Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase

Sporothrix schenckii is a dimorphic fungus existing as mould in the environment and as yeast in the host. The morphological shift between mycelial/yeast phases is crucial for its virulence, but the transcriptional networks implicated in dimorphic transition are still not fully understood. Here, we report the global transcriptomic differences occurring between mould and yeast phases of S. schenckii, including changes in gene expression profiles associated with these distinct cellular phenotypes. Moreover, we also propose a new genome annotation, which reveals a more complex transcriptional architecture than previously assumed. Using RNA-seq, we identified a total of 17 307 genes, of which 11 217 were classified as protein-encoding genes, whereas 6090 were designated as non-coding RNAs (ncRNAs). Approximately ~71 % of all annotated genes were found to overlap and the different-strand overlapping type was the most common. Gene expression analysis revealed that 8795 genes were differentially regulated among yeast and mould forms. Differential gene expression was also observed for antisense ncRNAs overlapping neighbouring protein-encoding genes. The release of transcriptome-wide data and the establishment of the Sporothrix Genome DataBase (http://sporothrixgenomedatabase.unime.it) represent an important milestone for Sporothrix research, because they provide a strong basis for future studies on the molecular pathways involved in numerous biological processes.

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GeneExpression in HL60 Granulocytoids and Human PolymorphonuclearLeukocytes Exposed to Candidaalbicans†

Infection and Immunity ◽

10.1128/iai.72.1.414-429.2004 ◽

2004 ◽

Vol 72 (1) ◽

pp. 414-429 ◽

Cited By ~ 29

Author(s):

Alaka Mullick ◽

Miria Elias ◽

Penelope Harakidas ◽

Anne Marcil ◽

Malcolm Whiteway ◽

...

Keyword(s):

Gene Expression ◽

Polymorphonuclear Leukocytes ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Dimorphic Fungus ◽

Granulocytic Differentiation ◽

Effector Cells ◽

Study Gene Expression ◽

Opportunistic Human Pathogen ◽

Human Polymorphonuclear Leukocytes

ABSTRACT Candida albicans is an opportunistic human pathogen causing both superficial and disseminated diseases. It is a dimorphic fungus, switching between yeast and hyphal forms, depending on cues from its microenvironment. Hyphae play an important role in the pathogenesis of candidiasis. The host's response to Candida infection is multifaceted and includes the participation of granulocytes as key effector cells. The aim of this investigation was to study host gene expression during granulocyte-Candida interaction. Effector cells were generated by the granulocytic differentiation of HL60 cells. The resulting cell population was shown to be morphologically and functionally equivalent to granulocytes and is therefore referred to as HL60 granulocytoids for the purposes of this study. Gene expression profiles were determined 1 h after hosts were infected with C. albicans. Three Candida-granulocytoid ratios were chosen to reflect different degrees of HL60 granulocytoid inhibition of C. albicans. The data demonstrate that at the high pathogen-host ratio, C. albicans modulated the HL60 granulocytoid's response by downregulating the expression of known antimicrobial genes. In addition, looking at the expression of a large number of genes, not all of which have necessarily been implicated in candidastatic or candidacidal mechanisms, it has been possible to describe the physiological response of the HL60 granulocytoid to an infectious challenge with C. albicans. Finally, some of the observed changes in HL60 granulocytoid gene expression were investigated in freshly isolated human polymorphonuclear leukocytes infected with C. albicans. Similar changes were seen in these primary human cells, lending support to the validity of this model.

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RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of Pinus Tabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte

International Journal of Molecular Sciences ◽

10.3390/ijms19082246 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2246 ◽

Cited By ~ 1

Author(s):

Yang Yao ◽

Rui Han ◽

Zaixin Gong ◽

Caixia Zheng ◽

Yuanyuan Zhao

Keyword(s):

Gene Expression ◽

Female Gametophyte ◽

Expression Profiles ◽

Signal Transduction Pathway ◽

Gene Expression Profiles ◽

Pinus Tabulaeformis ◽

Cdna Libraries ◽

Pcr Analysis ◽

Transcriptional Networks ◽

Ovule Development

The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.

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Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain

Translational Psychiatry ◽

10.1038/s41398-021-01528-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rizaldy C. Zapata ◽

Besma S. Chaudry ◽

Mariela Lopez Valencia ◽

Dinghong Zhang ◽

Scott A. Ochsner ◽

...

Keyword(s):

Gene Expression ◽

Weight Gain ◽

Regulatory Networks ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Whole Body ◽

Transcriptional Networks ◽

Gene Set ◽

P Gene ◽

Whole Body Metabolism

AbstractAlthough antipsychotics, such as olanzapine, are effective in the management of psychiatric conditions, some patients experience excessive antipsychotic-induced weight gain (AIWG). To illuminate pathways underlying AIWG, we compared baseline blood gene expression profiles in two cohorts of mice that were either prone (AIWG-P) or resistant (AIWG-R) to weight gain in response to olanzapine treatment for two weeks. We found that transcripts elevated in AIWG-P mice relative to AIWG-R are enriched for high-confidence transcriptional targets of numerous inflammatory and immunomodulatory signaling nodes. Moreover, these nodes are themselves enriched for genes whose disruption in mice is associated with reduced body fat mass and slow postnatal weight gain. In addition, we identified gene expression profiles in common between our mouse AIWG-P gene set and an existing human AIWG-P gene set whose regulation by immunomodulatory transcription factors is highly conserved between species. Finally, we identified striking convergence between mouse AIWG-P transcriptional regulatory networks and those associated with body weight and body mass index in humans. We propose that immunomodulatory transcriptional networks drive AIWG, and that these networks have broader conserved roles in whole body-metabolism.

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Gene expression profiles of RAW264.7 macrophages stimulated with preparations of LPS differing in isolation and purity

Innate Immunity ◽

10.1177/1753425910393540 ◽

2011 ◽

Vol 18 (1) ◽

pp. 80-88 ◽

Cited By ~ 14

Author(s):

Holly R Rutledge ◽

Weiwen Jiang ◽

Jun Yang ◽

Laura A Warg ◽

David A Schwartz ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Transcriptional Networks ◽

Molecular Pathways ◽

Raw264.7 Macrophages ◽

Lps Treatment

Lipopolysaccharide is a major component of the cell wall of Gram-negative bacteria and a potent stimulator of innate immune response via TLR4. Studies on the LPS action both in vivo and in vitro have used different preparations of LPS, including ultra-pure LPS (LIST) and a less pure but less expensive form (Sigma) isolated from Escherichia coli serotype O111:B4. The difference between the effects of these compounds has not been well studied although this information is important in understanding TLR stimulation. In this study, we compared response of RAW264.7 macrophage cells treated LIST or Sigma LPS for 6 h and 24 h. Gene expression data were analyzed to identify specific genes and pathways that are in common and unique to the two LPS preparations. Seven hundred fifty-five genes were differentially expressed at 6 h in response to Sigma LPS and 973 were differentially expressed following LIST LPS treatment, with 503 in common. At 24 h, Sigma LPS induced or repressed 901 genes while 1646 genes were differentially regulated by LIST LPS treatment; 701 genes were shared by two forms of LPS. Although considerably more genes were differentially expressed in response to LIST LPS, similar molecular pathways and transcriptional networks were activated by the two LPS preparations. We also treated bone marrow-derived macrophages (BMMs) from three strains of mice with different concentrations of LIST and Sigma LPS and showed that BMMs produced more IL-6 and TNF-α in response to LIST LPS at low LPS concentrations but, at higher LPS concentrations, more cytokines were produced in response to stimulation by Sigma LPS. Together, these findings suggest that, despite activation of similar molecular pathways by LIST and Sigma LPS preparations, residual protein impurities in the Sigma LPS preparation may nevertheless influence the transcriptional profile attributed to TLR4 stimulation.

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Transcription Profiling of the Stringent Response in Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.01092-07 ◽

2007 ◽

Vol 190 (3) ◽

pp. 1084-1096 ◽

Cited By ~ 254

Author(s):

Tim Durfee ◽

Anne-Marie Hansen ◽

Huijun Zhi ◽

Frederick R. Blattner ◽

Ding Jun Jin

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Stress Responses ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Stringent Response ◽

Maximum Growth ◽

Regulatory Processes ◽

K 12 ◽

Encoding Genes

ABSTRACT The bacterial stringent response serves as a paradigm for understanding global regulatory processes. It can be triggered by nutrient downshifts or starvation and is characterized by a rapid RelA-dependent increase in the alarmone (p)ppGpp. One hallmark of the response is the switch from maximum-growth-promoting to biosynthesis-related gene expression. However, the global transcription patterns accompanying the stringent response in Escherichia coli have not been analyzed comprehensively. Here, we present a time series of gene expression profiles for two serine hydroxymate-treated cultures: (i) MG1655, a wild-type E. coli K-12 strain, and (ii) an isogenic relAΔ251 derivative defective in the stringent response. The stringent response in MG1655 develops in a hierarchical manner, ultimately involving almost 500 differentially expressed genes, while the relAΔ251 mutant response is both delayed and limited in scope. We show that in addition to the down-regulation of stable RNA-encoding genes, flagellar and chemotaxis gene expression is also under stringent control. Reduced transcription of these systems, as well as metabolic and transporter-encoding genes, constitutes much of the down-regulated expression pattern. Conversely, a significantly larger number of genes are up-regulated. Under the conditions used, induction of amino acid biosynthetic genes is limited to the leader sequences of attenuator-regulated operons. Instead, up-regulated genes with known functions, including both regulators (e.g., rpoE, rpoH, and rpoS) and effectors, are largely involved in stress responses. However, one-half of the up-regulated genes have unknown functions. How these results are correlated with the various effects of (p)ppGpp (in particular, RNA polymerase redistribution) is discussed.

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Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients

Blood ◽

10.1182/blood-2013-02-485771 ◽

2014 ◽

Vol 123 (6) ◽

pp. 894-904 ◽

Cited By ~ 66

Author(s):

Nicolas Rapin ◽

Frederik Otzen Bagger ◽

Johan Jendholm ◽

Helena Mora-Jensen ◽

Anders Krogh ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Transcriptional Networks ◽

New Disease ◽

Expression Data ◽

Normal Cells ◽

Key Points ◽

Normal Gene ◽

Disease Entities

Key Points This study describes a method for the comparison of gene expression data of any type of cancer cells with their corresponding normal cells. Our analyses reveal novel disease entities, identify common deregulated transcriptional networks, and predict survival.

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Transcriptomic comparison between beetle strains selected for short and long durations of death feigning

Scientific Reports ◽

10.1038/s41598-019-50440-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Hironobu Uchiyama ◽

Ken Sasaki ◽

Shogo Hinosawa ◽

Keisuke Tanaka ◽

Kentarou Matsumura ◽

...

Keyword(s):

Gene Expression ◽

Metabolic Pathways ◽

Antipredator Behavior ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Pcr Analysis ◽

Quantitative Real Time Pcr ◽

Death Feigning ◽

Encoding Genes

Abstract The molecular basis of death feigning, an antipredator behavior that has received much attention recently, was analyzed. We compared the gene expression profiles of strains with different behaviors, i.e., different durations of death feigning, in the beetle Tribolium castaneum. Beetles artificially selected for short (S) and long (L) durations of death feigning for many generations were compared thoroughly by RNA sequencing. We identified 518 differentially expressed genes (DEGs) between the strains. The strains also showed divergence in unexpected gene expression regions. As expected from previous physiological studies, genes associated with the metabolic pathways of tyrosine, a precursor of dopamine, were differentially expressed between the S and L strains; these enzyme-encoding genes were expressed at higher levels in the L strain than in the S strain. We also found that several genes associated with insulin signaling were expressed at higher levels in the S strain than in the L strain. Quantitative real-time PCR analysis showed that the relative expression levels of Tchpd (encoding 4-hydroxyphenylpyruvate dioxygenase, Hpd) and Tcnat (encoding N-acetyltransferase, Nat) were significantly higher in the L strain than in the S strain, suggesting the influence of these enzymes on the supply of dopamine and duration of death feigning.

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Overexpression of Genes of the Cell Wall Stimulon in Clinical Isolates of Staphylococcus aureus Exhibiting Vancomycin-Intermediate- S. aureus-Type Resistance to Vancomycin

Journal of Bacteriology ◽

10.1128/jb.188.3.1120-1133.2006 ◽

2006 ◽

Vol 188 (3) ◽

pp. 1120-1133 ◽

Cited By ~ 114

Author(s):

Fionnuala McAleese ◽

Shang Wei Wu ◽

Krzysztof Sieradzki ◽

Paul Dunman ◽

Ellen Murphy ◽

...

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Cell Wall ◽

Heart Valve ◽

Genetic Relatedness ◽

Expression Profiles ◽

Altered Expression ◽

Vancomycin Mics ◽

Protein Encoding ◽

Encoding Genes

ABSTRACT Custom-designed gene chips (Affymetrix) were used to determine genetic relatedness and gene expression profiles in Staphylococcus aureus isolates with increasing MICs of vancomycin that were recovered over a period of several weeks from the blood and heart valve of a patient undergoing extensive vancomycin therapy. The isolates were found to be isogenic as determined by the GeneChip based genotyping approach and thus represented a unique opportunity to study changes in gene expression that may contribute to the vancomycin resistance phenotype. No differences in gene expression were detected between the parent strain, JH1, and JH15, isolated from the nares of a patient contact. Few expression changes were observed between blood and heart valve isolates with identical vancomycin MICs. A large number of genes had altered expression in the late stage JH9 isolate (MIC = 8 μg/ml) compared to JH1 (MIC = 1 μg/ml). Most genes with altered expression were involved in housekeeping functions or cell wall biosynthesis and regulation. The sortase-encoding genes, srtA and srtB, as well as several surface protein-encoding genes were downregulated in JH9. Two hypothetical protein-encoding genes, SAS016 and SA2343, were dramatically overexpressed in JH9. Interestingly, 27 of the genes with altered expression in JH9 grown in drug-free medium were found to be also overexpressed when the parental strain JH1 was briefly exposed to inhibitory concentrations of vancomycin, and more than half (17 of 27) of the genes with altered expression belonged to determinants that were proposed to form part of a general cell wall stress stimulon (S. Utaida et al., Microbiology 149:2719-2732, 2003).

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