scholarly journals Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots

Life ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1010
Author(s):  
James Sheppard ◽  
Eric S. Land ◽  
Tiffany Aurora Toennisson ◽  
Colleen J. Doherty ◽  
Imara Y. Perera
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Continuous Light ◽  
Continuous Variable ◽  
Plant Responses ◽  
Plant Signaling ◽  
Transcriptional Responses ◽  
Experimental Conditions ◽  
Experimental Container ◽  
Fractional Gravity

Although many reports characterize the transcriptional response of Arabidopsis seedlings to microgravity, few investigate the effect of partial or fractional gravity on gene expression. Understanding plant responses to fractional gravity is relevant for plant growth on lunar and Martian surfaces. The plant signaling flight experiment utilized the European Modular Cultivation System (EMCS) onboard the International Space Station (ISS). The EMCS consisted of two rotors within a controlled chamber allowing for two experimental conditions, microgravity (stationary rotor) and simulated gravity in space. Seedlings were grown for 5 days under continuous light in seed cassettes. The arrangement of the seed cassettes within each experimental container results in a gradient of fractional g (in the spinning rotor). To investigate whether gene expression patterns are sensitive to fractional g, we carried out transcriptional profiling of root samples exposed to microgravity or partial g (ranging from 0.53 to 0.88 g). Data were analyzed using DESeq2 with fractional g as a continuous variable in the design model in order to query gene expression across the gravity continuum. We identified a subset of genes whose expression correlates with changes in fractional g. Interestingly, the most responsive genes include those encoding transcription factors, defense, and cell wall-related proteins and heat shock proteins.

scholarly journals Transcriptional profiling of the murine airway response to acute ozone exposure

2019 ◽  
Author(s):  
Adelaide Tovar ◽  
Gregory J. Smith ◽  
Joseph M. Thomas ◽  
Jack R. Harkema ◽  
Samir N. P. Kelada
Keyword(s):  
Gene Expression ◽  
Airway Inflammation ◽  
Cellular Proliferation ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Ozone Exposure ◽  
Matrix Remodeling ◽  
Transcriptional Responses ◽  
Morphological Alterations ◽  
Cell Counts

AbstractExposure to ambient ozone (O3) pollution causes airway inflammation, epithelial injury, and decreased lung function. Long-term exposure is associated with increased mortality and exacerbations of respiratory conditions. While the adverse health effects of O3 exposure have been thoroughly described, less is known about the molecular processes that drive these outcomes. The aim of this study was to describe the cellular and molecular alterations observed in murine airways after exposure to either 1 or 2 ppm O3. After exposing adult, female C57BL/6J mice to filtered air, 1 or 2 ppm O3 for 3 hours, we assessed hallmark responses including airway inflammatory cell counts, epithelial permeability, cytokine secretion, and morphological alterations of the large airways. Further, we performed RNA-seq to profile gene expression in two critical tissues involved in O3 responses: conducting airways (CA) and airway macrophages (AM). We observed a concentration-dependent increase in airway inflammation and injury, and a large number of genes were differentially expressed in both target tissues at both concentrations of O3. Genes that were differentially expressed in CA were generally associated with barrier function, detoxification processes, and cellular proliferation. The differentially expressed genes in AM were associated with innate immune signaling, cytokine production, and extracellular matrix remodeling. Overall, our study has described transcriptional responses to acute O3 exposure, revealing both shared and unique gene expression patterns across multiple concentrations of O3 and in two important O3-responsive tissues. These profiles provide broad mechanistic insight into pulmonary O3 toxicity, and reveal a variety of targets for refined follow-up studies.

scholarly journals RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics

2019 ◽  
Vol 20 (23) ◽  
pp. 6098 ◽  
Author(s):  
Amarinder Singh Thind ◽  
Kumar Parijat Tripathi ◽  
Mario Rosario Guarracino
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Differential Gene

The comparison of high throughput gene expression datasets obtained from different experimental conditions is a challenging task. It provides an opportunity to explore the cellular response to various biological events such as disease, environmental conditions, and drugs. There is a need for tools that allow the integration and analysis of such data. We developed the “RankerGUI pipeline”, a user-friendly web application for the biological community. It allows users to use various rank based statistical approaches for the comparison of full differential gene expression profiles between the same or different biological states obtained from different sources. The pipeline modules are an integration of various open-source packages, a few of which are modified for extended functionality. The main modules include rank rank hypergeometric overlap, enriched rank rank hypergeometric overlap and distance calculations. Additionally, preprocessing steps such as merging differential expression profiles of multiple independent studies can be added before running the main modules. Output plots show the strength, pattern, and trends among complete differential expression profiles. In this paper, we describe the various modules and functionalities of the developed pipeline. We also present a case study that demonstrates how the pipeline can be used for the comparison of differential expression profiles obtained from multiple platforms’ data of the Gene Expression Omnibus. Using these comparisons, we investigate gene expression patterns in kidney and lung cancers.

Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium

2004 ◽  
Vol 20 (1) ◽  
pp. 117-130 ◽  
Author(s):  
Rafaela da Silva ◽  
Eliana Lucchinetti ◽  
Thomas Pasch ◽  
Marcus C. Schaub ◽  
Michael Zaugg
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Ischemia Reperfusion ◽  
Expression Patterns ◽  
Principal Component ◽  
Gene Clusters ◽  
Stable Gene ◽  
Transcriptional Responses ◽  
Rat Hearts

Pharmacological (PPC) and ischemic preconditioning (IschPC) provide comparable protection against ischemia in the heart. However, the genomic phenotype may depend on the type of preconditioning. Isolated perfused rat hearts were used to evaluate transcriptional responses to PPC and IschPC in the presence (mediator/effector response) or absence (trigger response) of 40 min of test ischemia using oligonucleotide microarrays. IschPC was induced by 3 cycles of 5 min of ischemia, and PPC by 15 min of 2.1 vol% isoflurane. Unsupervised analysis methods were used to identify gene expression patterns. PPC and IschPC were accompanied by marked alterations in gene expression. PPC and IschPC shared only ∼25% of significantly up- and downregulated genes after triggering. The two types of preconditioning induced a more uniform genomic response after ischemia/reperfusion. Numerous genes separated preconditioned from unprotected ischemic hearts. Three stable gene clusters were identified in the trigger response to preconditioning, while eight stable clusters related to cytoprotection, inflammation, remodeling, and long interspersed nucleotide elements (LINEs) were delineated after prolonged ischemia. A single stable sample cluster emerged from cluster analysis for both IschPC and unprotected myocardium, indicating a close molecular relationship between these two treatments. Principal component analysis revealed differences between PPC vs. IschPC, and trigger vs. mediator/effector responses in transcripts predominantly related to biosynthesis and apoptosis. IschPC and PPC similarly but distinctly reprogram the genetic response to ischemic injury. IschPC elicits a postischemic gene expression profile closer to unprotected myocardium than PPC, which may be therefore more advantageous as therapeutic strategy in cardioprotection.

scholarly journals Meta-analysis of gene expression profiles in granulosa cells during folliculogenesis

Reproduction ◽  
2016 ◽  
Vol 151 (6) ◽  
pp. R103-R110 ◽  
Author(s):  
Daulat Raheem Khan ◽  
Éric Fournier ◽  
Isabelle Dufort ◽  
François J Richard ◽  
Jaswant Singh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Granulosa Cell ◽  
Granulosa Cells ◽  
Expression Profiles ◽  
Post Partum ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Comprehensive Overview ◽  
Experimental Conditions ◽  
Physiological Conditions

Abstract Folliculogenesis involves coordinated profound changes in different follicular compartments and significant modifications of their gene expression patterns, particularly in granulosa cells. Huge datasets have accumulated from the analyses of granulosa cell transcriptomic signatures in predefined physiological contexts using different technological platforms. However, no comprehensive overview of folliculogenesis is available. This would require integration of datasets from numerous individual studies. A prerequisite for such integration would be the use of comparable platforms and experimental conditions. The EmbryoGENE program was created to study bovine granulosa cell transcriptomics under different physiological conditions using the same platform. Based on the data thus generated so far, we present here an interactive web interface called GranulosaIMAGE (Integrative Meta-Analysis of Gene Expression), which provides dynamic expression profiles of any gene of interest and all isoforms thereof in granulosa cells at different stages of folliculogenesis. GranulosaIMAGE features two kinds of expression profiles: gene expression kinetics during bovine folliculogenesis from small (6 mm) to pre-ovulatory follicles under different hormonal and physiological conditions and expression profiles of granulosa cells of dominant follicles from post-partum cows in different metabolic states. This article provides selected examples of expression patterns along with suggestions for users to access and generate their own patterns using GranulosaIMAGE. The possibility of analysing gene expression dynamics during the late stages of folliculogenesis in a mono-ovulatory species such as bovine should provide a new and enriched perspective on ovarian physiology.

scholarly journals Epigenomic Regulatory Mechanism of Flowering in Apple Demonstrated in Two Varieties with Contrasted Flowering Behaviors

2021 ◽  
Author(s):  
Hua Zhou ◽  
Chenguang Zhang ◽  
Mengxue Wang ◽  
Wei Zhang ◽  
Juanjuan Ma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cytosine Methylation ◽  
Floral Induction ◽  
Expression Patterns ◽  
Axillary Bud ◽  
Necessary Condition ◽  
Whole Genome ◽  
Transcriptional Responses ◽  
Flowering Genes

Abstract Background: Flowering is the necessary condition and yield basis for woody fruits in their life cycle. Although there has been considerable interest in the regulatory mechanisms underlying floral induction and flowering, the associated epigenetic modifications remain relatively uncharacterized. Results: We identified the genome-wide of DNA methylation changes and the transcriptional responses in axillary bud of ‘Qinguan’ (QA) and ‘Fuji’ (FA) varieties with contrasted flowering behaviors. The DNA methylations were19.35%, 62.96% and 17.68% for FA, and 19.64%, 62.49% and 17.86% for QA in the CG, CHG and CHH contexts, respectively. Number of hypermethylated or hypomethylated DMRs in different regions were contributed to significantly up/downregulated gene expression. DNA methylation can positively or negatively regulate gene expression based on the CG, CHG and CHH contexts in different regions. Additionally, the huge differences in transcription of MIKCc-Type MADS-box genes, and multiple flowering genes in multiple flowering pathways (i.e., light, age, GA and sugar) by changing DNA methylation, contributed to contrasted flowering behaviors in both QA and FA. Specifically, the floral meristem identify genes (i.e., FT, LEAFY, AP1 and SOC1) were significantly higher expression in QA than FA, but the floral repressor (i.e., SVP, AGL15, and AGL18) had an opposite result. Significant differences in multiple hormone levels were due to DEGs and their DMRs in their synthesis pathways, leading to both contrasted axillary bud outgrowth and flowering behaviors. Conclusions: The whole-genome bisulfite sequencing (BS) libraries of QA and FA with diverse flowering capabilities have been constructed for finding whole-genome cytosine methylation profiles. The RNA sequencing of QA and FA and diverse flowering capabilities have been combined together to identify the gene expression patterns and the correlation with their methylation states so that we can better understand the epigenetic regulation mechanisms of floral induction and formation in apple.

scholarly journals Optogenetic investigation of BMP target gene expression diversity

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Katherine W Rogers ◽  
Mohammad ElGamacy ◽  
Benjamin M Jordan ◽  
Patrick Müller
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression Patterns ◽  
Spatial Diversity ◽  
Bmp Signaling ◽  
Transcriptional Responses ◽  
Spatiotemporal Expression ◽  
Spatial Differences ◽  
Signaling Activation ◽  
Open Question

Signaling molecules activate distinct patterns of gene expression to coordinate embryogenesis, but how spatiotemporal expression diversity is generated is an open question. In zebrafish, a BMP signaling gradient patterns the dorsal-ventral axis. We systematically identified target genes responding to BMP and found that they have diverse spatiotemporal expression patterns. Transcriptional responses to optogenetically delivered high- and low-amplitude BMP signaling pulses indicate that spatiotemporal expression is not fully defined by different BMP signaling activation thresholds. Additionally, we observed negligible correlations between spatiotemporal expression and transcription kinetics for the majority of analyzed genes in response to BMP signaling pulses. In contrast, spatial differences between BMP target genes largely collapsed when FGF and Nodal signaling were inhibited. Our results suggest that, similar to other patterning systems, combinatorial signaling is likely to be a major driver of spatial diversity in BMP-dependent gene expression in zebrafish.

scholarly journals Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Shadi Eshghi Sahraei ◽  
Michelle Cleary ◽  
Jan Stenlid ◽  
Mikael Brandström Durling ◽  
Malin Elfstrand
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Expression Patterns ◽  
Fraxinus Excelsior ◽  
Differentially Expressed ◽  
Gene Expression Patterns ◽  
Transcriptional Responses ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Resistant Genotypes

Abstract Background With the expanding ash dieback epidemic that has spread across the European continent, an improved functional understanding of the disease development in afflicted hosts is needed. The study investigated whether differences in necrosis extension between common ash (Fraxinus excelsior) trees with different levels of susceptibility to the fungus Hymenoscyphus fraxineus are associated with, and can be explained by, the differences in gene expression patterns. We inoculated seemingly healthy branches of each of two resistant and susceptible ash genotypes with H. fraxineus grown in a common garden. Results Ten months after the inoculation, the length of necrosis on the resistant genotypes were shorter than on the susceptible genotypes. RNA sequencing of bark samples collected at the border of necrotic lesions and from healthy tissues distal to the lesion revealed relatively limited differences in gene expression patterns between susceptible and resistant genotypes. At the necrosis front, only 138 transcripts were differentially expressed between the genotype categories while 1082 were differentially expressed in distal, non-symptomatic tissues. Among these differentially expressed genes, several genes in the mevalonate (MVA) and iridoid pathways were found to be co-regulated, possibly indicating increased fluxes through these pathways in response to H. fraxineus. Comparison of transcriptional responses of symptomatic and non-symptomatic ash in a controlled greenhouse experiment revealed a relatively small set of genes that were differentially and concordantly expressed in both studies. This gene-set included the rate-limiting enzyme in the MVA pathway and a number of transcription factors. Furthermore, several of the concordantly expressed candidate genes show significant similarity to genes encoding players in the abscisic acid- or Jasmonate-signalling pathways. Conclusions A set of candidate genes, concordantly expressed between field and greenhouse experiments, was identified. The candidates are associated with hormone signalling and specialized metabolite biosynthesis pathways indicating the involvement of these pathways in the response of the host to infection by H. fraxineus.

scholarly journals Transcriptional Profiling of the Murine Airway Response to Acute Ozone Exposure

2019 ◽  
Vol 173 (1) ◽  
pp. 114-130 ◽  
Author(s):  
Adelaide Tovar ◽  
Gregory J Smith ◽  
Joseph M Thomas ◽  
Wesley L Crouse ◽  
Jack R Harkema ◽  
...  
Keyword(s):  
Gene Expression ◽  
Airway Inflammation ◽  
Cellular Proliferation ◽  
Expression Patterns ◽  
Ozone Exposure ◽  
Matrix Remodeling ◽  
Transcriptional Responses ◽  
Cell Counts ◽  
Response Expression ◽  
Conducting Airways

Abstract Ambient ozone (O3) exposure has serious consequences on respiratory health, including airway inflammation and injury. Decades of research have yielded thorough descriptions of these outcomes; however, less is known about the molecular processes that drive them. The aim of this study was to further describe the cellular and molecular responses to O3 exposure in murine airways, with a particular focus on transcriptional responses in 2 critical pulmonary tissue compartments: conducting airways (CA) and airway macrophages (AM). After exposing adult, female C57BL/6J mice to filtered air, 1 or 2 ppm O3, we assessed hallmark responses including airway inflammation (cell counts and cytokine secretion) and injury (epithelial permeability), followed by gene expression profiling of CA and AM by RNA-seq. As expected, we observed concentration-dependent increases in airway inflammation and injury. Conducting airways and AM both exhibited changes in gene expression to both 1 and 2 ppm O3 that were largely compartment-specific. In CA, genes associated with epithelial barrier function, detoxification processes, and cellular proliferation were altered, while O3 affected genes involved in innate immune signaling, cytokine production, and extracellular matrix remodeling in AM. Further, CA and AM also exhibited notable differences in concentration–response expression patterns for large numbers of genes. Overall, our study has described transcriptional responses to acute O3 exposure, revealing both shared and unique gene expression patterns across multiple concentrations of O3 and in 2 important O3-responsive tissues. These profiles provide broad mechanistic insight into pulmonary O3 toxicity, and reveal a variety of targets for focused follow-up studies.

scholarly journals Selection and validation of reference genes for quantitative gene expression normalization in Taxus spp.

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kaikai Zhang ◽  
Wei Fan ◽  
Duanfen Chen ◽  
Luyuan Jiang ◽  
Yunfeng Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Reference Genes ◽  
Expression Patterns ◽  
Future Research ◽  
Taxus Chinensis ◽  
Experimental Conditions ◽  
Taxol Biosynthesis ◽  
Qrt Pcr ◽  
Suitable Reference

AbstractQuantitative real-time PCR (qRT-PCR) is commonly used to measure gene expression to further explore gene function, while suitable reference genes must be stably expressed under different experimental conditions to obtain accurate and reproducible data for relative quantification. Taxol or paclitaxel is an important anticancer compound mainly identified in Taxus spp. The molecular mechanism of the regulation of taxol biosynthesis is current research goal. However, in the case of Taxus spp., few reports were published on screening suitable reference genes as internal controls for qRT-PCR. Here, eight reference genes were selected as candidate reference genes for further study. Common statistical algorithms geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder were used to analyze the data from samples collected from a cell line of Taxus × media under various experimental conditions and from tissues of Taxus chinensis var. mairei. The expression patterns of TcMYC under salicylic acid treatment differed significantly, with the best and worst reference genes in the cell line. This study screened out suitable reference genes (GAPDH1 and SAND) under different treatments and tissues for the accurate and reliable normalization of the qRT-PCR expression data of Taxus spp. At the same time, this study will aid future research on taxol biosynthesis-related genes expression in Taxus spp., and can also be directly used to other related species.

scholarly journals Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Anne Plessis ◽  
Christoph Hafemeister ◽  
Olivia Wilkins ◽  
Zennia Jean Gonzaga ◽  
Rachel Sarah Meyer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Linear Models ◽  
Expression Patterns ◽  
Environmental Parameters ◽  
Gene Clusters ◽  
Field Conditions ◽  
Published Data ◽  
Transcriptional Responses ◽  
Climatic Fluctuations ◽  
Environmental Models

Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field.

Sign in / Sign up

Export Citation Format

Share Document