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DNA fingerprints of human oral microbiome: a first step towards early diagnosis of oral diseases
Title
DNA fingerprints of human oral microbiome: a first step towards early diagnosis of oral diseases.
Creator
Chakraborty, Shreyasee, Esiobu, Nwadiuto, Florida Atlantic University, Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
This study evaluated the stability of oral bacteria in healthy subjects and documented community shifts in smokers and oral/periodontal disease by employing PCR-RFLP, DGGE and sequence analysis of the 16S rDNA gene from metagenomes and plate-wash (cultured) bacteria of oral wash from 15 participants,. A stable core of bacterial DNA fingerprint was detected within and between subjects and did not change over time when analyzed in smokers and healthy non-smokers. Signature bands in smokers, non...
Show moreThis study evaluated the stability of oral bacteria in healthy subjects and documented community shifts in smokers and oral/periodontal disease by employing PCR-RFLP, DGGE and sequence analysis of the 16S rDNA gene from metagenomes and plate-wash (cultured) bacteria of oral wash from 15 participants,. A stable core of bacterial DNA fingerprint was detected within and between subjects and did not change over time when analyzed in smokers and healthy non-smokers. Signature bands in smokers, non-smokers and periodontal disease subjects were evident suggesting the presence of potential indicators of health and poor oral health. Taxon diversity was higher in smokers including members of the genera Rothia, Synechococcus, Neisseria, Thiomargarita and Pyrobaculum but highest in periodontal disease. The two techniques successfully aligned the subjects within appropriate categories (based on their oral microbial genetic patterns)confirming their diagnostic suitability.
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Date Issued
2014
PURL
http://purl.flvc.org/fau/fd/FA00004184, http://purl.flvc.org/fau/fd/FA00004184
Subject Headings
Molecular microbiology., Mouth--Microbiology., Bacterial genetics., Cellular signal transduction., Microbial genomics.
Format
Document (PDF)
role for polynucleotide phosphorylase in protecting cells and controlling RNA quality under oxidative stress
Title
A role for polynucleotide phosphorylase in protecting cells and controlling RNA quality under oxidative stress.
Creator
Wu, Jinhua., Charles E. Schmidt College of Science, Department of Biological Sciences
Abstract/Description
RNA damage occurring under oxidative stress has been shown to cause RNA dysfunction and must be detrimental to cells and organisms. We propose that damaged RNA can be removed by specific RNA surveillance activities. In this work, we investigated the role of polynucleotide phosphorylase (PNPase), a 3'->5' exoribonuclease, in protecting the cells against oxidative stress and eliminating oxidatively-damaged RNA. Previously, it was reported that E. coli PNPase has a higher affinity to poly(8-oxoG...
Show moreRNA damage occurring under oxidative stress has been shown to cause RNA dysfunction and must be detrimental to cells and organisms. We propose that damaged RNA can be removed by specific RNA surveillance activities. In this work, we investigated the role of polynucleotide phosphorylase (PNPase), a 3'->5' exoribonuclease, in protecting the cells against oxidative stress and eliminating oxidatively-damaged RNA. Previously, it was reported that E. coli PNPase has a higher affinity to poly(8-oxoG:A). We further confirmed that E. coli PNPase can specifically bind to an oxidized RNA with a high affinity. An E. coli strain deficient in PNPase (pnp) is hypersensitive to hydrogen peroxide (H2O2). Importantly, the level of H2O2-induced RNA damage, measured by the content of 8-hydroxyguanosine, increases significantly in the pnp mutant cells. Consistent with the notion that PNPase plays a direct role in these processes, introduction of the pnp gene encoding E. coli PNPase can restore the viability and RNA oxidation level of the pnp mutant cells in response to H2O2 treatment. Interestingly, degradosome-association is not required for PNPase to protect cell against oxidative stress. PNPase is evolutionary conserved in most of organisms of all domains of life. The human polynucleotide phosphorylase (hPNPase) localizes mainly in mitochondria and plays pleiotropic roles in cell differentiation and has been previously shown to bind 8- oxoG-RNA with a high affinity. Here we show that similar to E. coli PNPase, hPNPase plays an indispensable role in protecting HeLa cells against oxidative stress. The viability in HeLa cell and 8-oxoG levels in RNA are inversely correlated in response to H2O2- treatment. After removal of oxidative challenge, the elevated level of 8-oxoG in RNA decreases, suggesting the existence of surveillance mechanism(s) for cleaning up oxidized RNA., We have shown that hPNPase may be responsible for the surveillance of oxidized RNA in mammalian cells.Overexpresion of hPNPase reduces RNA oxidation and increases HeLa cell viability against H2O2 insult. Conversely, hPNPase knockdown decreases the viability and increases 8-oxoG level in HeLa cells exposed to H2O2. Taken together, our results suggest that RNA oxidation is a challenging problem for living organisms, and PNPase may play an important role in protecting both prokaryotic and eukaryotic cells by limiting damage to RNA under oxidative stress.
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Date Issued
2008
PURL
http://purl.flvc.org/FAU/186302
Subject Headings
RNA, Metabolism, Biopolymers, Physiological transport, Bacterial genetics, Proteins, Synthesis, Cellular signal transduction
Format
Document (PDF)
Study on the Role oftmRNA in Protecting Escherichia coli Cell Under Oxidative stress.
Title
Study on the Role oftmRNA in Protecting Escherichia coli Cell Under Oxidative stress.
Creator
Kollipara, Gayatri, Li, Zhongwei, Florida Atlantic University, Charles E. Schmidt College of Medicine, Department of Biomedical Science
Abstract/Description
tmRNA is a small stable RNA present in Eubacteria. Through a mechanism called trans-translation, tmRNA mediates ribosome rescue and quality control of proteins and mRNA. In this study, the Escherichia coli (E. coli) mutant lacking tmRNA was demonstrated hypersensitive to oxidative stress. The role of tmRNA-mediated surveillance mechanism in protecting E. coli cell under oxidative stress condition was examined. The tmRNA-mediated tagged protein levels were elevated in cells under oxidative...
Show moretmRNA is a small stable RNA present in Eubacteria. Through a mechanism called trans-translation, tmRNA mediates ribosome rescue and quality control of proteins and mRNA. In this study, the Escherichia coli (E. coli) mutant lacking tmRNA was demonstrated hypersensitive to oxidative stress. The role of tmRNA-mediated surveillance mechanism in protecting E. coli cell under oxidative stress condition was examined. The tmRNA-mediated tagged protein levels were elevated in cells under oxidative stress condition, demonstrating the enhanced need for tmRNA under such condition. Our results suggest that mRNA damage by oxidative stress may cause reduced cell viability, and that tmRNA is required to rescue cells under such condition. Furthermore, our observations showed that tmRNA is required for the optimal growth of E. coli under normal aeration but not under anaerobic condition, suggesting that oxidation ofmRNA is the major reason for requirement oftmRNA during normal aeration.
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Date Issued
2007
PURL
http://purl.flvc.org/fau/fd/FA00000782
Subject Headings
Proteins--Synthesis, Bacterial genetics, Escherichia coli infections, Cells--Evolution
Format
Document (PDF)
The role of bacterial lipopolysaccharide in the production of the lupus B cell phenotype
Title
The role of bacterial lipopolysaccharide in the production of the lupus B cell phenotype.
Creator
Nikolic, Veljko., Florida Atlantic University, Hartmann, James X.
Abstract/Description
The purpose of this study was to determine the effect of bacterial lipopolysaccharide (LPS) on the expression of RP105 (CD180) in human B lymphocytes from normal, leukemic, and lupus patients. The percentage of cells that express RP105 on their surface increased following a 24 hour exposure to LPS. However, continued exposure for a total of four days resulted in a marked decrease in the expression of this receptor molecule. Human B cells were purified by a combination of density gradient and...
Show moreThe purpose of this study was to determine the effect of bacterial lipopolysaccharide (LPS) on the expression of RP105 (CD180) in human B lymphocytes from normal, leukemic, and lupus patients. The percentage of cells that express RP105 on their surface increased following a 24 hour exposure to LPS. However, continued exposure for a total of four days resulted in a marked decrease in the expression of this receptor molecule. Human B cells were purified by a combination of density gradient and negative magnetic bead selection and maintained in culture with and without LPS. Enzyme linked immunoassay for the detection of anti-dsDNA antibodies following LPS treatment of isolated B cells was negative. The percentage of RP105 positive or negative B cells from lupus patients could not be accurately determined because too few B cells were available from these lymphopenic patients following negative selection.
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Date Issued
2004
PURL
http://purl.flvc.org/fcla/dt/13177
Subject Headings
Microbial polysaccharides, Bacterial genetics, Systemic lupus erythematosus--Etiology, Systemic lupus erythematosus--Molecular aspects
Format
Document (PDF)