Microarray analysis of gene expression under in vitro growth conditions mimicking the in vivo environment

2005 ◽  
Vol 110 (3-4) ◽  
pp. 255-263 ◽  
Author(s):  
E MELNIKOW ◽  
S DORNAN ◽  
C SARGENT ◽  
M DUSZENKO ◽  
G EVANS ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Growth Conditions ◽  
In Vitro Growth

Rapid melanization of bomirski amelanotic melanoma cells in cell culture

1983 ◽  
Vol 3 (2) ◽  
pp. 189-194 ◽  
Author(s):  
A. Słominski
Keyword(s):  
Cell Culture ◽  
Primary Cell Culture ◽  
Growth Conditions ◽  
Melanoma Cells ◽  
Amelanotic Melanoma ◽  
Primary Cell ◽  
In Vitro Growth

Transfer of Bomirski amelanotic melanoma ceils from in vivo to in vitro growth conditions results in occurrence of rapid melanization in their cytoplasm. The melanized ceils from primary cell culture initiate tumours in hamsters, which do not contain traces of melanin and resemble typical amelanotic melanoma.

scholarly journals Analysis of theIn VivoTranscriptome ofBordetella pertussisduring Infection of Mice

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Ting Y. Wong ◽  
Jesse M. Hall ◽  
Evan S. Nowak ◽  
Dylan T. Boehm ◽  
Laura A. Gonyar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Iron Acquisition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Growth Conditions ◽  
Rna Seq ◽  
Content Type ◽  
Murine Lung

ABSTRACTBordetella pertussiscauses the disease whooping cough through coordinated control of virulence factors by theBordetellavirulence gene system. Microarrays and, more recently, RNA sequencing (RNA-seq) have been used to describein vitrogene expression profiles ofB. pertussisand other pathogens. In previous studies, we have analyzed thein vitrogene expression profiles ofB. pertussis, and we hypothesize that the infection transcriptome profilein vivois significantly different from that under laboratory growth conditions. To study the infection transcriptome ofB. pertussis, we developed a simple filtration technique for isolation of bacteria from infected lungs. The work flow involves filtering the bacteria out of the lung homogenate using a 5-μm-pore-size syringe filter. The captured bacteria are then lysed to isolate RNA for Illumina library preparation and RNA-seq analysis. Upon comparing thein vitroandin vivogene expression profiles, we identified 351 and 255 genes as activated and repressed, respectively, during murine lung infection. As expected, numerous genes associated with virulent-phase growth were activated in the murine host, including pertussis toxin (PT), the PT secretion apparatus, and the type III secretion system. A significant number of genes encoding iron acquisition and heme uptake proteins were highly expressed during infection, supporting iron acquisition as critical forB. pertussissurvivalin vivo. Numerous metabolic genes were repressed during infection. Overall, these data shed light on the gene expression profile ofB. pertussisduring infection, and this method will facilitate efforts to understand how this pathogen causes infection.IMPORTANCEIn vitrogrowth conditions for bacteria do not fully recapitulate the host environment. RNA sequencing transcriptome analysis allows for the characterization of the infection gene expression profiles of pathogens in complex environments. Isolation of the pathogen from infected tissues is critical because of the large amounts of host RNA present in crude lysates of infected organs. A filtration method was developed that enabled enrichment of the pathogen RNA for RNA-seq analysis. The resulting data describe the “infection transcriptome” ofB. pertussisin the murine lung. This strategy can be utilized for pathogens in other hosts and, thus, expand our knowledge of what bacteria express during infection.

Gene expression profiling of in vitro-derived and in vivo-derived bovine blastocysts using microarray analysis

2011 ◽  
Vol 22 ◽  
pp. S53-S54
Author(s):  
Digdem Aktoprakligil Aksu ◽  
Cansu Agca ◽  
Soner Aksu ◽  
Haydar Bagis ◽  
Tolga Akkoc ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Microarray Analysis ◽  
Expression Profiling

scholarly journals The Vitamin B 12 -Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters

mBio ◽  
2017 ◽  
Vol 8 (2) ◽  
Author(s):  
Mingxu Fang ◽  
Carl E. Bauer
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Light Absorption ◽  
Growth Conditions ◽  
Binding Activity ◽  
Regulatory Function ◽  
Vitamin B ◽  
Dna Binding Activity

ABSTRACT Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B 12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq) and ChIP-seq and exonuclease digestion (ChIP-exo) studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ 2 ) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ 2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function. IMPORTANCE Photoreceptors control a wide range of physiology often by regulating downstream gene expression in response to light absorption via a bound chromophore. Different photoreceptors are known to utilize a number of different compounds for light absorption, including the use of such compounds as flavins, linearized tetrapyrroles (bilins), and carotenoids. Recently, a novel class of photoreceptors that use vitamin B 12 (cobalamin) as a blue-light-absorbing chromophore have been described. In this study, we analyzed the mechanism by which the vitamin B 12 binding photoreceptor AerR controls the DNA binding activity of the photosystem regulator CrtJ. This study shows that a direct interaction between the vitamin B 12 binding photoreceptor AerR with CrtJ modulates CrtJ binding to DNA and importantly, the regulatory outcome of gene expression, as shown here with photosystem promoters.

scholarly journals Divergent Targets of Candida albicans Biofilm Regulator Bcr1In VitroandIn Vivo

2012 ◽  
Vol 11 (7) ◽  
pp. 896-904 ◽  
Author(s):  
Saranna Fanning ◽  
Wenjie Xu ◽  
Norma Solis ◽  
Carol A. Woolford ◽  
Scott G. Filler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Stress Response ◽  
Growth Conditions ◽  
Gene Expression Measurement ◽  
Content Type ◽  
New Genes

ABSTRACTCandida albicansis a causative agent of oropharyngeal candidiasis (OPC), a biofilm-like infection of the oral mucosa. Biofilm formation depends upon theC. albicanstranscription factor Bcr1, and previous studies indicate that Bcr1 is required for OPC in a mouse model of infection. Here we have used a nanoString gene expression measurement platform to elucidate the role of Bcr1 in OPC-related gene expression. We chose for assays a panel of 134 genes that represent a range of morphogenetic and cell cycle functions as well as environmental and stress response pathways. We assayed gene expression in whole infected tongue samples. The results sketch a portrait ofC. albicansgene expression in which numerous stress response pathways are activated during OPC. This one set of experiments identifies 64 new genes with significantly altered RNA levels during OPC, thus increasing substantially the number of known genes in this expression class. Thebcr1Δ/Δ mutant had a much more limited gene expression defect during OPC infection than previously reported forin vitrogrowth conditions. Among major functional Bcr1 targets, we observed thatALS3was Bcr1 dependentin vivowhileHWP1was not. We used null mutants and complemented strains to verify that Bcr1 and Hwp1 are required for OPC infection in this model. The role of Als3 is transient and mild, though significant. Our findings suggest that the versatility ofC. albicansas a pathogen may reflect its ability to persist in the face of multiple stresses and underscore that transcriptional circuitry during infection may be distinct from that detailed duringin vitrogrowth.

scholarly journals Expression of the Gonococcal Global Regulatory Protein Fur and Genes Encompassing the Fur and Iron Regulon during In Vitro and In Vivo Infection in Women

2008 ◽  
Vol 190 (9) ◽  
pp. 3129-3139 ◽  
Author(s):  
Sarika Agarwal ◽  
Shite Sebastian ◽  
Borys Szmigielski ◽  
Peter A. Rice ◽  
Caroline A. Genco
Keyword(s):  
Epithelial Cells ◽  
Microarray Analysis ◽  
Regulatory Protein ◽  
Growth Conditions ◽  
Pcr Analysis ◽  
Gonococcal Infection ◽  
Cervical Epithelial Cells ◽  
Female Subjects

ABSTRACT The ferric uptake regulatory protein, Fur, functions as a global regulatory protein of gene transcription in the mucosal pathogen Neisseria gonorrhoeae. We have shown previously that several N. gonorrhoeae Fur-repressed genes are expressed in vivo during mucosal gonococcal infection in men, which suggests that this organism infects in an iron-limited environment and that Fur is expressed under these conditions. In this study we have demonstrated expression of the gonococcal fur gene in vitro, in human cervical epithelial cells, and in specimens from female subjects with uncomplicated gonococcal infection. In vitro studies confirmed that the expression of the gonococcal fur gene was repressed during growth under iron-replete growth conditions but that a basal level of the protein was maintained. Using GFP transcriptional fusions constructed from specific Fur binding sequences within the fur promoter/operator region, we determined that this operator region was functional during N. gonorrhoeae infection of cervical epithelial cells. Furthermore, reverse transcription-PCR analysis, as well as microarray analysis, using a custom Neisseria Fur and iron regulon microarray revealed that several Fur- and iron-regulated genes were expressed during N. gonorrhoeae infection of cervical epithelial cells. Microarray analysis of specimens obtained from female subjects with uncomplicated gonococcal infection corroborated our in vitro findings and point toward a key role of gonococcal Fur- and iron-regulated genes in gonococcal disease.

Differential expression of the enolase gene under in vivo versus in vitro growth conditions of Aeromonas hydrophila

2003 ◽  
Vol 34 (4) ◽  
pp. 195-204 ◽  
Author(s):  
Jian Sha ◽  
C.L. Galindo ◽  
V. Pancholi ◽  
V.L. Popov ◽  
Y. Zhao ◽  
...  
Keyword(s):  
Differential Expression ◽  
Aeromonas Hydrophila ◽  
Growth Conditions ◽  
In Vitro Growth

scholarly journals Gene Expression of Commensal Lactobacillus johnsonii Strain NCC533 during In Vitro Growth and in the Murine Gut

2007 ◽  
Vol 189 (22) ◽  
pp. 8109-8119 ◽  
Author(s):  
Emmanuel Denou ◽  
Bernard Berger ◽  
Caroline Barretto ◽  
Jean-Michel Panoff ◽  
Fabrizio Arigoni ◽  
...  
Keyword(s):  
Stationary Phase ◽  
Viable Cell ◽  
Growth Conditions ◽  
In Vitro Growth ◽  
Lactobacillus Johnsonii ◽  
Cell Counts ◽  
Expression Of Genes ◽  
In Vivo Growth

ABSTRACT Work with pathogens like Vibrio cholerae has shown major differences between genes expressed in bacteria grown in vitro and in vivo. To explore this subject for commensals, we investigated the transcription of the Lactobacillus johnsonii NCC533 genome during in vitro and in vivo growth using the microarray technology. During broth growth, 537, 626, and 277 of the 1,756 tested genes were expressed during exponential phase, “adaptation” (early stationary phase), and stationary phase, respectively. One hundred one, 150, and 33 genes, respectively, were specifically transcribed in these three phases. To explore the in vivo transcription program, we fed L. johnsonii containing a resistance plasmid to antibiotic-treated mice. After a 2-day washout phase, we determined the viable-cell counts of lactobacilli that were in the lumina and associated with the mucosae of different gut segments. While the cell counts showed a rather uniform distribution along the gut, we observed marked differences with respect to the expression of the Lactobacillus genome. The largest number of transcribed genes was in the stomach (n = 786); the next-largest numbers occurred in the cecum (n = 391) and the jejunum (n = 296), while only 26 Lactobacillus genes were transcribed in the colon. In vitro and in vivo transcription programs overlapped only partially. One hundred ninety-one of the transcripts from the lactobacilli in the stomach were not detected during in vitro growth; 202 and 213 genes, respectively, were transcribed under all in vitro and in vivo conditions; but the core transcriptome for all growth conditions comprised only 103 genes. Forty-four percent of the NCC533 genes were not detectably transcribed under any of the investigated conditions. Nontranscribed genes were clustered on the genome and enriched in the variable-genome part. Our data revealed not only major differences between in vitro- and in vivo-expressed genes in a Lactobacillus gut commensal organism but also marked changes in the expression of genes along the digestive tract.

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