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Sesamum indicum Cytochrome P
No full text<i>4.11. Phylogenetic analysis of O. indicum cytochrome P 450</i> <p>Genes annotated as Cytochrome P 450 in the transcriptome were shortlisted (Supplementary Table 4). They were used to identify the full length ORFs of OinCyp450s with high FPKM values (above 5.5). Protein BLAST of the genes annotated as cytochrome P450 s was performed to identify the type /function of the specific Cytochrome P450. Phylogenetic tree of the newly identified, full length protein OinCyps was performed using MEGA7 by the maximum likelihood method (Kumar et al., 2016) (Fig. 5).</p> <p> <b>Conflicts of interest</b></p> <p>The authors declare no conflict of interest.</p> <p> <b>Acknowledgement</b></p> <p>The authors would like to acknowledge the Department of Biotechnology (DBT), Government of India for the DBT-BioCARE project to Dr. Vaijayanti Tamhane (BT/Bio-CARe/07/320/2012) and Departmental Research and Developmental Program (DRDP), Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India for funding this work. The authors are thankful to Ms. Meenakshi Kapse, Project Assistant, IBB, SPPU for helping with command line BLAST analysis of the transcriptome. The authors are grateful to Dr. Sneha Bansode, Department of Biotechnology, SPPU for her critical comments and suggestions. The transcriptome sequencing service was provided by Genotypic, Bangalore, India.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 211, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Oroxylum indicum subsp. root
No full text<i>2.1. Sequencing and De novo assembly of O. indicum root transcripts</i> <p> <i>De novo</i> transcriptome analysis is an excellent platform for generation of comprehensive information to deduce the basic biological, molecular and cellular processes for non-model organisms lacking whole genome sequences. To generate a transcriptome database for <i>O. indicum</i>, cDNA libraries of root tissue were sequenced using Illumina NextSeq 500. A total of 24,625,398 raw reads were generated comprising 3,718,435,098 nucleotides with an average size of 151 bp and 44% GC content (Table 1). Reads with Q <20 were removed. Reads were mapped to human reference transcriptome which showed absence of contamination of human transcripts. These high quality reads were used for <i>de novo</i> assembly using Trinity (Hass et al., 2013). It has been reported that the quality of a <i>de novo</i> assembly is dependent on many factors, such as the type of assembler used, followed by parameters like N50 value and coverage (Reddy et al., 2015). The data has been submitted to NCBI, Sequence Read Archive (SRA) submission: SUB2988844.</p> <p>The assembly resulted in a total of 121,286 transcripts with N50 value of 1783 bp with an average contig length of 1080 bp (Table 2). Furthermore, transcript clustering (CD-HIT-EST) resulted into 81,002 transcripts with an average contig length of 1071 bp and 1788 N50 value (Table 2). These 81,002 transcripts were further targeted for BLASTx analysis for functional annotation.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 202, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Oroxylum indicum subsp. root
No full text<i>2.6. Transcription factor analysis in the O. indicum root transcriptome</i> <p> At least six distinct transcription factors (TFs) namely myeloblastosis (MYB), basic helix-loop-helix (bHLH), WD or beta-transducin repeat (WD40), WRKY, Zinc finger and MADS box proteins are involved in flavonoid biosynthesis regulation (Terrier et al., 2009). Of these, three transcription factors MYB, bHLH and WD40 (MBW) were detected in the root transcriptome of <i>O. indicum</i> (Table 6; Supplementary Table 3). MYB11, MYB12 and MYB111 are known to control flavonol biosynthesis by activating the early biosynthetic steps (Nesi et al., 2002; Gou et al., 2011), while the MBW complex activates the late biosynthetic genes of flavonoid biosynthesis (Mehrtens et al., 2005; Stracke et al., 2007; Li, 2014). In the <i>O. indicum</i> root, the MYB transcription factor family was represented prominently, followed by WD40 and bHLH (Table 6; Supplementary Table 3). These transcription factors can either work individually or synergistically in controlling the multiple enzymatic steps involved in the flavonoid biosynthesis (Mano et al., 2007; Hichri et al., 2011).</p> <p> Among the MYB family TFs, MYB 4 and R2R3-MYB were highly abundant in <i>O. indicum</i> root (Table 6). R2R3-MYB protein is known to participate in the regulation of specialized metabolism including production of phenylpropanoids and flavonoids in plants (Vom Endt et al., 2002; Bomal et al., 2008; Taylor and Grotewold, 2005). The putative TF bHLH was highly expressed in the root transcriptome of <i>O. indicum.</i> bHLH interacts with R3 repeat domains of MYB proteins at the Nterminal acidic region to form the MYB –bHLH complex, involved in flavonoid biosynthesis pathway regulation (Feller et al., 2011). Transducin/WD-40 family isoform 5, of the WD40 family was abundant in <i>O. indicum</i> roots. WD40 proteins do not possess any catalytic activity, but it has been hypothesized that they act as a docking platform for regulating the anthocyanin and phenylalanine biosynthesis pathways (Feller et al., 2011).</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 205, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
Cold-induced sweetening in potato (Solanum tuberosum L.): genetic analysis of the apoplastic invertase inhibitor gene
No full textPotatoes are increasingly consumed in the form of processed foodstuffs such as French fries and crisps. After harvest, potatoes need to be kept at low temperature to prevent sprouting during storage for round-the-year processing. However, tubers accumulate reducing sugars at low temperatures, a phenomenon referred to as cold-induced sweetening (CIS). The processing of these high sugar potatoes into crisps or fries leads to a dark brown to black product that renders them unfit for human consumption and causes a great loss to the processing industry. To prevent sprouting and diseases, chemical treatments have been applied to tubers in storage. The recent withdrawal of these chemicals has increased the reliance on cold storage for potato tubers and highlighted the importance of CIS. Extensive research is required to produce a cultivar resistant to cold induced sweetening (CIS) along with good processing quality. The present work focused on increasing the understanding of the biological processes (physiological, biochemical and molecular) contributing to the initiation and/or controlling of CIS in potato tubers. The genetic basis of this trait was examined in progeny from a cross between potato cultivars with poor and excellent CIS response. This included molecular markers for candidate genes of known position on potato chromosomes to assess the role of different alleles involved in carbohydrate metabolism. Association studies between marker alleles and the phenotype of the progeny were performed. Among all the candidate genes, allele diversity for apoplastic invertase inhibitor gene was further studied from resistant and susceptible potato cultivars. In total five alleles were identified. Polymorphism was observed in both exon and intron regions. Three alleles had a unique substitution at the predicted junction of the signal peptide and mature protein. In order to identify the specific alleles that may play a role in resistance to CIS, transgenic potato plants have been produced with overexpression and antisense repression of apoplastic invertase inhibitor alleles. The results revealed that there were no consistent differences in CIS traits among the transgenic lines with the various alleles. However, the results of the transcript analysis showed much higher and stable transcripts levels of the apoplastic invertase inhibitor in the 1021/1 derived transgenic lines. This greater accumulation or stability of the apoplastic invertase inhibitor transcripts in 1021/1 may be a key factor contributing to the CIS trait of this cultivar.
A key difference from previous studies involves the use of 1021/1, a potato cultivar known to have the very high resistance to CIS. This study provided to help identify key genes for the future genetic improvement of tuber properties with respect to long-term storage and processing characteristics. The development of a potato that does not sweeten in the cold will revolutionize the potato industry as this problem currently contributes 20 percent losses after crop harvest. Once identified, clones resistance to CIS could be used in potato breeding programmes for the development of cold-resistant processing cultivars. Eliminating the need for chemical application of sprout inhibitors will be helpful to develop sustainable approaches to benefit both mankind and potato industries. These biotechnological tools will be used to identify elite potatoes with improved properties of the tuber with respect to long-term storage and processing characteristics (cold-sweetening and after-cooking darkening)
Oroxylum indicum subsp. root
No full text<i>2.7. Expression pattern of selected phenylpropanoid and flavonoid</i> <i>biosynthesis pathway genes in the young and mature roots of O. indicum</i> <p> Relative expression levels of seven genes namely, cinnamyl alcohol dehydrogenase (<i>OinCAD</i>), 4-coumarate–CoA ligase (<i>Oin4CL</i>), transcinnamate 4-monooxygenase (<i>OinC4H</i>), chalcone synthase (<i>OinCHS</i>), flavone synthase (<i>OinFNS</i>), chalcone isomerase (<i>OinCHI</i>) and flavanone 3-dioxygenase (<i>OinF3H</i>) were determined by a quantitative real time polymerase chain reaction (qRT-PCR) (Fig. 4) in young and old roots of <i>O. indicum</i>. The expression level of <i>OinCAD</i> was not significantly different in the two tissues. A two fold higher expression of <i>Oin4CL</i> was detected in old roots as compared to young roots. The expression of <i>OinC4H</i> was lower in both the young and old root of <i>O. indicum</i>. <i>OinCHS</i> showed around a four fold higher expression in the old root as compared to the young root (Fig. 4). <i>CHS</i> is the first rate-limiting enzyme in flavonoid biosynthesis pathway and higher levels of the enzyme is directly correlated with the higher level of flavonoids (Zuk et al., 2016). On the contrary, expression of <i>OinCHI</i>, <i>OinFNS</i> and <i>OinF3H</i> were at least ten fold higher in young roots as compared to old roots of <i>O. indicum</i> (Fig. 4). The higher expression of <i>CHI</i> in young roots may be linked to its role in auxin movement leading to plant growth and development (Peer and Murphy, 2007). Moreover, there are possibly different isoforms of the flavonoid biosynthesis genes which display spatial and temporal regulation, as reflected by their differential expression in young and old roots of <i>O. indicum</i>.</p>Published as part of <i>Deshmukh, Aaditi B., Datir, Sagar S., Bhonde, Yogesh, Kelkar, Natasha, Samdani, Pawan & Tamhane, Vaijayanti A., 2018, De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway, pp. 201-213 in Phytochemistry 156</i> on page 206, DOI: 10.1016/j.phytochem.2018.09.013, <a href="http://zenodo.org/record/10484692">http://zenodo.org/record/10484692</a>
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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