regulatory functions carried out by lncRNAs in plants, and our findings provide a basis for further study on these transcripts
The effect of altering autumn grazing management on sward structural characteristics, morphology and nutritive value
No full textAltering grazing management practices to increase the amount of herbage available on farm can help extend the grazing season, improve herbage utilization and, in turn, improve the sustainability and efficiency of pasture based dairy systems. Extended grazing happens at two pivotal time points - autumn and spring. Management for both incorporates building herbage masses; in autumn, the grazing rotation is extended from August to a peak in October, which in turn increases pre-grazing herbage mass. Increasing herbage in spring relies on accumulating herbage, over winter achieved by autumn closing date (CD). Accumulating herbage mass has the potential to impact various factors of sward production, morphology and physiology. The current thesis evaluated how management practices in autumn and spring affect the perennial ryegrass (Lolium perenne, L; PRG) plant. This research is important to identify areas where management can be improved which will allow for the increase in herbage available to be utilised, improve efficiencies, profitability and sustainability. The objective of this thesis was to investigate the impact of accumulating herbage masses for the extension of the grazing season in autumn, over winter and spring. Herbage masses in autumn were investigated at different defoliation dates (DD) across the final rotation (chapter 2 and 3). The effect of final defoliation in autumn (CD) over winter and into spring was investigated (chapter 4 and 5).
It was found accumulating herbage should begin in August and herbage masses > 2000 kg DM ha-1 should be defoliated before 7th November, as there is a large decline in herbage mass and sward quality. Low target herbage mass (THM; 500 kg DM ha-1) should have a later DD, as swards continue to accumulate herbage, while maintaining sward quality, however, low THM, can potentially be carried over winter, average farm cover is below farm targets for spring demand (i.e. above 750 kg DM ha-1; S.R. > 2.9 livestock units (LU) ha-1). Carrying swards with lower herbage masses over winter was demonstrated successfully in chapter 4 and 5. The medium THM, can maintain sward quality across the autumn period, despite losing herbage, so can be grazed later in the final rotation. Sward morphology was also affected by increasing herbage masses in autumn. Light transmitted to the base of the sward was reduced, which resulted in increased internode elongation. Very high THM had the greatest number of tillers with internode elongation and the longest length of internode elongation.
Autumn CD was found to affect herbage production, herbage quality, leaf, stem and dead proportions and tiller density over winter and in spring. Autumn CD is responsible for 50% of the herbage available in spring, with each day delay in closing resulting in an extra 16 kg DM-1. Swards closed earlier had a higher herbage mass in spring and lower sward quality compared to later closed swards; that had reduced herbage and a higher herbage quality. Autumn CD effected subsequent growth rates but not quality in spring (2nd rotation); swards closed early had a lower growth rate compared to swards closed later following the initial spring defoliation. Sward structure was negatively affected by early autumn CD. Early CD had greater parent and daughter tiller mortality than later CD. Early CD also resulted in greater leaf extension and leaf senescence rates in daughter tillers compared to late.
The results of this thesis have provided further insight into the grazing management practices in autumn and spring and the impact they have on sward structure, quality and herbage. These results will help improve grazing management practices into the future
Modulation of plant growth by day length dependent regulation of the TOR signaling pathway
No full textPlant growth occurs through cell growth and proliferation, which are high energy demanding processes. Plants need to coordinate growth responses with their environmental conditions to ensure the best use of their resources. This accurate regulation depends on the circadian clock, an internal time keeping mechanism that informs the plant of day length duration (photoperiod).
The TOR (Target of Rapamycin) kinase pathway is a central hub where cellular energy levels are perceived and translated into specific growth responses across kingdoms. In plants, the TOR pathway has been associated with rapid growing tissue including embryos, shoot and root meristems. Downstream of TOR, the 40S ribosomal protein S6 Kinase 1 (S6K1) modulates both cell growth and proliferation.
Since S6K1 accumulation is modulated by the circadian clock, this thesis investigated how changes in S6K1 levels would affect plant growth when the clock function is impaired by mutation in ZTL (ZEITLUPE) which encodes a F-box protein that targets for degradation several components of the Arabidopsis clock.
The findings show that de-regulation of TOR signaling pathway components impacts plant growth and development. This negative effect is reinforced by a defective circadian function, suggesting that plants require a running clock to match the TOR pathway activity with specific environmental conditions
An investigation into the tissue culture and transformation of embryonic callus from mature and immature embryos of the model grass species Brachypodium distachyon and Brachypodium sylvaticum
Get PDFIn recent years, the genus Brachypodium has become of great interest to researchers, for use as a model grass system for cereal crops. Exploring the traits of a model species provides researchers with a broader understanding of internal genetic operations of evolutionarily related plant species, leading to advances in selective breeding of crop plants for profitable and sustainable phenotypic traits. Model species process many favorable traits including rapid life cycles, ease of transformation, among others. Many advances have been made to optimise the Brachypodium genus as a model species, including whole-genome sequencing, BAC libraries, EST sequences, availability of many natural accessions. The most widely studied species in the Brachypodium genus, B. distachyon has rapidly soared to the frontline as a model species due it its short life cycle (annual), rapid generation time, small stature, known genetic sequence and amenability in tissue culture and field conditions. In contrast, the perennial relative B. sylvaticum is favoured for being a model species for perennial bioenergy crops including switchgrass and Miscanthus. Although not as widely studied as B. distachyon at present, B. sylvaticum is diploid, self-fertile, with a short generation time. These traits encourage the development of B. sylvaticum into a perennial crop model species. This thesis outlines tissue culture conditions needed to produce compact embryogenic callus (CEC) from both mature and immature embryos from the accessions, Bd21 of B. distachyon and Ain-1 of B. sylvaticum. Induction and propagation of embryogenic callus were promoted by different concentrations of 2,4-Dichlorophenoxyacetic acid (2,4-D) and 6-Benzylaminopurine (BAP) in the callus induction medium (CIM). An Agrobacterium-mediated transformation system was developed for immature and mature embryonic callus using the virulent strain AGL1 carrying the pCAMBIA 1305.2 vector. This vector possesses the nptII gene for bacterial selection with kanamycin, the β-glucuronidase GusPlus gene for histochemical staining and the hptII gene for plant hygromycin phosphotransferase II selection. The reporter beta-glucuronidase (GUS) gene was driven by the CaMV35S promoter and terminated by the CaMV35S polyA signal. Successful transformation was detected using polymerase chain reaction (PCR) technology. Detecting a positive result for the T-DNA hptII gene and a negative result for the intercistronic region between Vir B and Vir G genes indicated positive tissue transformation. A positive result intercistronic region would indicate the AGL1 was present on the outside of the plant tissue as this region would not be integrated into the plant tissue during transformation. Embryonic callus production, transformation efficiency (up to 22%) and regeneration efficiency (up to 26%) were compared between both species using this protocol. Production and transformation of mature and immature embryos of both species, along with regeneration of transformed plantlets, is another positive step in the journey to making B. distachyon and B. sylvaticum into model species
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
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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