scholarly journals The genomic response to courtship song stimulation in female Drosophila melanogaster

2011 ◽  
Vol 279 (1732) ◽  
pp. 1359-1365 ◽  
Author(s):  
Elina Immonen ◽  
Michael G. Ritchie
Keyword(s):  
Drosophila Melanogaster ◽  
Time Course ◽  
Expression Patterns ◽  
Mate Recognition ◽  
Courtship Song ◽  
Transcriptional Responses ◽  
Signal Perception ◽  
Real Time Quantitative Pcr ◽  
Immunity Genes ◽  
Male Wing

Courtship behaviour involves a complex exchange of signals and responses. These are usually studied at the phenotypic level, and genetic or transcriptional responses to courtship are still poorly understood. Here, we examine the gene-expression changes in Drosophila melanogaster females in response to one of the key male courtship signals in mate recognition, song produced by male wing vibration. Using long oligonucleotide microarrays, we identified several genes that responded differentially to the presence or absence of acoustic courtship stimulus. These changes were modest in both the number of genes involved and fold-changes, but notably dominated by antennal signalling genes involved in olfaction as well as neuropeptides and immune response genes. Second, we compared the expression patterns of females stimulated with synthetic song typical of either conspecific or heterospecific ( Drosophila simulans ) males. In this case, antennal olfactory signalling and innate immunity genes were also enriched among the differentially expressed genes. We confirmed and investigated the time course of expression differences of two identified immunity genes using real-time quantitative PCR. Our results provide novel insight into specific molecular changes in females in response to courtship song stimulation. These may be involved in both signal perception and interpretation and some may anticipate molecular interactions that occur between the sexes after mating.

Temperature affects the ontogeny of sexually dimorphic cuticular hydrocarbons in Drosophila melanogaster

2002 ◽  
Vol 205 (20) ◽  
pp. 3241-3249 ◽  
Author(s):  
Fabrice Savarit ◽  
Jean-François Ferveur
Keyword(s):  
Drosophila Melanogaster ◽  
Cuticular Hydrocarbons ◽  
Time Course ◽  
Mate Recognition ◽  
Effect Of Temperature ◽  
Sexually Dimorphic ◽  
Shock Pulse ◽  
Male And Female ◽  
Different Temperatures ◽  
Transgenic Strains

SUMMARY Hydrocarbons on the cuticle of mature Drosophila melanogasterflies play a crucial role in mate recognition, and protect against dehydration. We measured the effect of temperature on mature cuticular hydrocarbons (CHs) by (i) rearing two control strains at different temperatures, (ii) shifting the temperature after metamorphosis and (iii)inducing a single heat-shock pulse in control and heat-sensitive transgenic strains, over a period of 3 days following adult eclosion. This study describes the time course of the events involved in the production of male-and female-predominant CHs. We also found that `immature' CHs, sexually monomorphic CHs on younger flies, were not affected by these treatments.

scholarly journals Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model

2021 ◽  
pp. ASN.2021081150
Author(s):  
Eryn Dixon ◽  
Haojia Wu ◽  
Yoshiharu Muto ◽  
Parker Wilson ◽  
Benjamin Humphreys
Keyword(s):  
Gene Expression ◽  
Murine Model ◽  
Time Course ◽  
Spatial Information ◽  
Expression Patterns ◽  
Repair Time ◽  
Spatial Data Analysis ◽  
Transcriptional Responses ◽  
Injury And Repair ◽  
Cell Cell

Background Single cell sequencing technologies have advanced our understanding of kidney biology and disease but the loss of spatial information in these datasets hinders our interpretation of intercellular communication networks and regional gene expression patterns. New spatial transcriptomic sequencing platforms make it possible to measure the topography of gene expression at genome depth. Methods We optimized and validated a female bilateral ischemia reperfusion injury model. Using the 10X Genomics Visium Spatial Gene Expression solution, we generated spatial maps of gene expression across the injury and repair time course, and applied two open-source computational tools, Giotto and SPOTlight, to increase resolution and measure cell-cell interaction dynamics. Results An ischemia time of 34 minutes in a female murine model resulted in comparable injury to 22 minutes for males. We report a total of 16,856 unique genes mapped across injury and repair time course. Giotto, a computational toolbox for spatial data analysis, enabled increased resolution mapping of genes and cell types. Using a seeded non-negative matrix regression (SPOTlight) to deconvolute the dynamic landscape of cell-cell interactions, we find that injured proximal tubule cells are characterized by increasing macrophage and lymphocyte interactions even at 6 weeks after injury, potentially reflecting the AKI to CKD transition. Conclusions In this transcriptomic atlas, we defined region-specific and injury-induced loss of differentiation markers and their re-expression during repair, as well as region-specific injury and repair transcriptional responses. Lastly, we created a data visualization web application for the scientific community to explore these results (http://humphreyslab.com/SingleCell/; login: humphreyslab_visium password: irivisium).

scholarly journals Chromosome Unipolar Division and Low Expression of Tws May Cause Parthenogenesis of Rice Water Weevil (Lissorhoptrus oryzophilus Kuschel)

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 278
Author(s):  
Pengcheng Wang ◽  
Fangyuan Yang ◽  
Zhuo Ma ◽  
Runzhi Zhang
Keyword(s):  
Drosophila Melanogaster ◽  
Quantitative Pcr ◽  
Ovarian Tissue ◽  
Expression Patterns ◽  
Meiotic Spindle ◽  
Lissorhoptrus Oryzophilus ◽  
Rice Water Weevil ◽  
Rice Water ◽  
Beijing China ◽  
Low Expression

Rice water weevil (RWW) is divided into two types of population, triploid parthenogenesis and diploid bisexual reproduction. In this study, we explored the meiosis of triploid parthenogenesis RWW (Shangzhuang Town, Haidian District, Beijing, China) by marking the chromosomes and microtubules of parthenogenetic RWW oocytes via immunostaining. The immunostaining results show that there is a canonical meiotic spindle formed in the triploid parthenogenetic RWW oocytes, but chromosomes segregate at only one pole, which means that there is a chromosomal unipolar division during the oogenesis of the parthenogenetic RWW. Furthermore, we cloned the conserved sequences of parthenogenetic RWW REC8 and Tws, and designed primers based on the parthenogenetic RWW sequence to detect expression patterns by quantitative PCR (Q-PCR). Q-PCR results indicate that the expression of REC8 and Tws in ovarian tissue of bisexual Drosophila melanogaster is 0.98 and 10,000.00 times parthenogenetic RWW, respectively (p < 0.01). The results show that Tws had low expression in parthenogenetic RWW ovarian tissue, and REC8 was expressed normally. Our study suggests that the chromosomal unipolar division and deletion of Tws may cause parthenogenesis in RWW.

scholarly journals Jonckheere–Terpstra–Kendall-based non-parametric analysis of temporal differential gene expression

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Hitoshi Iuchi ◽  
Michiaki Hamada
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Time Course ◽  
Time Series Data ◽  
Expression Patterns ◽  
Detection Methods ◽  
Series Data ◽  
Expression Levels ◽  
Over Time ◽  
Non Parametric

Abstract Time-course experiments using parallel sequencers have the potential to uncover gradual changes in cells over time that cannot be observed in a two-point comparison. An essential step in time-series data analysis is the identification of temporal differentially expressed genes (TEGs) under two conditions (e.g. control versus case). Model-based approaches, which are typical TEG detection methods, often set one parameter (e.g. degree or degree of freedom) for one dataset. This approach risks modeling of linearly increasing genes with higher-order functions, or fitting of cyclic gene expression with linear functions, thereby leading to false positives/negatives. Here, we present a Jonckheere–Terpstra–Kendall (JTK)-based non-parametric algorithm for TEG detection. Benchmarks, using simulation data, show that the JTK-based approach outperforms existing methods, especially in long time-series experiments. Additionally, application of JTK in the analysis of time-series RNA-seq data from seven tissue types, across developmental stages in mouse and rat, suggested that the wave pattern contributes to the TEG identification of JTK, not the difference in expression levels. This result suggests that JTK is a suitable algorithm when focusing on expression patterns over time rather than expression levels, such as comparisons between different species. These results show that JTK is an excellent candidate for TEG detection.

scholarly journals Generalized Correlation Coefficient for Non-Parametric Analysis of Microarray Time-Course Data

2017 ◽  
Vol 14 (2) ◽  
Author(s):  
Qihua Tan ◽  
Mads Thomassen ◽  
Mark Burton ◽  
Kristian Fredløv Mose ◽  
Klaus Ejner Andersen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Correlation Coefficient ◽  
Parametric Analysis ◽  
Time Course ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Microarray Time Course ◽  
Time Course Data ◽  
Generalized Correlation ◽  
Non Parametric

AbstractModeling complex time-course patterns is a challenging issue in microarray study due to complex gene expression patterns in response to the time-course experiment. We introduce the generalized correlation coefficient and propose a combinatory approach for detecting, testing and clustering the heterogeneous time-course gene expression patterns. Application of the method identified nonlinear time-course patterns in high agreement with parametric analysis. We conclude that the non-parametric nature in the generalized correlation analysis could be an useful and efficient tool for analyzing microarray time-course data and for exploring the complex relationships in the omics data for studying their association with disease and health.

Combined expression patterns of QTL-linked candidate genes best predict thermotolerance in Drosophila melanogaster

2009 ◽  
Vol 55 (11) ◽  
pp. 1050-1057 ◽  
Author(s):  
Fabian M. Norry ◽  
Peter F. Larsen ◽  
Yongjie Liu ◽  
Volker Loeschcke
Keyword(s):  
Drosophila Melanogaster ◽  
Candidate Genes ◽  
Expression Patterns

scholarly journals Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Huiru Yang ◽  
Muhammad Mobeen Tahir ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr ◽  
Conserved Core

Abstract Background: Apple (Malus domestica Borkh.) is one of the most popular cultivated fruit crops in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

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.

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