scholarly journals Global Gene Expression Analysis during Germination in the Chytridiomycete Blastocladiella emersonii

2008 ◽  
Vol 8 (2) ◽  
pp. 170-180 ◽  
Author(s):  
Silvia M. Salem-Izacc ◽  
Tie Koide ◽  
Ricardo Z. N. Vêncio ◽  
Suely L. Gomes
Keyword(s):  
Cell Growth ◽  
Nutrient Medium ◽  
Time Course ◽  
Morphological Changes ◽  
Protein Biosynthesis ◽  
Cell Cycle Control ◽  
Global Gene Expression ◽  
Global Gene Expression Analysis ◽  
Blastocladiella Emersonii ◽  
Positive Effect

ABSTRACT Blastocladiella emersonii is an aquatic fungus of the Chytridiomycete class. During germination, the zoospore, a motile nongrowing cell, goes through a cascade of morphological changes that culminates with its differentiation into the germling cell, capable of coenocytic vegetative growth. Transcriptome analyses of B. emersonii cells were carried out during germination induced under various environmental conditions. Microarray data analyzing 3,563 distinct B. emersonii genes revealed that 26% of them are differentially expressed during germination in nutrient medium at at least one of the time points investigated. Over 500 genes are upregulated during the time course of germination under those conditions, most being related to cell growth, including genes involved in protein biosynthesis, DNA transcription, energetic metabolism, carbohydrate and oligopeptide transport, and cell cycle control. On the other hand, several transcripts stored in the zoospores are downregulated during germination in nutrient medium, such as genes involved in signal transduction, amino acid transport, and chromosome organization. In addition, germination induced in the presence of nutrients was compared with that triggered either by adenine or potassium ions in inorganic salt solution. Several genes involved in cell growth, induced during germination in nutrient medium, do not show increased expression when B. emersonii zoospores germinate in inorganic solution, suggesting that nutrients exert a positive effect on gene transcription. The transcriptome data also revealed that most genes involved in cell signaling show the same expression pattern irrespective of the initial germination stimulus.

scholarly journals Global Gene Expression Analysis during Sporulation of the Aquatic Fungus Blastocladiella emersonii

2009 ◽  
Vol 9 (3) ◽  
pp. 415-423 ◽  
Author(s):  
André L. G. Vieira ◽  
Suely L. Gomes
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Morphological Changes ◽  
Protein Biosynthesis ◽  
Global Gene Expression ◽  
Central Carbon Metabolism ◽  
Functional Categories ◽  
Content Type ◽  
Nutrient Sources ◽  
Blastocladiella Emersonii

ABSTRACTTheBlastocladiella emersoniilife cycle presents a number of drastic biochemical and morphological changes, mainly during two cell differentiation stages: germination and sporulation. To investigate the transcriptional changes taking place during the sporulation phase, which culminates with the production of the zoospores, motile cells responsible for the dispersal of the fungus, microarray experiments were performed. Among the 3,773 distinct genes investigated, a total of 1,207 were classified as differentially expressed, relative to time zero of sporulation, at at least one of the time points analyzed. These results indicate that accurate transcriptional control takes place during sporulation, as well as indicating the necessity for distinct molecular functions throughout this differentiation process. The main functional categories overrepresented among upregulated genes were those involving the microtubule, the cytoskeleton, signal transduction involving Ca2+, and chromosome organization. On the other hand, protein biosynthesis, central carbon metabolism, and protein degradation were the most represented functional categories among downregulated genes. Gene expression changes were also analyzed in cells sporulating in the presence of subinhibitory concentrations of glucose or tryptophan. Data obtained revealed overexpression of microtubule and cytoskeleton transcripts in the presence of glucose, probably causing the shape and motility problems observed in the zoospores produced under this condition. In contrast, the presence of tryptophan during sporulation led to upregulation of genes involved in oxidative stress, proteolysis, and protein folding. These results indicate that distinct physiological pathways are involved in the inhibition of sporulation due to these two classes of nutrient sources.

scholarly journals Brg1 Enables Rapid Growth of the Early Embryo by Suppressing Genes That Regulate Apoptosis and Cell Growth Arrest

2016 ◽  
Vol 36 (15) ◽  
pp. 1990-2010 ◽  
Author(s):  
Ajeet P. Singh ◽  
Julie F. Foley ◽  
Mark Rubino ◽  
Michael C. Boyle ◽  
Arpit Tandon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Growth ◽  
Cell Cycle Progression ◽  
Regulatory Region ◽  
Global Gene Expression ◽  
Early Embryo ◽  
Open Chromatin ◽  
Cycle Progression ◽  
Cell Growth Arrest ◽  
Global Gene Expression Analysis

SWI/SNF (switching/sucrose nonfermenting)-dependent chromatin remodeling establishes coordinated gene expression programs during development, yet important functional details remain to be elucidated. We show that the Brg1 (Brahma-related gene 1; Smarca4) ATPase is globally expressed at high levels during postimplantation development and its conditional ablation, beginning at gastrulation, results in increased apoptosis, growth retardation, and, ultimately, embryonic death. Global gene expression analysis revealed that genes upregulated inRosa26CreERT2;Brg1flox/floxembryos (here referred to asBrg1d/dembryos to describe embryos with deletion of theBrg1flox/floxalleles) negatively regulate cell cycle progression and cell growth. In addition, the p53 (Trp53) protein, which is virtually undetectable in early wild-type embryos, accumulated in theBrg1d/dembryos and activated the p53-dependent pathways. Using P19 cells, we show that Brg1 and CHD4 (chromodomain helicase DNA binding protein 4) coordinate to control target gene expression. Both proteins physically interact and show a substantial overlap of binding sites at chromatin-accessible regions adjacent to genes differentially expressed in theBrg1d/dembryos. Specifically, Brg1 deficiency results in reduced levels of the repressive histone H3 lysine K27 trimethylation (H3K27me3) histone mark and an increase in the amount of open chromatin at the regulatory region of thep53andp21(Cdkn1a) genes. These results provide insights into the mechanisms by which Brg1 functions, which is in part via the p53 program, to constrain gene expression and facilitate rapid embryonic growth.

scholarly journals Time Course Global Gene Expression Analysis of an In VivoCandidaBiofilm

2009 ◽  
Vol 200 (2) ◽  
pp. 307-313 ◽  
Author(s):  
Jeniel E. Nett ◽  
Alexander J. Lepak ◽  
Karen Marchillo ◽  
David R. Andes
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Time Course ◽  
Gene Expression Analysis ◽  
Global Gene Expression ◽  
Global Gene Expression Analysis

scholarly journals Exposure of Saccharomyces cerevisiae to Acetaldehyde Induces Sulfur Amino Acid Metabolism and Polyamine Transporter Genes, Which Depend on Met4p and Haa1p Transcription Factors, Respectively

2004 ◽  
Vol 70 (4) ◽  
pp. 1913-1922 ◽  
Author(s):  
Agustín Aranda ◽  
Marcel-lí del Olmo
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Biosynthesis ◽  
Sulfur Metabolism ◽  
Cell Cycle Control ◽  
Control Cell ◽  
Mitochondrial Protein ◽  
Vitamin B1 ◽  
Global Gene Expression ◽  
Growth Conditions ◽  
Yeast Cells

ABSTRACT Acetaldehyde is a toxic compound produced by Saccharomyces cerevisiae cells under several growth conditions. The adverse effects of this molecule are important, as significant amounts accumulate inside the cells. By means of global gene expression analyses, we have detected the effects of acetaldehyde addition in the expression of about 400 genes. Repressed genes include many genes involved in cell cycle control, cell polarity, and the mitochondrial protein biosynthesis machinery. Increased expression is displayed in many stress response genes, as well as other families of genes, such as those encoding vitamin B1 biosynthesis machinery and proteins for aryl alcohol metabolism. The induction of genes involved in sulfur metabolism is dependent on Met4p and other well-known factors involved in the transcription of MET genes under nonrepressing conditions of sulfur metabolism. Moreover, the deletion of MET4 leads to increased acetaldehyde sensitivity. TPO genes encoding polyamine transporters are also induced by acetaldehyde; in this case, the regulation is dependent on the Haa1p transcription factor. In this paper, we discuss the connections between acetaldehyde and the processes affected by this compound in yeast cells with reference to the microarray data.

scholarly journals Transcriptomic analysis of the development of skeletal muscle atrophy in cancer-cachexia in tumor-bearing mice

2018 ◽  
Vol 50 (12) ◽  
pp. 1071-1082 ◽  
Author(s):  
Thomas A. Blackwell ◽  
Igor Cervenka ◽  
Bhuwan Khatri ◽  
Jacob L. Brown ◽  
Megan E. Rosa-Caldwell ◽  
...  
Keyword(s):  
Time Course ◽  
Gastrocnemius Muscle ◽  
Cancer Cachexia ◽  
Muscle Wasting ◽  
Global Gene Expression ◽  
Skeletal Muscle Atrophy ◽  
Cytoskeletal Structure ◽  
Protein Ubiquitination ◽  
Global Gene Expression Analysis ◽  
Cellular Pathways

Cancer-cachexia (CC) is a wasting condition directly responsible for 20–40% of cancer-related deaths. The mechanisms controlling development of CC-induced muscle wasting are not fully elucidated. Most investigations focus on the postcachectic state and do not examine progression of the condition. We recently demonstrated mitochondrial degenerations precede muscle wasting in time course progression of CC. However, the extent of muscle perturbations before wasting in CC is unknown. Therefore, we performed global gene expression analysis in CC-induced muscle wasting to enhance understanding of intramuscular perturbations across the development of CC. Lewis lung carcinoma (LLC) was injected into the hind-flank of C57BL6/J mice at 8 wk of age with tumor allowed to develop for 1, 2, 3, or 4 wk and compared with PBS-injected control. Muscle wasting was evident at 4 wk LLC. RNA sequencing of gastrocnemius muscle samples showed widespread alterations in LLC compared with PBS animals with largest differences seen in 4 wk LLC, suggesting extensive transcriptomic alterations concurrent to muscle wasting. Commonly altered pathways included: mitochondrial dysfunction and protein ubiquitination, along with other less studied processes in this condition regulating transcription/translation and cytoskeletal structure. Current findings present novel evidence of transcriptomic shifts and altered cellular pathways in CC-induced muscle wasting.

scholarly journals Global gene expression analysis of the Myxococcus xanthus developmental time course

Genomics ◽  
2021 ◽  
Vol 113 (1) ◽  
pp. 120-134
Author(s):  
Gaurav Sharma ◽  
Andrew I. Yao ◽  
Gregory T. Smaldone ◽  
Jennifer Liang ◽  
Matt Long ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Time Course ◽  
Gene Expression Analysis ◽  
Myxococcus Xanthus ◽  
Global Gene Expression ◽  
Developmental Time ◽  
Global Gene Expression Analysis

Identification of temporal patterns of gene expression in the uteri of immature, ovariectomized mice following exposure to ethynylestradiol

2003 ◽  
Vol 15 (2) ◽  
pp. 127-141 ◽  
Author(s):  
K. C. Fertuck ◽  
J. E. Eckel ◽  
C. Gennings ◽  
T. R. Zacharewski
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Gene Annotation ◽  
Cell Cycle Control ◽  
Global Gene Expression ◽  
Ovariectomized Mice ◽  
Novel Approach ◽  
Annotation Information ◽  
Wet Weight ◽  
Physiological Outcomes

Estrogen induction of uterine wet weight provides an excellent model to investigate relationships between changes in global gene expression and well-characterized physiological responses. In this study, time course microarray GeneChip data were analyzed using a novel approach to identify temporal changes in uterine gene expression following treatment of immature ovariectomized C57BL/6 mice with 0.1 mg/kg 17α-ethynylestradiol. Functional gene annotation information from public databases facilitated the association of changes in gene expression with physiological outcomes, which allowed detailed mechanistic inferences to be drawn regarding cell cycle control and proliferation, transcription and translation, structural tissue remodeling, and immunologic responses. These systematic approaches confirm previously established responses, identify novel estrogen-regulated transcriptional effects, and disclose the coordinated activation of multiple modes of action that support the uterotrophic response elicited by estrogen. In particular, it was possible to elucidate the physiological significance of the dramatic induction of arginase, a classic estrogenic response, by elucidating its mechanistic relevance and delineating the role of arginine and ornithine utilization in the estrogen-stimulated induction of uterine wet weight.

Morphological Changes in the Brain of Acutely Ill and Weight-Recovered Patients with Anorexia Nervosa

2014 ◽  
Vol 42 (1) ◽  
pp. 7-18 ◽  
Author(s):  
Jochen Seitz ◽  
Katharina Bühren ◽  
Georg G. von Polier ◽  
Nicole Heussen ◽  
Beate Herpertz-Dahlmann ◽  
...  
Keyword(s):  
Anorexia Nervosa ◽  
Cognitive Deficits ◽  
Time Course ◽  
Morphological Changes ◽  
Meta Analysis ◽  
Short Term ◽  
Clinical Prognosis ◽  
Qualitative Review ◽  
Brain Changes ◽  
The Brain

Objective: Acute anorexia nervosa (AN) leads to reduced gray (GM) and white matter (WM) volume in the brain, which however improves again upon restoration of weight. Yet little is known about the extent and clinical correlates of these brain changes, nor do we know much about the time-course and completeness of their recovery. Methods: We conducted a meta-analysis and a qualitative review of all magnetic resonance imaging studies involving volume analyses of the brain in both acute and recovered AN. Results: We identified structural neuroimaging studies with a total of 214 acute AN patients and 177 weight-recovered AN patients. In acute AN, GM was reduced by 5.6% and WM by 3.8% compared to healthy controls (HC). Short-term weight recovery 2–5 months after admission resulted in restitution of about half of the GM aberrations and almost full WM recovery. After 2–8 years of remission GM and WM were nearly normalized, and differences to HC (GM: –1.0%, WM: –0.7%) were no longer significant, although small residual changes could not be ruled out. In the qualitative review some studies found GM volume loss to be associated with cognitive deficits and clinical prognosis. Conclusions: GM and WM were strongly reduced in acute AN. The completeness of brain volume rehabilitation remained equivocal.

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