scholarly journals Transcriptome Analysis of Hormone-and Cuticle-Related Genes in the Development Process of Deutonymph in Tetranychus urticae

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 736
Author(s):  
Gang Li ◽  
Xinyao Gu ◽  
Shunhua Gui ◽  
Jianjun Guo ◽  
Tianci Yi ◽  
...  
Keyword(s):  
Juvenile Hormone ◽  
Tetranychus Urticae ◽  
Transcriptome Analysis ◽  
Development Process ◽  
Developmental Process ◽  
Biosynthesis Pathway ◽  
Time Points ◽  
Cuticle Protein ◽  
Chitinase Genes ◽  
Related Pathway

Tetranychus urticae is an important agricultural pest that feeds on more than 1100 plant species. To investigate gene expression network in development process of deutonymph, a comprehensive transcriptome analysis of different developmental time points of deutonymph in T. urticae was performed. Comparing with expression profile of 7 h, 309, 876, 2736, and 3432 differential expression genes were detected at time points 14 h, 21 h, 28 h, and 35 h, respectively. The expression dynamic analysis indicated that genes in hormone- (ecdysteroid and juvenile hormone) and cuticle- (chitin and cuticle proteins) related pathways were indispensable for development process in deutonymph. Among hormone related pathway genes, the ecdysteroid biosynthesis pathway genes were highly expressed at the growth period of development process, which is opposite to the expression patterns of juvenile hormone biosynthesis pathway genes. For cuticle related pathway genes, 13 chitinase genes were identified in the genome of T. urticae, and 8 chitinase genes were highly expressed in different time points of developmental process in the deutonymph of T. urticae. Additionally, 59 cuticle protein genes were identified from genome, and most of the cuticle protein genes were expressed in the molting period of developmental process in deutonymph. This study reveals critical genes involved in the development process of deutonymph and also provides comprehensive development transcriptome information for finding more molecular targets to control this pest.

scholarly journals Elucidation of the core betalain biosynthesis pathway in Amaranthus tricolor

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu-Cheng Chang ◽  
Yi-Ching Chiu ◽  
Nai-Wen Tsao ◽  
Yuan-Lin Chou ◽  
Choon-Meng Tan ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Natural Antioxidants ◽  
Biosynthesis Pathway ◽  
Comparative Transcriptome ◽  
Amaranthus Tricolor ◽  
Enzymatic Assays ◽  
Comparative Transcriptome Analysis ◽  
Elevated Expression ◽  
Green Coloration

AbstractAmaranthus tricolor L., a vegetable Amaranthus species, is an economically important crop containing large amounts of betalains. Betalains are natural antioxidants and can be classified into betacyanins and betaxanthins, with red and yellow colors, respectively. A. tricolor cultivars with varying betalain contents, leading to striking red to green coloration, have been commercially produced. However, the molecular differences underlying betalain biosynthesis in various cultivars of A. tricolor remain largely unknown. In this study, A. tricolor cultivars with different colors were chosen for comparative transcriptome analysis. The elevated expression of AmCYP76AD1 in a red-leaf cultivar of A. tricolor was proposed to play a key role in producing red betalain pigments. The functions of AmCYP76AD1, AmDODAα1, AmDODAα2, and AmcDOPA5GT were also characterized through the heterologous engineering of betalain pigments in Nicotiana benthamiana. Moreover, high and low L-DOPA 4,5-dioxygenase activities of AmDODAα1 and AmDODAα2, respectively, were confirmed through in vitro enzymatic assays. Thus, comparative transcriptome analysis combined with functional and enzymatic studies allowed the construction of a core betalain biosynthesis pathway of A. tricolor. These results not only provide novel insights into betalain biosynthesis and evolution in A. tricolor but also provide a basal framework for examining genes related to betalain biosynthesis among different species of Amaranthaceae.

scholarly journals De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Nisha Dhiman ◽  
Anil Kumar ◽  
Dinesh Kumar ◽  
Amita Bhattacharya
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Analysis ◽  
Vegetative Growth ◽  
De Novo ◽  
Biosynthesis Pathway ◽  
De Novo Transcriptome ◽  
Tissue Specific ◽  
Nardostachys Jatamansi ◽  
Secondary Metabolite Biosynthesis

Abstract The study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.

scholarly journals Failures to further developing orphan medicinal products after designation granted in Europe: an analysis of marketing authorisation failures and abandoned drugs

BMJ Open ◽  
2017 ◽  
Vol 7 (9) ◽  
pp. e017358 ◽  
Author(s):  
Viviana Giannuzzi ◽  
Annalisa Landi ◽  
Enrico Bosone ◽  
Floriana Giannuzzi ◽  
Stefano Nicotri ◽  
...  
Keyword(s):  
Marketing Authorisation ◽  
Development Process ◽  
Developmental Process ◽  
Clinical Stage ◽  
Phase Iii ◽  
Marketing Approval ◽  
Medicinal Products ◽  
Safety Issues ◽  
Stage Of Development ◽  
Orphan Medicinal Products

ObjectivesThe research and development process in the field of rare diseases is characterised by many well-known difficulties, and a large percentage of orphan medicinal products do not reach the marketing approval.This work aims at identifying orphan medicinal products that failed the developmental process and investigating reasons for and possible factors influencing failures.DesignDrugs designated in Europe under Regulation (European Commission) 141/2000 in the period 2000–2012 were investigated in terms of the following failures: (1) marketing authorisation failures (refused or withdrawn) and (2) drugs abandoned by sponsors during development.Possible risk factors for failure were analysed using statistically validated methods.ResultsThis study points out that 437 out of 788 designations are still under development, while 219 failed the developmental process. Among the latter, 34 failed the marketing authorisation process and 185 were abandoned during the developmental process. In the first group of drugs (marketing authorisation failures), 50% reached phase II, 47% reached phase III and 3% reached phase I, while in the second group (abandoned drugs), the majority of orphan medicinal products apparently never started the development process, since no data on 48.1% of them were published and the 3.2% did not progress beyond the non-clinical stage.The reasons for failures of marketing authorisation were: efficacy/safety issues (26), insufficient data (12), quality issues (7), regulatory issues on trials (4) and commercial reasons (1). The main causes for abandoned drugs were efficacy/safety issues (reported in 54 cases), inactive companies (25.4%), change of company strategy (8.1%) and drug competition (10.8%). No information concerning reasons for failure was available for 23.2% of the analysed products.ConclusionsThis analysis shows that failures occurred in 27.8% of all designations granted in Europe, the main reasons being safety and efficacy issues. Moreover, the stage of development reached by drugs represents a specific risk factor for failures.

Adding Learning to the Cellular Development of Neural Networks: Evolution and the Baldwin Effect

1993 ◽  
Vol 1 (3) ◽  
pp. 213-233 ◽  
Author(s):  
Frédéric Gruau ◽  
Darrell Whitley
Keyword(s):  
Neural Networks ◽  
Boolean Functions ◽  
Development Process ◽  
Developmental Process ◽  
Fitness Landscape ◽  
Biological Cell ◽  
Baldwin Effect ◽  
Genetic Search ◽  
Lamarckian Evolution ◽  
The Baldwin Effect

A grammar tree is used to encode a cellular developmental process that can generate whole families of Boolean neural networks for computing parity and symmetry. The development process resembles biological cell division. A genetic algorithm is used to find a grammar tree that yields both architecture and weights specifying a particular neural network for solving specific Boolean functions. The current study particularly focuses on the addition of learning to the development process and the evolution of grammar trees. Three ways of adding learning to the development process are explored. Two of these exploit the Baldwin effect by changing the fitness landscape without using Lamarckian evolution. The third strategy is Lamarckian in nature. Results for these three modes of combining learning with genetic search are compared against genetic search without learning. Our results suggest that merely using learning to change the fitness landscape can be as effective as Lamarckian strategies at improving search.

Managing concurrent execution of multiple activities in product development process

2020 ◽  
Vol 28 (3) ◽  
pp. 210-221
Author(s):  
Gyesik Oh ◽  
Yoo Suk Hong
Keyword(s):  
Product Development ◽  
Concurrent Engineering ◽  
Information Transfer ◽  
Process Model ◽  
Development Process ◽  
Developmental Process ◽  
Quantitative Model ◽  
Product Development Process ◽  
Optimal Decision ◽  
Concurrent Execution

Many companies adopt concurrent engineering in their product-development projects in order to reduce time to market. Concurrent engineering requires careful management, since the uncertainty of transferred information leads to rework and renders a development process complex. Most of the existing studies on concurrent engineering have analyzed overlapping between two activities. The present study expanded the research scope by modeling the developmental process of the concurrent execution of multiple activities as the result of management decisions, the overlapping ratio, and the information transfer frequency. When multiple activities are overlapped, it is more difficult to model a development process, since the uncertainty of cascaded information has impacts on many activities. The quantitative model developed in the present study provides insights into the uncertainty of information and the product-development process. Based on the generalized process model for multiple-activity overlapping, the optimal decision to minimize project duration was considered. As a solution to the dilemma of the high computational burden of considering all feasible decision sets, this paper proposes a myopic heuristic. The project management heuristic proposed in this paper is intended to assist managers in the decision-making process, as well as reducing the intermediate deadlines in project main plan.

scholarly journals Phenotypic Characterization of Streptococcus pneumoniae Biofilm Development

2006 ◽  
Vol 188 (7) ◽  
pp. 2325-2335 ◽  
Author(s):  
Magee Allegrucci ◽  
F. Z. Hu ◽  
K. Shen ◽  
J. Hayes ◽  
Garth D. Ehrlich ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Biofilm Formation ◽  
Protein Identification ◽  
Development Process ◽  
Developmental Stages ◽  
Developmental Process ◽  
Phenotypic Characterization ◽  
Biofilm Growth ◽  
Cell Counts ◽  
Biofilm Development

ABSTRACT Streptococcus pneumoniae is among the most common pathogens associated with chronic otitis media with effusion, which has been hypothesized to be a biofilm disease. S. pneumoniae has been shown to form biofilms, however, little is known about the developmental process, the architecture, and the changes that occur upon biofilm development. In the current study we made use of a continuous-culture biofilm system to characterize biofilm development of 14 different S. pneumoniae strains representing at least 10 unique serotypes. The biofilm development process was found to occur in three distinct stages, including initial attachment, cluster formation, and biofilm maturation. While all 14 pneumococcal strains displayed similar developmental stages, the mature biofilm architecture differed significantly among the serotypes tested. Overall, three biofilm architectural groups were detected based on biomass, biofilm thickness, and cluster size. The biofilm viable cell counts and total protein concentration increased steadily over the course of biofilm development, reaching ∼8 × 108 cells and ∼15 mg of protein per biofilm after 9 days of biofilm growth. Proteomic analysis confirmed the presence of distinct biofilm developmental stages by the detection of multiple phenotypes over the course of biofilm development. The biofilm development process was found to correlate not only with differential production of proteins but also with a dramatic increase in the number of detectable proteins, indicating that biofilm formation by S. pneumoniae may be a far more complex process than previously anticipated. Protein identification revealed that proteins involved in virulence, adhesion, and resistance were more abundant under biofilm growth conditions. A possible role of the identified proteins in biofilm formation is discussed.

scholarly journals Transcriptomic Analysis Provides Insights into Grafting Union Development in Pecan (Carya illinoinensis)

2017 ◽  
Author(s):  
Zhenghai Mo ◽  
Gang Feng ◽  
Wenchuan Su ◽  
Zhuangzhuang Liu ◽  
Fangren Peng
Keyword(s):  
Secondary Cell Wall ◽  
Developmental Process ◽  
Carya Illinoinensis ◽  
Differentially Expressed ◽  
Vascular Bundles ◽  
Oxygen Species ◽  
Hormone Signaling ◽  
Graft Union ◽  
Time Points ◽  
Cell Wall Deposition

Pecan (Carya illinoinensis), as a popular nut tree, is widely planted in China in recent years. Grafting is an important technique for its cultivation. For a successful grafting, graft union development generally involves the formation of callus and vascular bundles at the graft union. To explore the molecular mechanism of graft union development, we applied high through-put RNA sequencing to investigate transcriptomic profiles of graft union at four time points (0d, 8d, 15d, and 30d) during pecan grafting process. We identified a total of 12,180 differentially expressed genes. In addition, we found that the content of auxin, cytokinin and gibberellin were accumulated at the graft unions during the grafting process. Correspondingly, genes involved in those hormone signaling were found to be differentially expressed. Interestingly, we found that most genes associated with cell division were up-regulated at callus formative stages, while genes related to cell elongation, secondary cell wall deposition, and programmed cell death were generally up-regulated at vascular bundle formative stages. In the meantime, genes responsible for reactive oxygen species were highly up-regulated across the graft union developmental process. These results will aid in our understanding of successful grafting in the future.

scholarly journals Dynamics and Transcriptome Analysis of Starch and Sucrose Metabolism During Corm Development in Freesia Hybrida

2020 ◽  
Author(s):  
Li Ma ◽  
Suqin Ding ◽  
Zi Yan ◽  
Dongqin Tang
Keyword(s):  
Transcriptome Analysis ◽  
Metabolic Regulation ◽  
Developmental Stages ◽  
Developmental Process ◽  
Soluble Sugars ◽  
Enrichment Analysis ◽  
Sucrose Phosphate Synthase ◽  
Sucrose Metabolism ◽  
Critical Pathway ◽  
Freesia Hybrida

Abstract Background Starch and sucrose metabolism plays a crucial role in the formation and development of bulbs in bulbous plants, which, however, remains unclear and unexplored in the corms of Freesia hybrida, one kind of famous bulbous flower. Herein, we investigated the dynamics of the major form of carbohydrates and related enzyme activities and profiled the transcriptome of freesia corms at four developmental stages with the aim to reveal the relation of starch and sucrose metabolism to corm development and the transcriptional regulation of this metabolic process.Results The content of starch, sucrose and soluble sugars followed an overall upward trend across the corm developmental stages. Activities of the adenosine diphosphoglucose pyrophosphorylase, starch branching enzyme and β-amylase generally followed the pattern of the starch and sucrose level. Activities of sucrose phosphate synthase increased from corm formation till the initial swelling stage and subsequently reached a plateau. Activities of invertase and sucrose synthase peaked at the later rapid swelling stage. Transcriptome analysis revealed a total of 100,999 unigenes, out of which 44,405 unigenes were annotated. Analysis based on Clusters of Orthologous Groups suggested that carbohydrate transport and metabolism (9.34% of the sequences) was prominent across the corm developmental process. Totally 3427 differentially expressed genes were identified and the enrichment analysis directed starch and sucrose metabolism a critical pathway in corm development especially at the rapid swelling stage. Genes encoding key carbohydrate-metabolizing enzymes were identified and their differential expression related to corm development was explored.Conclusions The comparative transcriptome analysis discloses essential roles of starch and sucrose metabolism and the genetic mechanism related to the corm development. The results construct a valuable resource pool for further molecular-level studies, which are helpful for metabolic regulation of carbohydrates and improvement in molecular breeding of Freesia hybrida.

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