@article {720,
	title = {Disassembly of simian virus 40 during passage through the endoplasmic reticulum and in the cytoplasm.},
	journal = {J Virol},
	volume = {86},
	year = {2012},
	month = {2012 Feb},
	pages = {1555-62},
	abstract = {The nonenveloped polyomavirus simian virus 40 (SV40) is taken up into cells by a caveola-mediated endocytic process that delivers the virus to the endoplasmic reticulum (ER). Within the ER lumen, the capsid undergoes partial disassembly, which exposes its internal capsid proteins VP2 and VP3 to immunostaining with antibodies. We demonstrate here that the SV40 genome does not become accessible to detection while the virus is in the ER. Instead, the genome becomes accessible two distinct detection procedures, one using anti-bromodeoxyuridine antibodies and the other using a 5-ethynyl-2-deoxyuridine-based chemical reaction, only after the emergence of partially disassembled SV40 particles in the cytoplasm. These cytoplasmic particles retain some of the SV40 capsid proteins, VP1, VP2, and VP3, in addition to the viral genome. Thus, SV40 particles undergo discrete disassembly steps during entry that are separated temporally and topologically. First, a partial disassembly of the particles occurs in the ER, which exposes internal capsid proteins VP2 and VP3. Then, in the cytoplasm, disassembly progresses further to also make the genomic DNA accessible to immune detection.},
	keywords = {Animals, Cell Line, Cercopithecus aethiops, Cytoplasm, Endoplasmic Reticulum, Genome, Viral, Microscopy, Fluorescence, Simian virus 40, Virus Assembly},
	issn = {1098-5514},
	doi = {10.1128/JVI.05753-11},
	author = {Kuksin, Dmitry and Norkin, Leonard C}
}
@article {806,
	title = {RecA4142 causes SOS constitutive expression by loading onto reversed replication forks in Escherichia coli K-12.},
	journal = {J Bacteriol},
	volume = {192},
	year = {2010},
	month = {2010 May},
	pages = {2575-82},
	abstract = {Escherichia coli initiates the SOS response when single-stranded DNA (ssDNA) produced by DNA damage is bound by RecA and forms a RecA-DNA filament. recA SOS constitutive [recA(Con)] mutants induce the SOS response in the absence of DNA damage. It has been proposed that recA(Con) mutants bind to ssDNA at replication forks, although the specific mechanism is unknown. Previously, it had been shown that recA4142(F217Y), a novel recA(Con) mutant, was dependent on RecBCD for its high SOS constitutive [SOS(Con)] expression. This was presumably because RecA4142 was loaded at a double-strand end (DSE) of DNA. Herein, it is shown that recA4142 SOS(Con) expression is additionally dependent on ruvAB (replication fork reversal [RFR] activity only) and recJ (5{\textquoteright}-->3{\textquoteright} exonuclease), xonA (3{\textquoteright}-->5{\textquoteright} exonuclease) and partially dependent on recQ (helicase). Lastly, sbcCD mutations (Mre11/Rad50 homolog) in recA4142 strains caused full SOS(Con) expression in an ruvAB-, recBCD-, recJ-, and xonA-independent manner. It is hypothesized that RuvAB catalyzes RFR, RecJ and XonA blunt the DSE (created by the RFR), and then RecBCD loads RecA4142 onto this end to produce SOS(Con) expression. In sbcCD mutants, RecA4142 can bind other DNA substrates by itself that are normally degraded by the SbcCD nuclease.},
	keywords = {Bacterial Proteins, Deoxyribonucleases, DNA Helicases, DNA Replication, Endodeoxyribonucleases, Escherichia coli K12, Escherichia coli Proteins, Exodeoxyribonuclease V, Exodeoxyribonucleases, Exonucleases, Microscopy, Fluorescence, Mutation, Rec A Recombinases, SOS Response (Genetics)},
	issn = {1098-5530},
	doi = {10.1128/JB.01623-09},
	author = {Long, Jarukit Edward and Massoni, Shawn C and Sandler, Steven J}
}
@article {853,
	title = {Occurrence of Chlamydia trachomatis and Chlamydia pneumoniae in paediatric respiratory infections.},
	journal = {Eur Respir J},
	volume = {33},
	year = {2009},
	month = {2009 Feb},
	pages = {360-7},
	abstract = {An emerging body of evidence suggests that half of asthma in both children and adults is associated with chronic lung infection. The aim of the present study was to determine the frequency of viable Chlamydia pneumoniae (Cp) and C. trachomatis (Ct) in the respiratory tracts of paediatric patients with chronic respiratory diseases. Bronchoalveolar lavage fluid (BALF) samples obtained from 182 children undergoing bronchoscopy for clinical reasons were assayed using PCR analysis, in vitro tissue culture and immunofluorescence staining for the presence of Cp and Ct. Chlamydia-specific DNA was detected by PCR in 124 (68\%) out of 182 patients; 79 were positive for Cp, 77 positive for Ct and 32 for both organisms; 75 patients had cultivable Chlamydia. Ct DNA prevalence decreased, whereas Cp positivity generally increased with age. A total of 59 out of 128 asthma patients and 16 out of 54 nonasthmatics were Chlamydia culture positive. When the patients were divided into inflammatory versus noninflammatory airway disease, there were 69 (46\%) out of 150 and six (18\%) out of 32 BALF samples with cultivable Chlamydia, respectively. Viable Chlamydia pneumoniae and Chlamydia trachomatis occur frequently in children with chronic respiratory diseases and may be more prevalent in asthma patients. To the current authors{\textquoteright} knowledge, this is the first report of viable Chlamydia trachomatis in the lungs of children.},
	keywords = {Adolescent, Bronchoalveolar Lavage Fluid, Bronchoscopy, Child, Child, Preschool, Chlamydia Infections, Chlamydia trachomatis, Chlamydophila pneumoniae, Cohort Studies, Female, Humans, Infant, Infant, Newborn, Male, Microscopy, Fluorescence, Prospective Studies, Respiratory Tract Infections},
	issn = {1399-3003},
	doi = {10.1183/09031936.00019508},
	author = {Webley, W C and Tilahun, Y and Lay, K and Patel, K and Stuart, E S and Andrzejewski, C and Salva, P S}
}
@article {393,
	title = {Two functions of the C-terminal domain of Escherichia coli Rob: mediating "sequestration-dispersal" as a novel off-on switch for regulating Rob{\textquoteright}s activity as a transcription activator and preventing degradation of Rob by Lon protease.},
	journal = {J Mol Biol},
	volume = {388},
	year = {2009},
	month = {2009 May 8},
	pages = {415-30},
	abstract = {In Escherichia coli, Rob activates transcription of the SoxRS/MarA/Rob regulon. Previous work revealed that Rob resides in three to four immunostainable foci, that dipyridyl and bile salts are inducers of its activity, and that inducers bind to Rob{\textquoteright}s C-terminal domain (CTD). We propose that sequestration inactivates Rob by blocking its access to the transcriptional machinery and that inducers activate Rob by mediating its dispersal, allowing interaction with RNA polymerase. To test "sequestration-dispersal" as a new mechanism for regulating the activity of transcriptional activators, we fused Rob{\textquoteright}s CTD to SoxS and used indirect immunofluorescence microscopy to determine the effect of inducers on SoxS-Rob{\textquoteright}s cellular localization. Unlike native SoxS, which is uniformly distributed throughout the cell, SoxS-Rob is sequestered without an inducer, but is rapidly dispersed when cells are treated with an inducer. In this manner, Rob{\textquoteright}s CTD serves as an anti-sigma factor in regulating the co-sigma-factor-like activity of SoxS when fused to it. Rob{\textquoteright}s CTD also protects its N-terminus from Lon protease, since Lon{\textquoteright}s normally rapid degradation of SoxS is blocked in the chimera. Accordingly, Rob{\textquoteright}s CTD has novel regulatory properties that can be bestowed on another E. coli protein.},
	keywords = {Decanoic Acids, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Reporter, Microscopy, Fluorescence, Models, Biological, Protease La, Protein Structure, Tertiary, Pyridines, Recombinant Fusion Proteins, Trans-Activators, Transcription, Genetic},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2009.03.023},
	author = {Griffith, Kevin L and Fitzpatrick, M Megan and Keen, Edward F and Wolf, Richard E}
}
@article {492,
	title = {Fluorescent properties of c-type cytochromes reveal their potential role as an extracytoplasmic electron sink in Geobacter sulfurreducens.},
	journal = {Environ Microbiol},
	volume = {10},
	year = {2008},
	month = {2008 Feb},
	pages = {497-505},
	abstract = {A novel fluorescence technique for monitoring the redox status of c-type cytochromes in Geobacter sulfurreducens was developed in order to evaluate the capacity of these extracytoplasmic cytochromes to store electrons during periods in which an external electron acceptor is not available. When intact cells in which the cytochromes were in a reduced state were excited at a wavelength of 350 nm, they fluoresced with maxima at 402 and 437 nm. Oxidation of the cytochromes resulted in a loss of fluorescence. This method was much more sensitive than the traditional approach of detecting c-type cytochromes via visible light absorbance. Furthermore, fluorescence of reduced cytochromes in individual cells could be detected via fluorescence microscopy, and the cytochromes in a G. sulfurreducens biofilm, remotely excited with an optical fibre, could be detected at distances as far as 5 cm. Fluorescence analysis of cytochrome oxidation and reduction of the external electron acceptor, anthraquinone-2,6-disulfonate, suggested that the extracytoplasmic cytochromes of G. sulfurreducens could store approximately 10(7) electrons per cell. Independent analysis of the haem content of the cells determined from analysis of incorporation of (55)Fe into cytochromes provided a similar estimate of cytochrome electron-storage capacity. This electron-storage capacity could, in the absence of an external electron acceptor, permit continued electron transfer across the inner membrane sufficient to supply the maintenance energy requirements for G. sulfurreducens for up to 8 min or enough proton motive force to power flagella motors for G. sulfurreducens motility. The fluorescence approach described here provides a sensitive method for evaluating the redox status of Geobacter species in culture and/or its environments. Furthermore, these results suggest that the periplasmic and outer-membrane cytochromes of Geobacter species act as capacitors, allowing continued electron transport, and thus viability and motility, for Geobacter species as they move between heterogeneously dispersed Fe(III) oxides during growth in the subsurface.},
	keywords = {Anthraquinones, Cytochromes c, Electron Transport, Ferric Compounds, Flagella, Fluorescence, Geobacter, Microscopy, Fluorescence, Oxidation-Reduction},
	issn = {1462-2920},
	doi = {10.1111/j.1462-2920.2007.01470.x},
	author = {Esteve-N{\'u}{\~n}ez, Abraham and Sosnik, Julian and Visconti, Pablo and Lovley, Derek R}
}
@article {855,
	title = {Detection of Chlamydia in the peripheral blood cells of normal donors using in vitro culture, immunofluorescence microscopy and flow cytometry techniques.},
	journal = {BMC Infect Dis},
	volume = {6},
	year = {2006},
	month = {2006},
	pages = {23},
	abstract = {BACKGROUND: Chlamydia trachomatis (Ct) and Chlamydia pneumoniae (Cp) are medically significant infectious agents associated with various chronic human pathologies. Nevertheless, specific roles in disease progression or initiation are incompletely defined. Both pathogens infect established cell lines in vitro and polymerase chain reaction (PCR) has detected Chlamydia DNA in various clinical specimens as well as in normal donor peripheral blood monocytes (PBMC). However, Chlamydia infection of other blood cell types, quantification of Chlamydia infected cells in peripheral blood and transmission of this infection in vitro have not been examined.

METHODS: Cp specific titers were assessed for sera from 459 normal human donor blood (NBD) samples. Isolated white blood cells (WBC) were assayed by in vitro culture to evaluate infection transmission of blood cell borne chlamydiae. Smears of fresh blood samples (FB) were dual immunostained for microscopic identification of Chlamydia-infected cell types and aliquots also assessed using Flow Cytometry (FC).

RESULTS: ELISA demonstrated that 219 (47.7\%) of the NBD samples exhibit elevated anti-Cp antibody titers. Imunofluorescence microscopy of smears demonstrated 113 (24.6\%) of samples contained intracellular Chlamydia and monoclonals to specific CD markers showed that in vivo infection of neutrophil and eosinophil/basophil cells as well as monocytes occurs. In vitro culture established WBCs of 114 (24.8\%) of the NBD samples harbored infectious chlamydiae, clinically a potentially source of transmission, FC demonstrated both Chlamydia infected and uninfected cells can be readily identified and quantified.

CONCLUSION: NBD can harbor infected neutrophils, eosinophil/basophils and monocytes. The chlamydiae are infectious in vitro, and both total, and cell type specific Chlamydia carriage is quantifiable by FC.},
	keywords = {Adult, Blood Donors, Chlamydophila pneumoniae, Female, Flow Cytometry, Humans, Leukocytes, Male, Microscopy, Fluorescence},
	issn = {1471-2334},
	doi = {10.1186/1471-2334-6-23},
	author = {Cirino, Frances and Webley, Wilmore C and West, Corrie and Croteau, Nancy L and Andrzejewski, Chester and Stuart, Elizabeth S}
}
@article {823,
	title = {Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy.},
	journal = {Mol Microbiol},
	volume = {53},
	year = {2004},
	month = {2004 Sep},
	pages = {1343-57},
	abstract = {Many recombination, DNA repair and DNA replication mutants have high basal levels of SOS expression as determined by a sulAp-lacZ reporter gene system on a population of cells. Two opposing models to explain how the SOS expression is distributed in these cells are: (i) the {\textquoteright}Uniform Expression Model (UEM){\textquoteright} where expression is evenly distributed in all cells or (ii) the {\textquoteright}Two Population Model (TPM){\textquoteright} where some cells are highly induced while others are not at all. To distinguish between these two models, a method to quantify SOS expression in individual bacterial cells was developed by fusing an SOS promoter (sulAp) to the green fluorescent protein (gfp) reporter gene and inserting it at attlambda on the Escherichia coli chromosome. It is shown that the fluorescence in sulAp-gfp cells is regulated by RecA and LexA. This system was then used to distinguish between the two models for several mutants. The patterns displayed by priA, dnaT, recG, uvrD, dam, ftsK, rnhA, polA and xerC mutants were explained best by the TPM while only lexA (def), lexA3 (ind-) and recA defective mutants were explained best by the UEM. These results are discussed in a context of how the processes of DNA replication and recombination may affect cells in a population differentially.},
	keywords = {Adenosine Triphosphatases, DNA Damage, DNA Helicases, DNA Repair, Escherichia coli K12, Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Reporter, Microscopy, Fluorescence, Models, Genetic, Promoter Regions, Genetic, Recombinant Fusion Proteins, SOS Response (Genetics), Ultraviolet Rays},
	issn = {0950-382X},
	doi = {10.1111/j.1365-2958.2004.04225.x},
	author = {McCool, Jesse D and Long, Edward and Petrosino, Joseph F and Sandler, Hilary A and Rosenberg, Susan M and Sandler, Steven J}
}
