scholarly journals Time Course Transcriptome Analysis of Spina Bifida Progression in Fetal Rats

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.

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

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

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.

scholarly journals Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

2020 ◽  
Author(s):  
Lingtong Ren ◽  
Anfang Liu ◽  
Qigui Wang ◽  
Honggan Wang ◽  
Deqiang Dong ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Muscle Development ◽  
Muscle Fibers ◽  
Differentially Expressed ◽  
Embryonic Stage ◽  
Time Points ◽  
Embryonic Muscle ◽  
Embryonic Muscle Development

Abstract Background: Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. Results: Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P<0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,251 (E12vsE16), 4,324 (E12vsE19), and 5,224 (E12vsE21), 1,274 (E16vsE19), 2,735 (E16vsE21) and 857 (E19vsE21) differentially expressed mRNAs were identified. It is worth noting that 6,726 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The downward trend was the most important and was enriched in 3,963 DEGs. GO enrichment analysis provided three significantly enriched categories of the down-trending genes, including 91 cellular components, 53 molecular functions, and 248 biological processes. Through KEGG analysis, we explored the pathway of downtrend genes. A total of 183 KEGG pathways were enriched, including 17 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P<0.05), MAPK signalingpathway, TGF-beta signaling pathway, and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. Conclusion: Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.

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

2019 ◽  
Author(s):  
Guiling Sun ◽  
Yan Qin ◽  
Shenglong Bai ◽  
Wenzheng Li ◽  
Ting Sun ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Nicotiana Tabacum ◽  
Time Course ◽  
Differential Expression Analysis ◽  
Gene Families ◽  
Differentially Expressed ◽  
Agricultural Practice ◽  
Transcriptional Responses ◽  
Time Points ◽  
Nicotine Biosynthesis

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.

scholarly journals Transcriptome analysis of embryonic muscle development in Chengkou Mountain Chicken

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lingtong Ren ◽  
Anfang Liu ◽  
Qigui Wang ◽  
Honggan Wang ◽  
Deqiang Dong ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Muscle Development ◽  
Muscle Fibers ◽  
Differentially Expressed ◽  
Embryonic Stage ◽  
Time Points ◽  
Embryonic Muscle ◽  
Embryonic Muscle Development

Abstract Background Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. Results Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P < 0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,262 in E12vsE16, 5,058 in E12vsE19, 6139 in E12vsE21, 1,282 in E16vsE19, 2,920 in E16vsE21, and 646 in E19vsE21differentially expressed mRNAs were identified. It is worth noting that 7,572 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The significant enrichment trends included 3,150 DEGs. GO enrichment analysis provided three significantly enriched categories of significantly enriched differential genes, including 65 cellular components, 88 molecular functions, and 453 biological processes. Through KEGG analysis, we explored the biological metabolic pathways involved in differentially expressed genes. A total of 177 KEGG pathways were enriched, including 19 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P < 0.05), MAPK signalingpathway, TGF-beta signaling pathway, PI3K-Akt signaling pathway and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. Conclusions Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.

Time Course of Simulator Sickness in Asian Military Pilots

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.

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

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.

scholarly journals Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arika Fukushima ◽  
Masahiro Sugimoto ◽  
Satoru Hiwa ◽  
Tomoyuki Hiroyasu
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Response To Therapy ◽  
Hcv Infection ◽  
Entire Treatment Period ◽  
Time Points ◽  
Time Course Data ◽  
Conventional Methods

Abstract Background Historical and updated information provided by time-course data collected during an entire treatment period proves to be more useful than information provided by single-point data. Accurate predictions made using time-course data on multiple biomarkers that indicate a patient’s response to therapy contribute positively to the decision-making process associated with designing effective treatment programs for various diseases. Therefore, the development of prediction methods incorporating time-course data on multiple markers is necessary. Results We proposed new methods that may be used for prediction and gene selection via time-course gene expression profiles. Our prediction method consolidated multiple probabilities calculated using gene expression profiles collected over a series of time points to predict therapy response. Using two data sets collected from patients with hepatitis C virus (HCV) infection and multiple sclerosis (MS), we performed numerical experiments that predicted response to therapy and evaluated their accuracies. Our methods were more accurate than conventional methods and successfully selected genes, the functions of which were associated with the pathology of HCV infection and MS. Conclusions The proposed method accurately predicted response to therapy using data at multiple time points. It showed higher accuracies at early time points compared to those of conventional methods. Furthermore, this method successfully selected genes that were directly associated with diseases.

scholarly journals Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2311
Author(s):  
Hao Ding ◽  
Yueyue Lin ◽  
Tao Zhang ◽  
Lan Chen ◽  
Genxi Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Growth And Development ◽  
Muscle Development ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Growth Stages ◽  
Gene Expression And Regulation

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.

scholarly journals PSVII-2 Differentially expressed genes and their biological function in skeletal muscle of calves born from cows with or without protein supplementation during mid-gestation

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 165-166
Author(s):  
Elisa B Carvalho ◽  
Letícia P Sanglard ◽  
Karolina B Nascimento ◽  
Javier M Meneses ◽  
Daniel R Casagrande ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Muscle Development ◽  
Negative Binomial ◽  
Muscle Protein ◽  
Basal Diet ◽  
Protein Supplementation ◽  
Differentially Expressed ◽  
Control Group ◽  
Q Value

Abstract Gestating cows have an increased nutrient demand to meet the needs of developing the fetus and the mid-gestation is a critical period for the fetal skeletal muscle development. The aim of this study was to evaluate the skeletal muscle transcriptome in the progeny as a function of the maternal protein nutrition during mid-gestation. Eleven Tabapuã cows and their male calves were used in this study. In the first third of gestation (0 to 100 days of gestation; dg), all cows were kept on pasture. From 100 to 200 dg, the control group (CTRL; 7 animals) received a basal diet achieving 5.5% crude protein (CP), whereas the supplemented group (SUPPL; 4 animals) received a basal diet plus protein supplementation (40% CP). After 200 dg, all animals received the same diet. Weaning was performed at 205 ± 7.5 days of age and animals were kept on pasture until reaching 240 days of age, when they were transferred to a feedlot. Muscle samples were collected at 260 days of age and RNA was extracted for RNA-seq analysis. Gene expression data was analyzed with a negative binomial model to identify (q-value ≤ 0.05) differentially expressed genes (DEG) between treatments. A total of 716 DEG were identified (289 DEG up-regulated and 427 down-regulated in SUPPL group; q-value ≤ 0.05). From the 10 most significant down-regulated DEG in the SUPPL group, two genes associated with apoptotic process were identified: MAPK8IP1 and GRINA, with log2 Fold-Changes (log2FC) of 1.04 and 0.49, respectively. From the 10 most significant up-regulated DEG in the SUPPL group, mTOR was identified, with log2FC=0.31. This is a well-known gene involved in muscle protein synthesis. In conclusion, maternal protein supplementation during mid-gestation affects the expression of genes related to energy metabolism and muscle development, which can lead to long-term impacts on production efficiency.

Cutaneous wound healing is impaired in hemophilia B

Blood ◽  
2006 ◽  
Vol 108 (9) ◽  
pp. 3053-3060 ◽  
Author(s):  
Maureane Hoffman ◽  
Anna Harger ◽  
Angela Lenkowski ◽  
Ulla Hedner ◽  
Harold R. Roberts ◽  
...  
Keyword(s):  
Wound Healing ◽  
Time Course ◽  
Ferric Iron ◽  
Hemophilia B ◽  
Cutaneous Wound Healing ◽  
Delayed Wound Healing ◽  
Cutaneous Wound ◽  
Time Points ◽  
Hemophilic Arthropathy ◽  
Healing Wounds

Abstract We used a mouse model to test the hypothesis that the time course and histology of wound healing is altered in hemophilia B. Punch biopsies (3 mm) were placed in the skin of normal mice and mice with hemophilia. The size of the wounds was measured daily until the epidermal defect closed. All wounds closed in mice with hemophilia by 12 days, compared with 10 days in normal animals. Skin from the area of the wound was harvested at different time points and examined histologically. Hemophilic animals developed subcutaneous hematomas; normal animals did not. Macrophage infiltration was significantly delayed in hemophilia B. Unexpectedly, hemophilic mice developed twice as many blood vessels in the healing wounds as controls, and the increased vascularity persisted for at least 2 weeks. The deposition and persistence of ferric iron was also greater in hemophilic mice. We hypothesize that iron plays a role in promoting excess angiogenesis after wounding as it had been proposed to do in hemophilic arthropathy. We have demonstrated that impaired coagulation leads to delayed wound healing with abnormal histology. Our findings have significant implications for treatment of patients with hemophilia, and also highlight the importance of rapidly establishing hemostasis following trauma or surgery.

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