1,721,035 research outputs found
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
Diagnosis and genome analysis of lettuce necrotic yellows virus subgroups
No full textLettuce necrotic yellows virus is the type species of Cytorhabdovirus. This plant virus causes a disease that is most frequently reported in lettuce in Australia and New Zealand. The lettuce necrotic yellows virus (LNYV) population comprises two subgroups; subgroup I and subgroup II. The subgroups were previously identified by phylogenetic analysis of LNYV, and a diagnostic method distinguishing these subgroups has not yet been developed. In the current study, a diagnostic test for the LNYV subgroups based on reverse transcription polymerase chain reaction (RT-PCR) and RT-PCR- restriction fragment length polymorphism (RFLP) was developed and used for subgroup diagnosis. Subgroup specific primers were designed and tested on known infected samples. RT-PCR diagnosis of LNYV subgroups with these primers requires the subgroup specific primers are used in separate reactions, requiring two reactions for each sample being tested. The RT-PCR-RFLP diagnostic test allows amplification of an LNYV sequence using all the subgroup primers combined, followed by a restriction digest to generate a diagnostic pattern of DNA fragments that can be identified by gel electrophoresis.. The previously designed primers, BCNG1/BCNG2, and LNYV_440F/LNYV_1185R primer pairs were used for LNYV diagnosis. The conditions of these primers were re-optimised for the use in AUT laboratory. The as above mentioned primers were used to test for LNYV and its subgroup on potentially LNYV infected plants collected from Auckland, Waikato and Canterbury. A total of ten samples were tested positive for LNYV; three were subgroup I, six were subgroup II and one sample was LNYV subgroup unknown. LNYV subgroups can now be diagnosed more rapidly than by the previously used sequencing and phylogenetic analysis. The results also showed that LNYV_440F/LNYV_1185R primer pair was more efficient than BCNG1/BCNG2 primers to detect LNYV. The false negative results caused by BCNG1/BCNG2 primer pair could be due to RNA degradation.
Only one complete genome of LNYV (subgroup I) has been reported, which was obtained from an Australian isolate. In this study, the complete genomes of LNYV subgroups I and II from New Zealand isolates were sequenced by Illumina HiSeq. Phylogenetic analyses of LNYV genomes and all the available cytorhabdovirus and nucleorhabdovirus genomes were carried out. The results showed that LNYV subgroup I genomes are most closely related to each other than to subgroup II. Lettuce yellow mottle virus was the most closely related to LNYV. Phylogenetic analyses of the LNYV nucleocapsid gene sequences were also performed. The amino acid phylogenetic analysis shows that the AU9 isolate (subgroup II from Australia) appears to be closely related to the common ancestor, which indicates the origin of subgroup II. Since the complete genome or other gene sequences from the AU9 isolate are not available, the origin of LNYV cannot be confirmed. More samples from both Australia and New Zealand are necessary to understand these relationships more clearly.
LNYV subgroup I isolate has not been detected in Australia since 1993 and subgroup II may have outcompeted subgroup I in Australia, while this has not occurred in New Zealand. It was hypothesised by previously that subgroup II may have a more efficient relationship with the insect vectors and hosts. The glycoprotein was specifically analysed in the current study because rhabdoviruses use glycoprotein to attach and penetrate to the insect vectors/plant hosts. It was hypothesised that analysis of the glycoprotein may help to determine if subgroup II has a higher efficient relationship with insect/plant hosts than subgroup I. Six characteristics of glycoprotein sequence and 2D structure were analysed. It showed there were differences between the subgroups. However, a 3D structure and mutational analysis are needed to determine if the differences affect its association with the insect/plant hosts
Identification of Reference Genes and Quantification of Gene Expression Changes in Nicotiana glutinosa Plants Infected by Subgroups I & II of Lettuce Necrotic Yellows Virus
No full textLettuce necrotic yellows virus (LNYV) is a plant virus that has been reported to cause widespread crop losses in lettuce in Australia and New Zealand for the last 60 years. Phylogenetic analysis has determined two subgroups of the virus exist within the population, identified as subgroup I and II. It appears subgroup II has emerged more recently than subgroup I and currently has a wider geographical distribution, with subgroup I appearing to now be extinct in Australia.
Limited research has been undertaken into understanding the molecular mechanisms by which the virus operates upon establishing infection within a host plant. It is not known whether the two different subgroups influence different molecular pathways which may explain the current distribution of the virus in the environment. This study was designed to determine the expression of four target genes in the host plant Nicotiana glutinosa after inoculation by subgroup I and subgroup II of LNYV.
A reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay was utilised to determine the relative gene expression of the target genes CPK3, SGS3, WRKY26 and WRKY70 in response to LNYV infection. For a RT-qPCR experiment, a set of validated reference genes are necessary to act as internal controls and need to be specifically selected for studies in a particular host. Currently, no validated reference genes have been reported in the literature for N. glutinosa, so candidates were selected to determine their suitability for this purpose; Actin, EF1α, F-BOX, L23 Ntubc2, PDF2, PP2A, SAND and Ubiquitin. No full genome has been published for N. glutinosa, so molecular data from related species had to be obtained to infer the structure of these genes in order to design primers to amplify the genes in a qPCR experiment. Primers could not be designed for F-BOX, L23 and Ubiquitin, and non-specific products were amplified during amplification of WRKY26, EF1α and PDF2. The remaining candidate reference and target gene primers specifically amplified a single product and were considered suitable for testing in the gene expression study.
To obtain sufficient LNYV infected biological replicates for the qPCR experiment, N. glutinosa plants were grown from seed and inoculated with LNYV subgroup I or II. Infection rates varied between 0% and 15% for subgroup 1 and was 26.6% for subgroup II after 28 days of growth. After failing to grow enough replicates to study the virus across six time points, the experimental design was amended to determine target gene expression after 28 days in both subgroups.
Normalised, outlier removed qPCR data was processed using GeNorm and Normfinder algorithms and the values obtained suggested of the remaining candidate reference genes tested, SAND and Ntubc2 were suitable to be used in subsequent experiments based on their stable expression, though additional reference genes are required, and further biological replicates may be necessary to confirm this.
Using these reference genes and comparing the data of the genes of interest, it was determined that CPK3, SGS3 and WRKY70 were upregulated between uninfected and subgroup I infected conditions, and CPK3 and SGS3 were downregulated between uninfected and subgroup II infected conditions, whilst WRKY70 was upregulated. Differences were identified between the subgroups, with all three genes being more highly expressed in subgroup I compared to subgroup II with an approximate 7-fold difference in WRKY70 expression, suggesting that subgroup I isolates may induce transcription and signalling pathways in hosts to a higher degree than subgroup II during infection. Though this was a small scale study it indicates that the biological impact of the different subgroups of the LNYV subgroups may differ which may have influenced the current geographical distribution of the virus. Further research could focus on identifying additional reference genes for qPCR-based studies utilising N. glutinosa, or research additional target genes to try and identify additional molecular pathways the subgroups impact
Assessment of Ethanol, Honey, Milk and Essential Oils as Potential Postharvest Treatments of New Zealand Grown Fruit
No full textBrown and Penicillium rot (blue and green mould) are the most common postharvest diseases in New Zealand, causing significant postharvest fruit losses. Current practice uses fungicides to control the postharvest diseases; however there are perceived health risks associated with the use of such chemicals. Recently, there has been substantial interest in chemicals that are considered Generally Regarded as Safe or GRAS and natural products as alternative postharvest treatments to replace currently used fungicides. In this study, ethanol (GRAS chemical) and the natural products honey, milk and essential oils (lemon, lemongrass, manuka and orange) were assessed as potential alternative treatments to replace the currently used fungicides on both peaches and oranges. In pilot studies ethanol was applied to the fruit by either vapour or dipping (30 seconds or 1.5 minutes). Honey, milk and essential oils were applied by dipping at 30 seconds. Essential oils were also tested using a microtiter assay. Exposing fruit to ethanol vapour proved effective at inhibiting fungal growth, but impacted negatively on fruit quality. Peaches that were exposed to 70% to 100% ethanol vapour were protected against fungal infection for up to 30 days when stored at either 4ºC or room temperature. This is compared to two days for untreated peaches and three days for fungicide -treated peaches. However, the ethanol-treated peaches suffered from severe browning. In contrast, 20% ethanol protected peaches for ten days when stored at 4ºC and two days at room temperature. The fruit that were exposed to 20% ethanol did not brown as a result of the treatment. Oranges that were exposed to 20%, 50%, 70% and 100% ethanol vapour were protected from fungal inhibition for 30 days at both 4ºC and room temperature, but they too suffered from severe browning. Dipping was not as effective as vapour at protecting against fungal infection, but had a little effect on fruit quality. Peaches dipped in 20% to 100% ethanol were completely rotten by ten days when stored at room temperature, but the peaches experienced little to no browning. Untreated and fungicide-treated fruit were protected for one day and two days, respectively. Milk and honey do not appear to have potential as postharvest treatments. Peaches that were treated with 20%, 50% and 100% whole milk and 50% manuka honey showed greater degree of fungal infection compared to untreated peaches after both room temperature and 4ºC storage. At room temperature, peaches that were exposed to 20%, 50% and 100% milk were completely rotten at eight days, compared with ten days for untreated peaches. In contrast, at 4ºC, peaches that were treated with 100% milk were completely rotten at 30 days, while only a slight fungal infection observed on untreated fruit. Similar to milk, honey-treated peaches were also completely rotten at 30 days at 4ºC storage.In vitro (microtiter) assay of the essential oils showed that orange and manuka oils appeared to be effective only at high concentrations. In contrast, lemongrass and lemon oils appeared to be effective even at low concentrations. Of the essential oils tested in the in vivo assay, lemongrass and lemon oils have the greatest potential. Oranges that were exposed to 0.05% lemongrass oil, 0.25% and 0.5% lemon oil were protected for 30 days when stored at 4ºC or room temperature. They provided the best antifungal activity compared to the other concentrations of all four essential oils tested as well as fungicide treatment for 30 days. Of all the treatment tested, 0.05% lemongrass oil, 0.25% and 0.5% lemon oil appeared to be the most promising treatments. However, these treatments need to be tested for antifungal effects, fruit quality, flavour and nutritional effects in large scale experiments before they can be applied as replacements to currently used fungicides. Also, essential oils are complex compounds; therefore it would be of interest to determine the active compound(s) of the lemongrass and lemon oils
Genetic variability of Dasheen mosaic virus and consequences for detection
No full textThe genus Potyvirus is one of the largest groups of plant viruses having RNA genomes. RNA viruses show high genetic diversity which can influence virus infectivity and host selection. In this study, deep sequencing profiles of a potyvirus, namely Dasheen mosaic virus (DsMV) were analysed to determine the level of genetic variation occurring in two different DsMV strains (DsMV-NZ1 and DsMV-B) and isolates (DsMV-NZ1.1, NZ1.2, B1.1 and B1.2).
Potyviruses are one of the most important groups of plant viruses that cause severe damage to agricultural, horticultural and ornamental crops. Within this genus, DsMV is an important viral pathogen of cultivated aroids worldwide, causing a 40-60% reduction in total crop yield. Therefore, the precise and accurate identification of DsMV infection is important for developing appropriate control mechanisms. The first objectives of this study was to test the effectiveness of universal potyvirus primers in detection and identification of DsMV infection in taro. Three pairs of universal primers, namely HPFor-HPRev, CIFor-CIRev and NIb2F-NIb3R were tested in this study using reverse-transcriptase polymerase reaction (RT-PCR). After testing each of these primer pairs, it was concluded that these primers can be used for detection and identification of the DsMV infection of taro, but only under the experimental conditions used in this study.
The second objective was to determine the level of variation within each strain/isolate of the DsMV. For that Illumina HiSeq 2000 platform was used for creating the deep sequencing profiles of each sample. The bioinformatics analysis revealed that the level of variation across all the samples was consistent and an average 20% of genetic variation was observed within each strain/isolate from the DsMV reference genome. It was also found that the level of variation within the isolates of a same strain was lower than variation between the strains. A phylogenetic tree constructed based on the whole genome nucleotide sequences of the DsMV showed that DsMV belongs to the Bean common mosaic virus (BCMV) group. The phylogenetic analysis also revealed that DsMV is most closely related to Vanilla mosaic virus (VaMV) than to any other virus of the BCMV group.
The third objective of this study was to determine the level of variation within each region of the DsMV genome. The bioinformatics analysis of the Illumina sequencing data showed that the variation within the 5’ and 3’ untranslated regions was ~28% and 30%, respectively. With the protein coding genes, the P1 gene showed the highest level of genetic variation (~30%) while NIa-VPg gene showed the lowest (~16%). The low level of variation in the NIa-VPg gene suggested that this gene may be functionally very important for the DsMV while the high variation of the P1 may provide a mechanism for altering the host range. Each region needs to be investigated in more detail, which may help in identification of the regions of conservation within the potyviral genome.
The results showed that genetic variability can interfere with the efficient detection and identification of potyviral infection in plants. The findings of this study, helped in understanding the pattern of genetic variability among potyviruses. and in developing a better understanding of the functionality of the potyviral genome. The findings of this study can also be used for identifying the conserved regions within the potyviral genome, which would be expected to assist designing better universal primers for precise and accurate detection of potyvirus infection in plants, as well as deepening or understanding of viral processes such as translation replication
Genetic Variability of Dasheen Mosaic Virus and Consequences for Detection
No full textThe genus Potyvirus is one of the largest groups of plant viruses having RNA genomes. RNA viruses show high genetic diversity which can influence virus infectivity and host selection. In this study, deep sequencing profiles of a potyvirus, namely Dasheen mosaic virus (DsMV) were analysed to determine the level of genetic variation occurring in two different DsMV strains (DsMV-NZ1 and DsMV-B) and isolates (DsMV-NZ1.1, NZ1.2, B1.1 and B1.2).
Potyviruses are one of the most important groups of plant viruses that cause severe damage to agricultural, horticultural and ornamental crops. Within this genus, DsMV is an important viral pathogen of cultivated aroids worldwide, causing a 40-60% reduction in total crop yield. Therefore, the precise and accurate identification of DsMV infection is important for developing appropriate control mechanisms. The first objectives of this study was to test the effectiveness of universal potyvirus primers in detection and identification of DsMV infection in taro. Three pairs of universal primers, namely HPFor-HPRev, CIFor-CIRev and NIb2F-NIb3R were tested in this study using reverse-transcriptase polymerase reaction (RT-PCR). After testing each of these primer pairs, it was concluded that these primers can be used for detection and identification of the DsMV infection of taro, but only under the experimental conditions used in this study.
The second objective was to determine the level of variation within each strain/isolate of the DsMV. For that Illumina HiSeq 2000 platform was used for creating the deep sequencing profiles of each sample. The bioinformatics analysis revealed that the level of variation across all the samples was consistent and an average 20% of genetic variation was observed within each strain/isolate from the DsMV reference genome. It was also found that the level of variation within the isolates of a same strain was lower than variation between the strains. A phylogenetic tree constructed based on the whole genome nucleotide sequences of the DsMV showed that DsMV belongs to the Bean common mosaic virus (BCMV) group. The phylogenetic analysis also revealed that DsMV is most closely related to Vanilla mosaic virus (VaMV) than to any other virus of the BCMV group.
The third objective of this study was to determine the level of variation within each region of the DsMV genome. The bioinformatics analysis of the Illumina sequencing data showed that the variation within the 5’ and 3’ untranslated regions was ~28% and 30%, respectively. With the protein coding genes, the P1 gene showed the highest level of genetic variation (~30%) while NIa-VPg gene showed the lowest (~16%). The low level of variation in the NIa-VPg gene suggested that this gene may be functionally very important for the DsMV while the high variation of the P1 may provide a mechanism for altering the host range. Each region needs to be investigated in more detail, which may help in identification of the regions of conservation within the potyviral genome.
The results showed that genetic variability can interfere with the efficient detection and identification of potyviral infection in plants. The findings of this study, helped in understanding the pattern of genetic variability among potyviruses. and in developing a better understanding of the functionality of the potyviral genome. The findings of this study can also be used for identifying the conserved regions within the potyviral genome, which would be expected to assist designing better universal primers for precise and accurate detection of potyvirus infection in plants, as well as deepening or understanding of viral processes such as translation replication
Towards the Analysis of Potyvirus VPg Interacting Protein (PVIP) Gene Expression in Response to Potyvirus Infection
No full textPotyvirus is the largest genus in the RNA plant virus family of Potyviridae. Potyviruses infect most of the economically important agricultural and ornamental crops; Dasheen mosaic virus (DsMV) is a potyvirus which infects edible aroid plants such as taro, particularly in the South Pacific region. These viruses rely on various host plant proteins for their movement and replication. One such plant protein which is known to interact with the viral protein called virus genome linked protein (VPg) is potyvirus VPg interacting protein (PVIP). Dunoyer et al., (2004) suggested role for PVIP in potyvirus movement, in disease development and as an important factor for virus replication. Further, through bioinformatics sequence analysis of homologous Arabidopsis thaliana and Nicotiana benthamiana PVIP sequences, the PVIP gene was found to be homologous to OBERON 1 and OBERON 2 in A. thaliana, suggesting a role for PVIP in meristem maintenance (Saiga et al, 2008; Anand, 2010). This analysis also suggested that PVIP may have a role independent of virus infection, it may be an important factor in plant development. Anand (2010) analysed the effect of abiotic stress on PVIP mRNA accumulation. The PVIP mRNA levels were assessed in leaf tissue of N. benthamiana under various dark and light conditions. A decline in the PVIP mRNA accumulation was observed when these plants were placed in continuous dark, suggesting that light induces the expression of PVIP mRNA. This study concluded that PVIP gene is responsive to this type of abiotic stress; however, the responsiveness of PVIP mRNA level to biotic stress such as virus infection is yet to be unravelled.
The aim of this study was to determine the variation of PVIP mRNA accumulation in healthy and DsMV infected taro using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR). To conduct this analysis, the first objective was to identify appropriate reference genes for use in virus infected studies in taro.
There are several methods to conduct gene quantification studies such as northern hybridization, microarray data analysis; among these RT-qPCR has become the most reliable, common and sensitive method for the quantification of gene expression. According to the MIQE guidelines, there are many factors that need to be considered while conducting RT-qPCR analysis, one such important variable is the use of appropriate reference genes (Bustin et al., 2010). A reference gene is defined as having a stable expression under different experimental treatments (Taylor et al., 2011). Housekeeping genes such as glyceraldehydes-3-phosphate dehdrogenase (GAPDH), ubiquitin (UBQ), actin 18S rRNA have been used as reference genes; however, it has been found that the expression level of many of these housekeeping genes vary under various experimental conditions.
Lilly et al., (2011) assessed the stability of 12 candidate reference genes in virus infected A. thaliana. Among these 12 genes studied such as actin, UBQ, only four genes were shown to have stable expression. These four genes were namely, F-box family protein (F-box), SAND family protein, protodermal factor 2 (PDF2) and elongation factor α (EF1α). These genes were suggested to be suitable reference genes for analysis of all virus infected plants; however, this would need to be tested in other species before using them. Therefore, in this study the expression stability of these four reference genes namely, EF1α, F-box, SAND and PDF2 in healthy taro and N. benthamiana was assessed using RT-PCR. Various parameters such as annealing temperatures were tested using gradient PCR to optimise for efficient amplification of these genes in taro and N. benthamiana; however, efficient amplification was not achieved in taro and N. benthamiana using these primer pairs. Further, sequence analysis of homologous A. thaliana EF1α, PDF2, F-box and SAND genes against other publicly available monocot and dicot sequences, suggested significant variation within the primer target sequences, particularly in the 3’ end of the reverse primers. This may account for the inefficient amplification of these genes in taro and N. benthamiana. Therefore, new generic primers, specific to both monocot and dicot species were designed; however, due to limited availability of sequence information for PDF2 and SAND in publicly available databases along with significant variations among monocots and dicots, new generic primers were only designed for the amplification of EF1α and F-box genes. A EF1α primer pair suitable for both monocots and dicots was designed. For F-box, two primer pairs were designed one for monocots and one for dicots. The newly designed primers were then tested on taro, N. benthamiana and A. thaliana using RT-PCR and optimum PCR conditions was obtained.
Next step was to validate the EF1α and F-box genes as reference gene in virus infected taro using RT-qPCR. The data obtained was analysed statistically to determine any significant variation in the mRNA accumulation of EF1α and F-box between healthy and DsMV infected taro. Both these genes were shown to have similar and constant expression in healthy and DsMV infected taro. This suggests that these genes could be used as suitable reference gene for gene quantification studies in taro. For other species such as N. benthamiana and other monocot and dicots, this would need to be tested and confirmed empirically.
For the analysis of PVIP mRNA accumulation in healthy and DsMV infected taro, PVIP primers designed for N. benthamiana were tested on taro and A. thaliana using RT-PCR. A very faint product of expected size was observed for both taro and A. thaliana using this primer pair; however, it was assumed that the observed amplification would be sufficient for the efficient amplification of PVIP in taro for RT-qPCR analysis. The mRNA accumulation of PVIP was normalised against the EF1α and F-box reference genes for the RT-qPCR analysis. However, efficient amplification was not achieved from either healthy or DsMV infected taro using the N. benthamiana specific PVIP primer pair. Hence, generic monocot and dicot PVIP primers need to be designed and tested for future gene quantification studies in taro and other monocot and dicot species, to determine the variation in the mRNA accumulation of PVIP in virus infected plants
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