scholarly journals Time Course of Gene Expression during Porphyromonas gingivalis Strain ATCC 33277 Biofilm Formation

2011 ◽  
Vol 77 (18) ◽  
pp. 6733-6736 ◽  
Author(s):  
Reiko Yamamoto ◽  
Yuichiro Noiri ◽  
Mikiyo Yamaguchi ◽  
Yoko Asahi ◽  
Hazuki Maezono ◽  
...  
Keyword(s):  
Gene Expression ◽  
Porphyromonas Gingivalis ◽  
Biofilm Formation ◽  
Time Course ◽  
Growth Stage ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Strain Atcc ◽  
Content Type ◽  
Number Of Genes

ABSTRACTChronological gene expression patterns of biofilm-forming cells are important to understand bioactivity and pathogenicity of biofilms. ForPorphyromonas gingivalisATCC 33277 biofilm formation, the number of genes differentially regulated by more than 1.5-fold was highest during the growth stage (312/2,090 genes), and some pathogen-associated genes were time-dependently controlled.

scholarly journals Growth, Development, and Gene Expression in a Persistent Streptococcus gordonii Biofilm

2003 ◽  
Vol 71 (8) ◽  
pp. 4759-4766 ◽  
Author(s):  
Keeta S. Gilmore ◽  
Pravina Srinivas ◽  
Darrin R. Akins ◽  
Kenneth L. Hatter ◽  
Michael S. Gilmore
Keyword(s):  
Gene Expression ◽  
Biofilm Formation ◽  
Bacterial Population ◽  
Morphological Changes ◽  
Expression Patterns ◽  
Nutrient Flux ◽  
Gene Expression Patterns ◽  
Significant Shift ◽  
Streptococcus Gordonii ◽  
Growth Development

ABSTRACT A model for the protracted (30-day) colonization of smooth surfaces by Streptococcus gordonii that incorporates the nutrient flux that occurs in the oral cavity was developed. This model was used to characterize the biphasic expansion of the adherent bacterial population, which corresponded with the emergence of higher-order architectures characteristic of biofilms. Biofilm formation by S. gordonii was observed to be influenced by the presence of simple sugars including sucrose, glucose, and fructose. Real-time PCR was used to quantify changes in expression of S. gordonii genes known or thought to be involved in biofilm formation. Morphological changes were accompanied by a significant shift in gene expression patterns. The majority of S. gordonii genes examined were observed to be downregulated in the biofilm phase. Genes found to be upregulated in the biofilm state were observed to encode products related to environmental sensing and signaling.

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.

scholarly journals Discovering gene expression patterns in time course microarray experiments by ANOVA–SCA

2007 ◽  
Vol 23 (14) ◽  
pp. 1792-1800 ◽  
Author(s):  
María José Nueda ◽  
Ana Conesa ◽  
Johan A. Westerhuis ◽  
Huub C. J. Hoefsloot ◽  
Age K. Smilde ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Microarray Experiments

scholarly journals Sensitivity of White and Opaque Candida albicans Cells to Antifungal Drugs

2017 ◽  
Vol 61 (8) ◽  
Author(s):  
Veronica B. Craik ◽  
Alexander D. Johnson ◽  
Matthew B. Lohse
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Antifungal Agents ◽  
Expression Patterns ◽  
Antifungal Drugs ◽  
Gene Expression Patterns ◽  
Metabolic Profiles ◽  
Strain Variation ◽  
Content Type ◽  
Terbinafine Hydrochloride

ABSTRACT White and opaque cells of Candida albicans have the same genome but differ in gene expression patterns, metabolic profiles, and host niche preferences. We tested whether these differences, which include the differential expression of drug transporters, resulted in different sensitivities to 27 antifungal agents. The analysis was performed in two different strain backgrounds; although there was strain-to-strain variation, only terbinafine hydrochloride and caspofungin showed consistent, 2-fold differences between white and opaque cells across both strains.

scholarly journals Time-course transcriptome landscape of achene development in lettuce

2020 ◽  
Author(s):  
Chen Luo ◽  
Shenglin Wang ◽  
Kang Ning ◽  
Zijing Chen ◽  
Jingjing Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Expression Patterns ◽  
Morphological Characteristics ◽  
Gene Expression Patterns ◽  
Biological Processes ◽  
Transcriptome Data ◽  
Development Stages ◽  
Functional Studies ◽  
Lettuce Seeds

AbstractLettuce (Lactuca sativa L.), which belongs to the large Asteraceae (Compositae) family, breeds by sexual reproduction and produce seeds. Actually, lettuce seeds are achenes, which are defined as fruits. However, few studies have described the morphological characteristics of the lettuce achenes, and genes essential for achene development are largely unknown in lettuce. To investigate the gene activity during achene development and determine the possible mechanisms that influence achene development in lettuce, we performed a time-course transcriptome analysis of lettuce achenes. A total of 23,790 expressed genes were detected at the five achene development stages. We investigated the gene expression patterns during achene development and identified the enriched biological processes at the corresponding stages. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed a variety of transcriptomic similarities and differentiation at different achene development stages. Further, transcription factors and phytohormones were found to play important roles during achene development. Finally, we proposed a working model to illustrate the gene expression modules and possible molecular mechanism underlying achene development. Our time-course transcriptome data also provides a foundation for future functional studies to reveal the genetic control of achene development in lettuce.

scholarly journals Time course Analysis of Gene expression patterns in ZebrafIsh Eye during Optic Nerve Regeneration

2010 ◽  
Vol 4 ◽  
pp. JEN.S5006 ◽  
Author(s):  
Amy T. Mccurley ◽  
Gloria V. Callard
Keyword(s):  
Gene Expression ◽  
Optic Nerve ◽  
Nerve Regeneration ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Neural Cells ◽  
Nerve Crush ◽  
Optic Nerve Regeneration

It is well-established that neurons in the adult mammalian central nervous system (CNS) are terminally differentiated and, if injured, will be unable to regenerate their connections. In contrast to mammals, zebrafish and other teleosts display a robust neuroregenerative response. Following optic nerve crush (ONX), retinal ganglion cells (RGC) regrow their axons to synapse with topographically correct targets in the optic tectum, such that vision is restored in ~21 days. What accounts for these differences between teleostean and mammalian responses to neural injury is not fully understood. A time course analysis of global gene expression patterns in the zebrafish eye after ONX can help to elucidate cellular and molecular mechanisms that contribute to a successful neuroregeneration. To define different phases of regeneration after ONX, alpha tubulin 1 ( tuba1) and growth-associated protein 43 ( gap43), markers previously shown to correspond to morphophological events, were measured by real time quantitative PCR (qPCR). Microarray analysis was then performed at defined intervals (6 hours, 1, 4, 12, and 21 days) post-ONX and compared to SHAM. Results show that optic nerve damage induces multiple, phase-related transcriptional programs, with the maximum number of genes changed and highest fold-change occurring at 4 days. Several functional groups affected by optic nerve regeneration, including cell adhesion, apoptosis, cell cycle, energy metabolism, ion channel activity, and calcium signaling, were identified. Utilizing the whole eye allowed us to identify signaling contributions from the vitreous, immune and glial cells as well as the neural cells of the retina. Comparisons between our dataset and transcriptional profiles from other models of regeneration in zebrafish retina, heart and fin revealed a subset of commonly regulated transcripts, indicating shared mechanisms in different regenerating tissues. Knowledge of gene expression patterns in all components of the eye in a model of successful regeneration provides an entry point for functional analyses, and will help in devising hypotheses for testing normal and toxic regulatory factors.

scholarly journals Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium

2014 ◽  
Vol 80 (18) ◽  
pp. 5828-5835 ◽  
Author(s):  
Jill Gaskell ◽  
Amber Marty ◽  
Michael Mozuch ◽  
Philip J. Kersten ◽  
Sandra Splinter BonDurant ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phanerochaete Chrysosporium ◽  
Expression Patterns ◽  
Hybrid Poplar ◽  
Wood Decay ◽  
Transcript Abundance ◽  
Gene Expression Patterns ◽  
Parental Line ◽  
Content Type ◽  
Liquid Chromatography Tandem Mass

ABSTRACTWe examined gene expression patterns in the lignin-degrading fungusPhanerochaete chrysosporiumwhen it colonizes hybrid poplar (Populus alba×tremula) and syringyl (S)-rich transgenic derivatives. A combination of microarrays and liquid chromatography-tandem mass spectrometry (LC-MS/MS) allowed detection of a total of 9,959 transcripts and 793 proteins. Comparisons ofP. chrysosporiumtranscript abundance in medium containing poplar or glucose as a sole carbon source showed 113 regulated genes, 11 of which were significantly higher (>2-fold,P< 0.05) in transgenic line 64 relative to the parental line. Possibly related to the very large amounts of syringyl (S) units in this transgenic tree (94 mol% S), several oxidoreductases were among the upregulated genes. Peptides corresponding to a total of 18 oxidoreductases were identified in medium consisting of biomass from line 64 or 82 (85 mol% S) but not in the parental clone (65 mol% S). These results demonstrate thatP. chrysosporiumgene expression patterns are substantially influenced by lignin composition.

Sign in / Sign up

Export Citation Format

Share Document