Transcriptome Analysis Reveals Key Genes Involved in the Regulation of Nicotine Biosynthesis at Early Time Points after Topping in Tobacco (Nicotiana tabacum L.)

Abstract Background： Nicotiana tabacum is an important economic crop. Topping, a common agricultural practice employed with flue-cured tobacco, is designed to increase leaf nicotine contents. Many genes are found to be differentially expressed in response to topping, particularly genes involved in nicotine biosynthesis, but comprehensive analyses of early transcriptional responses induced by topping are not yet available. To develop a detailed understanding of the mechanisms regulating nicotine biosynthesis after topping, we have sequenced the transcriptomes of N. tabacum roots at seven time points following topping. Results： Differential expression analysis revealed that 4,830 genes respond to topping across all time points. Amongst these, nine gene families involved in nicotine biosynthesis and two gene families involved in nicotine transport showed significant changes during the immediate 24 hour period following topping. No obvious preference to the parental species was detected in the differentially expressed genes (DEGs). Significant changes in transcript levels of nine genes involved in nicotine biosynthesis and phytohormone signal transduction were validated by qRT-PCR assays. 549 genes encoding transcription factors (TFs), found to exhibit significant changes in gene expression after topping, formed 15 clusters based on similarities of their transcript level time-course profiles. 336 DEGs involved in phytohormone signal transduction, including genes functionally related to the phytohormones jasmonic acid, abscisic acid, auxin, ethylene, and gibberellin, were identified at the earliest time point after topping. Conclusions： Our research provides the first detailed analysis of the early transcriptional responses to topping in N. tabacum , and identifies excellent candidates for further detailed studies concerning the regulation of nicotine biosynthesis in tobacco roots.

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Transcriptome Analysis Reveals Key Genes Involved in the Regulation of Nicotine Biosynthesis at Early Time Points after Topping in Tobacco (Nicotiana tabacum L.)

10.21203/rs.2.16109/v2 ◽

2019 ◽

Author(s):

Yan Qin ◽

Shenglong Bai ◽

Wenzheng Li ◽

Ting Sun ◽

David W. Galbraith ◽

...

Keyword(s):

Signal Transduction ◽

Nicotiana Tabacum ◽

Time Course ◽

Differential Expression Analysis ◽

Gene Families ◽

Differentially Expressed ◽

Agricultural Practice ◽

Transcriptional Responses ◽

Time Points ◽

Nicotine Biosynthesis

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Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera

BMC Genomics ◽

10.1186/s12864-021-08081-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Neetu Goyal ◽

Garima Bhatia ◽

Naina Garewal ◽

Anuradha Upadhyay ◽

Kashmir Singh

Keyword(s):

Vitis Vinifera ◽

Downy Mildew ◽

Defense Mechanisms ◽

Molecular Mechanisms ◽

Differential Expression Analysis ◽

Gene Families ◽

Pathogen Resistance ◽

Differentially Expressed ◽

Phylogenetic Study ◽

In Planta

Abstract Background Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes. Results In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions. Conclusion The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.

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Time Course Transcriptome Analysis of Spina Bifida Progression in Fetal Rats

Brain Sciences ◽

10.3390/brainsci11121593 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1593

Author(s):

Kendall P. Murphy ◽

Bedika Pathak ◽

Jose L. Peiro ◽

Marc Oria

Keyword(s):

Spina Bifida ◽

Hedgehog Signaling ◽

Time Course ◽

Muscle Development ◽

Interaction Analysis ◽

Differentially Expressed ◽

Significant Variable ◽

Spinal Cord Regeneration ◽

Surgical Interventions ◽

Time Points

A better understanding of the transcriptomic modifications that occur in spina bifida may lead to identify mechanisms involved in the progression of spina bifida in utero and the development of new therapeutic strategies that aid in spinal cord regeneration after surgical interventions. In this study, RNA-sequencing was used to identify differentially expressed genes in fetal spinal cords from rats with retinoic acid-induced spina bifida at E15, E17, and E20. Gene ontology, KEGG, and protein–protein interaction analysis were conducted to predict pathways involved in the evolution of the disease. Approximately 3000, 1000 and 300 genes were differentially expressed compared to the control groups at E15, E17 and E20, respectively. Overall, the results suggest common alterations in certain pathways between gestational time points, such as upregulation in p53 and sonic hedgehog signaling at E15 and E17 and downregulation in the myelin sheath at E17 and E20. However, there were other modifications specific to gestational time points, including skeletal muscle development at E15, downregulated glucose metabolism at E17, and upregulated inflammation at E20. In conclusion, this work provides evidence that gestational age during spina bifida repair may be a significant variable to consider during the development of new regenerative therapeutics approaches.

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Enhanced Biosynthesis of Chlorogenic Acid and Its Derivatives in Methyl-Jasmonate-Treated Gardenia jasminoides Cells: A Study on Metabolic and Transcriptional Responses of Cells

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2020.604957 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zebo Liu ◽

Ali Mohsin ◽

Zejian Wang ◽

Xiaofeng Zhu ◽

Yingping Zhuang ◽

...

Keyword(s):

Signal Transduction ◽

Methyl Jasmonate ◽

Chlorogenic Acid ◽

Molecular Mechanism ◽

Time Course ◽

Transcriptional Responses ◽

Gardenia Jasminoides ◽

Meja Treatment ◽

Insight Into ◽

Precursor Supply

Chlorogenic acid and its derivatives (CQAs) are considered as important bioactive secondary metabolites in Gardenia jasminoides Ellis (G. jasminoides). However, few studies have investigated the biosynthesis and regulation of CQAs in G. jasminoides. In this study, methyl jasmonate (MeJA) was used to enhance CQAs accumulation in cultured G. jasminoides cells. Moreover, the possible molecular mechanism of MeJA-mediated accumulation of CQAs is also explored. To this end, time-course transcriptional profiles of G. jasminoides cells responding to MeJA were used to investigate the mechanism from different aspects, including jasmonate (JAs) biosynthesis, signal transduction, biosynthesis of precursor, CQAs biosynthesis, transporters, and transcription factors (TFs). A total of 57,069 unigenes were assembled from the clean reads, in which 80.7% unigenes were successfully annotated. Furthermore, comparative transcriptomic results indicated that differentially expressed genes (DEGs) were mainly involved in JAs biosynthesis and signal transduction (25 DEGs), biosynthesis of precursor for CQAs (18 DEGs), CQAs biosynthesis (19 DEGs), and transporters (29 DEGs). Most of these DEGs showed continuously upregulated expressions over time, which might activate the jasmonic acid (JA) signal transduction network, boost precursor supply, and ultimately stimulate CQAs biosynthesis. Additionally, various TFs from different TF families also responded to MeJA elicitation. Interestingly, 38 DEGs from different subgroups of the MYB family might display positive or negative regulations on phenylpropanoids, especially on CQAs biosynthesis. Conclusively, our results provide insight into the possible molecular mechanism of regulation on CQAs biosynthesis, which led to a high CQAs yield in the G. jasminoides cells under MeJA treatment.

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Gene Expression Analysis in Critically Ill Patients

Inquiry@Queen's Undergraduate Research Conference Proceedings ◽

10.24908/iqurcp.11657 ◽

2018 ◽

Author(s):

Mary Hoekstra

Keyword(s):

Gene Expression ◽

Critically Ill ◽

Expression Analysis ◽

Nosocomial Infections ◽

Single Gene ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Bovine Lactoferrin ◽

Time Points ◽

The Impact

Nosocomial infections are associated with increased morbidity and mortality in intensive care units (ICUs) and remain an important target for intervention. Several studies have explored bovine lactoferrin as a potential tool for preventing infection and modulating the immune response. One clinical trial, the PREVAIL study, investigated the efficacy of lactoferrin in preventing nosocomial infections in critically ill, mechanically ventilated patients. A subset of patients in this study had blood samples collected at up to 6 different time points during their stay in the ICU, which were used to extract RNA for gene expression profiling. The resulting gene expression data were analyzed to determine the impact of lactoferrin on gene expression. Differential expression analysis was performed using both a single-gene approach and weighted gene co-expression network analysis (WGCNA). A single-gene analysis revealed that there was an increased number of differentially expressed genes in the lactoferrin group at all time points, including genes associated with the inflammatory response. Results from WGCNA revealed that groups of genes associated with innate immunity and defence response to virus were significantly differentially expressed over time in the lactoferrin group. These results contribute to our understanding of critical illness at the molecular level and provide evidence that lactoferrin has a biological effect.

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Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

BMC Plant Biology ◽

10.1186/s12870-020-2241-9 ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 2

Author(s):

Yan Qin ◽

Shenglong Bai ◽

Wenzheng Li ◽

Ting Sun ◽

David W. Galbraith ◽

...

Keyword(s):

Nicotiana Tabacum ◽

Transcriptome Analysis ◽

Early Time ◽

Time Points ◽

Nicotiana Tabacum L ◽

Key Genes ◽

Nicotine Biosynthesis

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A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)

BMC Genomics ◽

10.1186/s12864-019-6236-6 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Xi Chen ◽

Shuo Sun ◽

Fangjie Liu ◽

Enhui Shen ◽

Lu Liu ◽

...

Keyword(s):

Nicotiana Tabacum ◽

High Throughput Sequencing ◽

Potential Role ◽

Interaction Network ◽

Differentially Expressed ◽

Circular Rnas ◽

Biological Functions ◽

Non Coding Rnas ◽

Nicotine Biosynthesis ◽

Tobacco Roots

Abstract Background Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), accomplish remarkable variety of biological functions. However, the composition of ncRNAs and their interactions with coding RNAs in modulating and controlling of cellular process in plants is largely unknown. Using a diverse group of high-throughput sequencing strategies, the mRNA, miRNA, lncRNA and circRNA compositions of tobacco (Nicotiana tabacum) roots determined and their alteration and potential biological functions in response to topping treatment analyzed. Results A total of 688 miRNAs, 7423 non-redundant lncRNAs and 12,414 circRNAs were identified, among which, some selected differentially expressed RNAs were verified by quantitative real-time PCR. Using the differentially expressed RNAs, a co-expression network was established that included all four types of RNAs. The number of circRNAs identified were higher than that of miRNAs and lncRNAs, but only two circRNAs were present in the co-expression network. LncRNAs appear to be the most active ncRNAs based on their numbers presented in the co-expression network, but none of them seems to be an eTM (endogenous Target Mimicry) of miRNAs. Integrated with analyses of sequence interaction, several mRNA-circRNA-miRNA interaction networks with a potential role in the regulation of nicotine biosynthesis were uncovered, including a QS-circQS-miR6024 interaction network. In this network miR6024 was significantly down-regulated, while the expression levels of its two targets, circQS and its host gene QS, were sharply increased following the topping treatment. Conclusions These results illustrated the transcriptomic profiles of tobacco roots, the organ responsible for nicotine biosynthesis. mRNAs always play the most important roles, while ncRNAs are also expressed extensively for topping treatment response, especially circRNAs are the most activated in the ncRNA pool. These studies also provided insights on the coordinated regulation module of coding and non-coding RNAs in a single plant biological sample. The findings reported here indicate that ncRNAs appear to form interaction complex for the regulation of stress response forming regulation networks with transcripts involved in nicotine biosynthesis in tobacco.

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Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage

BMC Genomics ◽

10.1186/s12864-021-07888-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ailing Zhang ◽

Yang Ji ◽

Min Sun ◽

Chuang Lin ◽

Puding Zhou ◽

...

Keyword(s):

Signal Transduction ◽

Drought Tolerance ◽

Pearl Millet ◽

Differentially Expressed Genes ◽

Drought Resistance ◽

Pennisetum Glaucum ◽

Seedling Stage ◽

Differentially Expressed ◽

Drought Treatment ◽

Time Points

Abstract Background Drought is one of the major environmental stresses resulting in a huge reduction in crop growth and biomass production. Pearl millet (Pennisetum glaucum L.) has excellent drought tolerance, and it could be used as a model plant to study drought resistance. The root is a very crucial part of plant that plays important roles in plant growth and development, which makes it a focus of research. Results In this study, we explored the mechanism of drought tolerance of pearl millet by comparing physiological and transcriptomic data under normal condition and drought treatment at three time points (1 h, 3 h and 7 h) in the root during the seedling stage. The relative electrical conductivity went up from 1 h to 7 h in both control and drought treatment groups while the content of malondialdehyde decreased. A total of 2004, 1538 and 605 differentially expressed genes were found at 1 h, 3 h and 7 h respectively and 12 genes showed up-regulation at all time points. Some of these differentially expressed genes were significantly enriched into ‘metabolic processes’, ‘MAPK signaling pathway’ and ‘plant hormone signal transduction’ such as the ABA signal transduction pathway in GO and KEGG enrichment analysis. Conclusions Pearl millet was found to have a quick drought response, which may occur before 1 h that contributes to its tolerance against drought stress. These results can provide a theoretical basis to enhance the drought resistance in other plant species.

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Time Course of Simulator Sickness in Asian Military Pilots

Aerospace Medicine and Human Performance ◽

10.3357/amhp.5674.2020 ◽

2020 ◽

Vol 91 (11) ◽

pp. 892-896

Author(s):

Janine En Qi Loi ◽

Magdalene Li Ling Lee ◽

Benjamin Boon Chuan Tan ◽

Brian See

Keyword(s):

Air Force ◽

Time Course ◽

Simulator Training ◽

Simulator Sickness ◽

Time Points ◽

True Prevalence ◽

Subjective Scale ◽

Significant Difference ◽

Simulator Sickness Questionnaire ◽

Military Pilots

INTRODUCTION: This study sought to determine the incidence, severity, and time-course of simulator sickness (SS) among Asian military pilots following flight simulator training.METHODS: A survey was conducted on Republic of Singapore Air Force pilots undergoing simulator training. Each subject completed a questionnaire immediately after (0H), and at the 3-h (3H) and 6-h (6H) marks. The questionnaire included the simulator sickness questionnaire (SSQ) and a subjective scale to rate their confidence to fly.RESULTS: In this study, 258 pilots with a median age of 31.50 yr (range, 2155 yr) and mean age of 32.61 6.56 yr participated. The prevalence of SS was 48.1% at 0H, 30.8% at 3H, and 16.4% at 6H. Based on a threshold of an SSQ score >10, the prevalence of operationally significant SS was 33.3% at 0H, 13.2% at 3H, and 8.1% at 6H. The most frequent symptoms were fatigue (38.1%), eye strain (29.0%), and fullness of head (19.9%). There was no significant difference in mean scores between rotary and fixed wing pilots. Older, more experienced pilots had greater scores at 0H, but this association did not persist. A correlation was found between SSQ score and self-reported confidence.DISCUSSION: To our knowledge, this study is the first to report the prevalence of operationally significant SS in Asian military pilots over serial time points. Most pilots with SS are able to subjectively judge their fitness to fly. Sensitivity analysis suggests the true prevalence of SS symptoms at 3H and 6H to be closer to 23.8% and 12.0%, respectively.Loi JEQ, Lee MLL, Tan BBC, See B. Time course of simulator sickness in Asian military pilots. Aerosp Med Hum Perform. 2020; 91(11):892896.

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Serial computed tomography findings of Coronavirus disease 2019 (COVID-19) pneumonia treated with favipiravir and steroid therapy: report of 11 cases

Bulletin of the National Research Centre ◽

10.1186/s42269-021-00553-7 ◽

2021 ◽

Vol 45 (1) ◽

Author(s):

Naoki Irizato ◽

Hiroshi Matsuura ◽

Atsuya Okada ◽

Ken Ueda ◽

Hitoshi Yamamura

Keyword(s):

Computed Tomography ◽

Mechanical Ventilation ◽

Steroid Therapy ◽

Time Course ◽

Ground Glass ◽

Time Points ◽

Ct Findings ◽

Mixed Pattern ◽

Bronchial Dilatation

Abstract Background This study evaluated the time course of computed tomography (CT) findings of patients with COVID-19 pneumonia who required mechanical ventilation and were treated with favipiravir and steroid therapy. Results Eleven patients with severe COVID-19 pneumonia were included. CT findings assessed at the three time points showed that all patients had ground-glass opacities (GGO) and consolidation and mixed pattern at intubation. Consolidation and mixed pattern disappeared in most of the patients whereas GGO persisted in all patients at 1-month follow-up. In addition to GGO, a subpleural line and bronchus distortion and bronchial dilatation were frequent findings. The degree of resolution of GGO varied depending on each patient. The GGO score correlated significantly with the time from symptoms onset to initiation of steroid therapy (ρ = 0.707, p = 0.015). Conclusions At 1-month follow-up after discharge, non-GGO lesions were absorbed almost completely, and GGO were a predominant CT manifestation. Starting steroid therapy earlier after onset of symptoms in severe COVID-19 pneumonia may reduce the extent of GGO at 1-month follow-up.

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