scholarly journals Differential Gene Expression Profiling of Staphylococcus aureus Cultivated under Biofilm and Planktonic Conditions

2005 ◽  
Vol 71 (5) ◽  
pp. 2663-2676 ◽  
Author(s):  
Alexandra Resch ◽  
Ralf Rosenstein ◽  
Christiane Nerz ◽  
Friedrich Götz
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Dna Microarrays ◽  
Cell Envelope ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Immune Defense ◽  
Biochemical Tests ◽  
Biofilm Growth ◽  
Ammonium Production

ABSTRACT It is well known that biofilm formation by pathogenic staphylococci on implanted medical devices leads to “chronic polymer-associated infections.” Bacteria in these biofilms are more resistant to antibiotics and the immune defense system than their planktonic counterparts, which suggests that the cells in a biofilm have altered metabolic activity. To determine which genes are up-regulated in Staphylococcus aureus biofilm cells, we carried out a comparative transcriptome analysis. Biofilm growth was simulated on dialysis membranes laid on agar plates. Staphylococci were cultivated planktonically in Erlenmeyer flasks with shaking. mRNA was isolated at five time points from cells grown under both conditions and used for hybridization with DNA microarrays. The gene expression patterns of several gene groups differed under the two growth conditions. In biofilm cells, the cell envelope appeared to be a very active compartment since genes encoding binding proteins, proteins involved in the synthesis of murein and glucosaminoglycan polysaccharide intercellular adhesin, and other enzymes involved in cell envelope synthesis and function were significantly up-regulated. In addition, evidence was obtained that formate fermentation, urease activity, the response to oxidative stress, and, as a consequence thereof, acid and ammonium production are up-regulated in a biofilm. These factors might contribute to survival, persistence, and growth in a biofilm environment. Interestingly, toxins and proteases were up-regulated under planktonic growth conditions. Physiological and biochemical tests for the up-regulation of urease, formate dehydrogenase, proteases, and the synthesis of staphyloxanthin confirmed the microarray data.

scholarly journals Global Transcriptome Analysis of Staphylococcus aureus Biofilms in Response to Innate Immune Cells

2013 ◽  
Vol 81 (12) ◽  
pp. 4363-4376 ◽  
Author(s):  
Tyler D. Scherr ◽  
Christelle M. Roux ◽  
Mark L. Hanke ◽  
Amanda Angle ◽  
Paul M. Dunman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Defense Mechanisms ◽  
Bacterial Infections ◽  
Expression Patterns ◽  
Immune Defense ◽  
Innate Immune ◽  
Gene Expression Patterns ◽  
Content Type ◽  
Affymetrix Microarrays

ABSTRACTThe potent phagocytic and microbicidal activities of neutrophils and macrophages are among the first lines of defense against bacterial infections. YetStaphylococcus aureusis often resistant to innate immune defense mechanisms, especially when organized as a biofilm. To investigate howS. aureusbiofilms respond to macrophages and neutrophils, gene expression patterns were profiled using Affymetrix microarrays. The addition of macrophages toS. aureusstatic biofilms led to a global suppression of the biofilm transcriptome with a wide variety of genes downregulated. Notably, genes involved in metabolism, cell wall synthesis/structure, and transcription/translation/replication were among the most highly downregulated, which was most dramatic at 1 h compared to 24 h following macrophage addition to biofilms. Unexpectedly, few genes were enhanced in biofilms after macrophage challenge. Unlike coculture with macrophages, coculture ofS. aureusstatic biofilms with neutrophils did not greatly influence the biofilm transcriptome. Collectively, these experiments demonstrate thatS. aureusbiofilms differentially modify their gene expression patterns depending on the leukocyte subset encountered.

Building Gene Networks by Analyzing Gene Expression Profiles

2019 ◽  
pp. 27-44
Author(s):  
Crescenzio Gallo
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Gene Networks ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Expression Data ◽  
Gene Expressions ◽  
Over Time

The possible applications of modeling and simulation in the field of bioinformatics are very extensive, ranging from understanding basic metabolic paths to exploring genetic variability. Experimental results carried out with DNA microarrays allow researchers to measure expression levels for thousands of genes simultaneously, across different conditions and over time. A key step in the analysis of gene expression data is the detection of groups of genes that manifest similar expression patterns. In this chapter, the authors examine various methods for analyzing gene expression data, addressing the important topics of (1) selecting the most differentially expressed genes, (2) grouping them by means of their relationships, and (3) classifying samples based on gene expressions.

An FLT3 gene-expression signature predicts clinical outcome in normal karyotype AML

Blood ◽  
2008 ◽  
Vol 111 (9) ◽  
pp. 4490-4495 ◽  
Author(s):  
Lars Bullinger ◽  
Konstanze Döhner ◽  
Raphael Kranz ◽  
Christoph Stirner ◽  
Stefan Fröhling ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Outcome ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Signature ◽  
Normal Karyotype ◽  
Mutation Status ◽  
Signature Genes ◽  
Starting Point

Abstract Acute myeloid leukemia with normal karyotype (NK-AML) represents a cytogenetic grouping with intermediate prognosis but substantial molecular and clinical heterogeneity. Within this subgroup, presence of FLT3 (FMS-like tyrosine kinase 3) internal tandem duplication (ITD) mutation predicts less favorable outcome. The goal of our study was to discover gene-expression patterns correlated with FLT3-ITD mutation and to evaluate the utility of a FLT3 signature for prognostication. DNA microarrays were used to profile gene expression in a training set of 65 NK-AML cases, and supervised analysis, using the Prediction Analysis of Microarrays method, was applied to build a gene expression–based predictor of FLT3-ITD mutation status. The optimal predictor, composed of 20 genes, was then evaluated by classifying expression profiles from an independent test set of 72 NK-AML cases. The predictor exhibited modest performance (73% sensitivity; 85% specificity) in classifying FLT3-ITD status. Remarkably, however, the signature outperformed FLT3-ITD mutation status in predicting clinical outcome. The signature may better define clinically relevant FLT3 signaling and/or alternative changes that phenocopy FLT3-ITD, whereas the signature genes provide a starting point to dissect these pathways. Our findings support the potential clinical utility of a gene expression–based measure of FLT3 pathway activation in AML.

scholarly journals Transcriptomic Analysis of Starch Biosynthesis in the Developing Grain of Hexaploid Wheat

2009 ◽  
Vol 2009 ◽  
pp. 1-23 ◽  
Author(s):  
Boryana S. Stamova ◽  
Debbie Laudencia-Chingcuanco ◽  
Diane M. Beckles
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Soluble Sugars ◽  
Starch Synthesis ◽  
Gene Families ◽  
Starch Accumulation ◽  
Protein Accumulation ◽  
High Accumulation

The expression of genes involved in starch synthesis in wheat was analyzed together with the accumulation profiles of soluble sugars, starch, protein, and starch granule distribution in developing caryopses obtained from the same biological materials used for profiling of gene expression using DNA microarrays. Multiple expression patterns were detected for the different starch biosynthetic gene isoforms, suggesting their relative importance through caryopsis development. Members of the ADP-glucose pyrophosphorylase, starch synthase, starch branching enzyme, and sucrose synthase gene families showed different expression profiles; expression of some members of these gene families coincided with a period of high accumulation of starch while others did not. A biphasic pattern was observed in the rates of starch and protein accumulation which paralleled changes in global gene expression. Metabolic and regulatory genes that show a pattern of expression similar to starch accumulation and granule size distribution were identified, suggesting their coinvolvement in these biological processes.

scholarly journals Vancomycin Tolerance in Methicillin-Resistant Staphylococcus aureus: Influence of Vancomycin, Daptomycin, and Telavancin on Differential Resistance Gene Expression

2012 ◽  
Vol 56 (8) ◽  
pp. 4422-4427 ◽  
Author(s):  
Warren E. Rose ◽  
Michael Fallon ◽  
John J. M. Moran ◽  
Joshua P. Vanderloo
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Gene Regulation ◽  
Cell Envelope ◽  
Differential Resistance ◽  
Accessory Gene ◽  
Methicillin Resistant ◽  
Content Type ◽  
Mrsa Strains ◽  
Time Kill

ABSTRACTMethicillin-resistantStaphylococcus aureus(MRSA) isolates that are susceptible to vancomycin but are tolerant to its killing effect may present a potential challenge for effective treatment. This study compared the microbiologic characteristics of clinical vancomycin-tolerant (VT-MRSA) and vancomycin-susceptible (VS-MRSA) strains using phenotypic and gene regulation studies. MRSA isolates collected from vancomycin-treated patients with bacteremia over a 5-year period were analyzed for vancomycin, daptomycin, and telavancin susceptibility, as well as accessory gene regulator (agr) group and function. Vancomycin tolerance was defined by a minimum bactericidal concentration (MBC)/minimum inhibitor concentration (MIC) ratio of ≥32 mg/liter. VT-MRSA isolates were compared to VS-MRSA isolates for differences in antimicrobial susceptibility, time-kill activity, and gene expression of key cell envelope response genesvraSR,dltA, andmprF. All 115 isolates evaluated were susceptible to vancomycin, daptomycin, and telavancin. Seven isolates (6%) were VT-MRSA.agrgroup II was more prevalent in isolates with vancomycin MBC/MIC ratios of ≥8. In time-kill analyses, VT-MRSA had reduced vancomycin killing, but daptomycin and telavancin activities were maintained. Significantly greater gene expression was observed in VT-MRSA after 72 h of subinhibitory antibiotic exposures. Vancomycin most notably increasedvraSRexpression (P= 0.002 versus VS-MRSA strains). Daptomycin and telavancin increased expression of all genes studied, most significantlymprFexpression (P< 0.001). Longer durations of antibiotic exposure (72 h versus 24 h) resulted in substantial increases in gene expression in VT-MRSA. Although the clinical impact of VT-MRSA is not fully recognized, these data suggest that VT-MRSA strains, while still susceptible, have altered gene regulation to adapt to the antimicrobial effects of glyco- and lipopeptides that may emerge during prolonged durations of exposure.

scholarly journals Bioinformatics Study on the Response of Human Endothelial Cells to Different Strains of Staphylococcus Aureus

2020 ◽  
Author(s):  
Tian-ao Xie ◽  
Ke-ying Fang ◽  
Wen-chao Cao ◽  
Jie Lv ◽  
Jia-xin Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Endothelial Cells ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Human Endothelial Cells ◽  
Different Strains ◽  
Differential Genes

Abstract BackgroundStaphylococcus aureus-induced bacteremia has an impact on human health due to its high mortality rate of 20–30%. To better study the invasion process of staphylococcus aureus, we conducted a study in human endothelial cells to try to find a link between the infection process and bacteremia at the molecular level.MethodsIn this study, the datasets GSE13736, GSE82036 were analyzed using R software to identify differentially expressed genes. Only the infection samples of four different strains had differential gene expression compared to the control samples. Then the GO analysis and KEGG analysis were conducted to construct a protein-protein interaction (PPI) network which shows the interaction and influence relationship between these differential genes. Finally, the central gene of the selected CytoHubba plug-in was verified using GraphPad Prism 8.ResultsThere were 421 differential genes in the Strain 6850, including 64 up-regulated and 357 down-regulated; There were 319 differential genes in the Strain 8325-4, including 14 up-regulated and 305 down-regulated. There were 90 differential genes in the Strain K70058396, including 12 up-regulated and 78 down-regulated. There were 876 differential genes in the Strain K1801/10, accompanied by 261 up-regulated and 615 down-regulated. An analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways associated with immune response and cytokines; Verification of the hub gene can provide a molecular basis for studying the relationship between invasive endothelial infection and bacteremia.ConclusionsWe found specific gene expression patterns in endothelial cells in response to infection with Strain K70058396, and these central genes and their expression products (RSAD2, DDX58, IFITT3, and IFIH1) play a key role in this process of infection.

scholarly journals Detection of icaA Gene Expression in Clinical Biofilm-Producing Staphylococcus Aureus Isolates

2020 ◽  
pp. 3154-3163
Author(s):  
Shaimaa W. Mohammed ◽  
Hala M. Radif
Keyword(s):  
Gene Expression ◽  
Staphylococcus Aureus ◽  
Bacterial Infections ◽  
Pcr Assay ◽  
Biochemical Tests ◽  
Slime Layer ◽  
Tract Infections ◽  
Strip Test ◽  
Icaa Gene ◽  
Quantitative Pcr Assay

The pathogenicity resulting from Staphylococcus aureus infection has remarkable importance as one of the community-associated bacterial infections, due to the virulent ability of these bacteria to produce biofilms. This study was designed to detect biofilm production in clinical isolates from samples of wounds and urinary tract infections. The expression levels of the icaA gene that is responsible of slime layer production in biofilms was compared in isolates with different biofilm producing capabilities. Fifty seven samples that included 32 samples from urine and 25 samples from wounds were collected from Alwasti Hospital, Al-Kindi Teaching Hospital, and Alzahraa Clinic, Baghdad, Iraq. The bacteria was identified according to biochemical tests, API20 strip test, and PCR assay. The results of 16S rRNA PCR detection revealed that nine isolates were identified as S. aureus. The biofilm assay showed that 46.15% of the isolates were strong biofilm producers, 46.15% had moderate ability to produce biofilm, and 7.70% were weak producers. Quantitative PCR assay was carried out on three isolates with different biofilm-producing abilities. The results demonstrated  that the strong biofilm-producing isolates had significantly higher (P ≤0.01) gene expression level (6.508) compared with the moderate (1.624) and the weak (1.231) isolates.

The graft response to transplantation: a gene expression profile analysis

2003 ◽  
Vol 15 (1) ◽  
pp. 52-64 ◽  
Author(s):  
Kenneth Christopher ◽  
Thomas F. Mueller ◽  
Rachel DeFina ◽  
Yurong Liang ◽  
Jianhua Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Constitutive Expression ◽  
Biological Processes ◽  
Heart Transplants ◽  
Self Organizing Maps ◽  
Gene Ontology Database ◽  
Expression Profile Analysis

Little is known regarding the graft response to transplantation injury. This study investigates the posttransplantation response of genes that are constitutively expressed in the heart. Constitutive heart and lymph node tissue-restricted gene expression was first analyzed with DNA microarrays. To demonstrate changes following transplantation in genes constitutively expressed in the heart, we performed vascularized murine heart transplants in allogeneic (BALB/c to B6), syngeneic (B6 to B6), and alymphoid (BALB/c-RAG2−/− to B6-RAG1−/−) experimental groups. Temporal induction of genes posttransplant relative to constitutive expression was evaluated with DNA microarrays. Dendrograms and self-organizing maps were generated to determine the dissimilarity between the experimental groups and to identify subsets of differentially expressed genes within the groups, respectively. Expression patterns of selected genes were confirmed by real-time PCR. Biological processes were assigned to genes induced posttransplant using the AnnBuilder package via the Gene Ontology Database. Post-transplant, a shift was noted in genes classified as defense, communication, and metabolism. Our results identify novel components of the graft response to transplantation injury and rejection.

scholarly journals Global Gene Expression Profiling of Yersinia pestis Replicating inside Macrophages Reveals the Roles of a Putative Stress-Induced Operon in Regulating Type III Secretion and Intracellular Cell Division

2010 ◽  
Vol 78 (9) ◽  
pp. 3700-3715 ◽  
Author(s):  
Hana S. Fukuto ◽  
Anton Svetlanov ◽  
Lance E. Palmer ◽  
A. Wali Karzai ◽  
James B. Bliska
Keyword(s):  
Gene Expression ◽  
Yersinia Pestis ◽  
Type Iii Secretion ◽  
Dna Microarrays ◽  
Cell Envelope ◽  
Global Gene Expression ◽  
Reading Frame ◽  
Type Iii ◽  
Global Gene Expression Profiling ◽  
High Level

ABSTRACT Yersinia pestis, the causative agent of plague, is a facultative intracellular pathogen. Previous studies have indicated that the ability of Y. pestis to survive inside macrophages may be critical during the early stages of plague pathogenesis. To gain insights into the biology of intracellular Y. pestis and its environment following phagocytosis, we determined the genome-wide transcriptional profile of Y. pestis KIM5 replicating inside J774.1 macrophage-like cells using DNA microarrays. At 1.5, 4, and 8 h postinfection, a total of 801, 464, and 416 Y. pestis genes were differentially regulated, respectively, compared to the level of gene expression of control bacteria grown in tissue culture medium. A number of stress-response genes, including those involved in detoxification of reactive oxygen species, as well as several metabolic genes involved in macromolecule synthesis, were significantly induced in intracellular Y. pestis, consistent with the presence of oxidative stress and nutrient starvation inside Yersinia-containing vacuoles. A putative stress-induced operon consisting of y2313, y2315, and y2316 (y2313-y2316), and a previously unidentified open reading frame, orfX, was studied further on the basis of its high level of intracellular expression. Mutant strains harboring either deletion, Δy2313-y2316 or ΔorfX, exhibited diverse phenotypes, including reduced effector secretion by the type III secretion system, increased intracellular replication, and filamentous morphology of the bacteria growing inside macrophages. The results suggest a possible role for these genes in regulating cell envelope characteristics in the intracellular environment.

scholarly journals Salt-Induced Stress Stimulates a Lipoteichoic Acid-Specific Three-Component Glycosylation System inStaphylococcus aureus

2018 ◽  
Vol 200 (12) ◽  
Author(s):  
Kelvin Kho ◽  
Timothy C. Meredith
Keyword(s):  
Staphylococcus Aureus ◽  
Sigma Factor ◽  
Cell Envelope ◽  
Normal Growth ◽  
Lipoteichoic Acid ◽  
Growth Conditions ◽  
Growth Media ◽  
Alternative Sigma Factor ◽  
Content Type

ABSTRACTLipoteichoic acid (LTA) inStaphylococcus aureusis a poly-glycerophosphate polymer anchored to the outer surface of the cell membrane. LTA has numerous roles in cell envelope physiology, including regulating cell autolysis, coordinating cell division, and adapting to environmental growth conditions. LTA is often further modified with substituents, includingd-alanine and glycosyl groups, to alter cellular function. While the genetic determinants ofd-alanylation have been largely defined, the route of LTA glycosylation and its role in cell envelope physiology have remained unknown, in part due to the low levels of basal LTA glycosylation inS. aureus. We demonstrate here thatS. aureusutilizes a membrane-associated three-component glycosylation system composed of an undecaprenol (Und)N-acetylglucosamine (GlcNAc) charging enzyme (CsbB; SAOUHSC_00713), a putative flippase to transport loaded substrate to the outside surface of the cell (GtcA; SAOUHSC_02722), and finally an LTA-specific glycosyltransferase that adds α-GlcNAc moieties to LTA (YfhO; SAOUHSC_01213). We demonstrate that this system is specific for LTA with no cross recognition of the structurally similar polyribitol phosphate containing wall teichoic acids. We show that while wild-typeS. aureusLTA has only a trace of GlcNAcylated LTA under normal growth conditions, amounts are raised upon either overexpressing CsbB, reducing endogenousd-alanylation activity, expressing the cell envelope stress responsive alternative sigma factor SigB, or by exposure to environmental stress-inducing culture conditions, including growth media containing high levels of sodium chloride.IMPORTANCEThe role of glycosylation in the structure and function ofStaphylococcus aureuslipoteichoic acid (LTA) is largely unknown. By defining key components of the LTA three-component glycosylation pathway and uncovering stress-induced regulation by the alternative sigma factor SigB, the role ofN-acetylglucosamine tailoring during adaptation to environmental stresses can now be elucidated. As thedltand glycosylation pathways compete for the same sites on LTA and induction of glycosylation results in decreasedd-alanylation, the interplay between the two modification systems holds implications for resistance to antibiotics and antimicrobial peptides.

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