Cytoplasmic Bacteria and the Autophagic Pathway

Cytoplasmic bacteria may assist in our study of the autophagic pathway. This review highlights the use of Listeria monocytogenes for examining the assembly of autophagic vacuoles in mammalian cells. Inhibiting protein synthesis of cytoplasmic L. monocytogenes results in their being sequestered into the autophagic pathway. Autophagic vacuoles form around the easily identified bacterial particles making the assembly process easy to study using morphological and biochemical methods. L. monocytogenes, which appears to be ideally adapted to life in the cell cytoplasm, does not normally become a target of autophagy. In model systems the bacteria thrive within host cell cytoplasm, indicating the importance of de novo protein synthesis in avoiding the autophagic pathway. This observation indicates an interesting opportunity for identifying the bacterial mechanisms that are mobilized to avoid the autophagic pathway.

Biofilm-specific extracellular matrix proteins of nontypeable Haemophilus influenzae

Nontypeable Haemophilus influenzae (NTHi), a human respiratory tract pathogen, can form colony biofilms in vitro. Bacterial cells and the amorphous extracellular matrix (ECM) constituting the biofilm can be separated using sonication. The ECM from 24- and 96-h NTHi biofilms contained polysaccharides and proteinaceous components as detected by nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) spectroscopy. More conventional chemical assays on the biofilm ECM confirmed the presence of these components and also DNA. Proteomics revealed eighteen proteins present in biofilm ECM that were not detected in planktonic bacteria. One ECM protein was unique to 24-h biofilms, two were found only in 96-h biofilms, and fifteen were present in the ECM of both 24- and 96-h NTHi biofilms. All proteins identified were either associated with bacterial membranes or cytoplasmic proteins. Immunocytochemistry showed two of the identified proteins, a DNA-directed RNA polymerase and the outer membrane protein OMP P2, associated with bacteria and biofilm ECM. Identification of biofilm-specific proteins present in immature biofilms is an important step in understanding the in vitro process of NTHi biofilm formation. The presence of a cytoplasmic protein and a membrane protein in the biofilm ECM of immature NTHi biofilms suggests that bacterial cell lysis may be a feature of early biofilm formation.

Beta- lactam antibiotics stimulate biofilm formation in non-typeable haemophilus influenzae by up-regulating carbohydrate metabolism

Non-typeable Haemophilus influenzae (NTHi) is a common acute otitis media pathogen, with an incidence that is increased by previous antibiotic treatment. NTHi is also an emerging causative agent of other chronic infections in humans, some linked to morbidity, and all of which impose substantial treatment costs. In this study we explore the possibility that antibiotic exposure may stimulate biofilm formation by NTHi bacteria. We discovered that sub-inhibitory concentrations of beta-lactam antibiotic (i.e., amounts that partially inhibit bacterial growth) stimulated the biofilm-forming ability of NTHi strains, an effect that was strain and antibiotic dependent. When exposed to sub-inhibitory concentrations of beta-lactam antibiotics NTHi strains produced tightly packed biofilms with decreased numbers of culturable bacteria but increased biomass. The ratio of protein per unit weight of biofilm decreased as a result of antibiotic exposure. Antibiotic-stimulated biofilms had altered ultrastructure, and genes involved in glycogen production and transporter function were up regulated in response to antibiotic exposure. Down-regulated genes were linked to multiple metabolic processes but not those involved in stress response. Antibiotic-stimulated biofilm bacteria were more resistant to a lethal dose (10 µg/mL) of cefuroxime. Our results suggest that beta-lactam antibiotic exposure may act as a signaling molecule that promotes transformation into the biofilm phenotype. Loss of viable bacteria, increase in biofilm biomass and decreased protein production coupled with a concomitant up-regulation of genes involved with glycogen production might result in a biofilm of sessile, metabolically inactive bacteria sustained by stored glycogen. These biofilms may protect surviving bacteria from subsequent antibiotic challenges, and act as a reservoir of viable bacteria once antibiotic exposure has ended.

Tacrolimus is an effective treatment for lupus nephritis in pregnancy

Lupus nephritis during pregnancy increases morbidity and mortality for mother and baby. Flares are difficult to treat as many therapeutic options are teratogenic or fetotoxic. Steroids alone may be unable to control disease activity and are associated with higher rates of preterm delivery, sepsis and gestational diabetes. Reports of using tacrolimus to treat lupus nephritis in pregnancy are limited. We describe the pregnancies of nine women in whom tacrolimus was successfully used to treat lupus nephritis flare (six patients) or maintain stable disease (three patients). Introduction or dose escalation of oral steroids was avoided in five of the patients who developed active disease and steroid dose was rapidly reduced in the sixth patient. All women with disease flare attained partial or complete remission after starting tacrolimus. None of the women on maintenance treatment developed active disease. We propose tacrolimus as an effective adjuvant or alternative therapy to steroids for treating lupus nephritis flare or maintaining stable disease during pregnancy.

Bacterial biofilms and increased bacterial counts are associated with airway stenosis

OBJECTIVES

Most airway stenoses are acquired secondary to the use of prolonged endotracheal intubation. Antibiotics have been shown to decrease local inflammation and granulation tissue formation in the trachea. However, antibiotic therapy is not 100% effective in preventing or treating granulation tissue formation. Development of bacterial biofilms may explain this finding. This study evaluates the difference between tracheal stenotic segments and normal trachea in terms of (1) presence of bacterial biofilms, (2) quantitative bacterial counts, and (3) inflammatory markers.

STUDY DESIGN

Cross-sectional study.

SETTING

Tertiary care academic medical center.

SUBJECTS

A total of 12 patients were included in the study. Tissue from stenotic segments from 6 patients with airway stenosis undergoing open airway procedures were compared with tracheal tissue from 6 patients without airway stenosis undergoing tracheostomy.

METHODS

Scanning electron microscopy for biofilm detection, quantitative polymerase chain reaction for quantitative analysis of bacterial count, and immunohistochemistry were performed for inflammatory markers transforming growth factor β1 (TGF-β1) and SMAD3.

RESULTS

Compared with the patients without airway stenosis, patients in the airway stenosis group showed presence of bacterial biofilms, a significantly higher expression of 16S rRNA gene copies per microgram of tissue (187.5 vs 7.33, P = .01), and higher expression of TGF-β1 (91% vs 8%, P < .001) and SMAD3 (83.5% vs 17.8%, P < .001).

CONCLUSION

Bacterial biofilms, increased bacterial counts, and higher expression of TGF-β1 and SMAD3 are associated with airway stenosis.

Experimental approaches to investigating the vaginal biofilm microbiome

Unraveling the complex ecology of the vaginal biofilm microbiome relies on a number of complementary techniques. Here, we describe the experimental approaches for studying vaginal microbial biofilm samples with a focus on specimen preparation for subsequent analysis. The techniques include fluorescence microscopy, fluorescence in situ hybridization, and scanning and transmission electron microscopy. Isolation of microbial DNA and RNA from these samples is covered along with a brief discussion of chemical analysis methods.

Cryosectioning fixed and cryoprotected biological material for immunocytochemistry

Immunocytochemistry for electron microscopy provides important information on the location and relative abundance of proteins inside cells. Gaining access to this information without extracting or disrupting the location of target proteins requires specialized preparation methods. Sectioning frozen blocks of chemically fixed and cryoprotected biological material is one method for obtaining immunocytochemical data. Once the cells or tissues are cut, the cryosections are thawed, mounted onto coated grids, and labeled with specific antibodies and colloidal gold probes. They are then embedded in a thin film of plastic containing a contrasting agent. Subcellular morphology can then be correlated with specific affinity labeling by examination in the transmission electron microscope (TEM). The major advantage of using thawed cryosections for immunolabeling is that the sections remain fully hydrated through the immunolabeling steps, reducing the possibility of dehydration-induced antigen modification. Modern technical advancements both in preparation protocols and equipment design make cryosectioning a routine and rapid approach for immunocytochemistry that may provide increased sensitivity for some antibodies.

Microwave-assisted processing and embedding for transmission electron microscopy

Microwave processors can provide a means of rapid processing and resin embedding for biological specimens that are to be sectioned and examined by transmission electron microscopy. This chapter describes a microwave-assisted protocol for processing, dehydrating and embedding biological material, taking them from living specimens to blocks embedded in sectionable resin in 4 h or less.

The periductal channels of the endolymphatic duct, hydrodynamic implications

OBJECTIVE

To describe the anatomy of a small network of channels surrounding the human endolymphatic duct.

STUDY DESIGN

Archival temporal bone sections and a surgical specimen were studied using a variety of techniques.

SETTING

Temporal bone laboratory of the House Research Institute.

SUBJECTS AND METHODS

Archival temporal bone sections were examined by light microscopy, 3D reconstruction, and immunohistochemical labeling. A surgical specimen was examined using electron microscopy. Sections from temporal bones with blocked endolymphatic ducts or amputated sacs were examined for the manifestations of endolymphatic hydrops.

RESULTS

Peri-endolymphatic duct channels were found to extend from the proximal cisternal part of the endolymphatic sac to the supporting tissue of the saccule and utricle. Tissue in the channels, as seen by conventional and electron microscopy, is continuous with and identical with the tissue surrounding the endolymphatic duct. Tissue in the channels labels with the S100 antibody similar to the spiral ligament and supporting tissue of the vestibular end organs and suggests a neural crest origin, as did the presence of melanocytes. Obstruction of the endolymphatic duct resulted in endolymphatic hydrops whereas amputation of the sac did not.

CONCLUSION

Endolymph is probably absorbed in the endolymphatic duct. The peri-endolymphatic duct channels that extend from the proximal sac to the supporting tissue of the saccule label with the S100 antibody and contain melanocytes suggest a neural crest origin and involvement in fluid and potassium hydrodynamics similar to those described for the similarly staining spiral ligament of the cochlea.

Bacterial Biofilms and Increased Bacterial Counts Are Associated with Airway Stenosis

Objectives:

The majority of airway stenoses are acquired secondary to the use of prolonged endotracheal intubation (ETT). Pressure exerted on the tracheal mucosa by the presence of ETT leads to irritation, ulceration, and granulation tissue formation and eventual fibrosis. An excess of granulation tissue promotes excess wound contracture. Antibiotics have been shown to decrease local inflammation and granulation tissue formation in the trachea. However, antibiotic therapy is not 100% effective in preventing or treating granulation tissue formation. Development of bacterial biofilms may explain this finding. This study was done to evaluate the difference between stenotic segment and normal trachea in terms of 1) presence of bacterial biofilms; 2) quantitative analysis of bacterial count; 3) inflammatory markers within tracheal tissue.

Methods:

Institutional review board approved case-control study, where cases were patients with airway stenosis and controls were patients without airway stenosis. We performed scanning electron microscopy (SEM) for biofilm, quantitative polymerase chain reaction (qPCR) for quantitative analysis of bacterial count, and immunohistochemistry (IHC) for inflammatory markers.

Results:

SEM showed presence of biofilm in cases compared to controls. The number of 16S rRNA gene copies using qPCR, a surrogate for the number of bacterial cells, was significantly higher in cases (mean=198) compared to controls (mean=30 ) ( P < 0.05). Pediatric cases showed a significantly higher bacterial count than adult cases. IHC showed stronger staining for SMAD3 and transforming growth factor β (TGF-β).

Conclusions:

Biofilms are present in airway stenotic segments, and there exists a difference in tracheal microbiomes and inflammatory markers between patients with airway stenosis and normal controls.

Development of a new model system to study microbial colonization on dentures

PURPOSE

Dentures are often colonized with a variety of microorganisms, including Candida albicans, that contribute to denture stomatitis. Several in vitro models have been previously established to study denture-related microbial colonization and evaluate treatment efficacy of denture cleansers; however, those models typically fail to appreciate the complex topology and heterogeneity of denture surfaces and lack effective ways to accurately measure microbial colonization. The purpose of this study was to study microbial colonization with a new model system based on real dentures, to more realistically mimic in vivo conditions.

MATERIALS AND METHODS

Scanning electron microscopy was used to observe topological structures among surfaces from different parts of the denture. Employing C. albicans as a model microorganism, we established microbial colonization on different denture surfaces. Moreover, we applied a modified MTT (3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide) colorimetric assay to quantify C. albicans colonization on dentures without the necessity of biofilm removal and to evaluate treatment efficacy of denture cleansers.

RESULTS

There were significant variations in topological structures among surfaces from different parts of the denture, with the unpolished side having the highest amounts of indentations and pores. The distinct denture surfaces support microbial colonization differently, with the unpolished side containing the highest level of microbial colonization and biofilm formation. Furthermore, the modified MTT colorimetric assay proved to be an accurate assay to measure biofilm formation on dentures and evaluate treatment efficacy of denture cleansers.

CONCLUSION

This new denture model system in conjunction with the MTT colorimetric assay is a valuable tool to study denture-related microbiology and treatment approaches.

Quantification by energy dispersive x-ray spectroscopy of alendronate in the diseased jaw bone of patients with bisphosphonate-related jaw osteonecrosis

OBJECTIVE

Recently, specific in vitro bisphosphonate concentrations have been established for reaching a toxic threshold that could result in the induction of bisphosphonate-related osteonecrosis of the jaw (BRONJ), but these data have not been validated in vivo. The purpose of this study was to quantify the concentration of bisphosphonates (BPs) in the diseased jaw bone of patients experiencing BRONJ.

STUDY DESIGN

We hypothesized that if the average natural nitrogen content of mammalian bone is known, the excess of nitrogen in the jaw bone of BRONJ patients is likely to reflect the concentration of amino-BP. To test our hypothesis, jaw bone specimens from patients with BRONJ were acquired after sequestrectomy and analyzed by energy-dispersive X-ray spectroscopy (EDS).

RESULTS

The EDS analysis of the bone demonstrated a highly linear correlation between increasing concentrations of BP and the increasing percentage of nitrogen measured at the bone surfaces (R(2) = .9851, P = .0149).

CONCLUSIONS

SEM/EDS can be a valuable tool for assessing BP concentration in jaw bone and provides important insight into BP pharmacokinetics and BRONJ.

Phenotypic characterization of the foldase homologue PrsA in Streptococcus mutans

Streptococcus mutans is generally considered to be the principal etiological agent for dental caries. Many of the proteins necessary for its colonization of the oral cavity and pathogenesis are exported to the cell surface or the extracellular matrix, a process that requires the assistance of the export machineries. Bioinformatic analysis revealed that the S. mutans genome contains a prsA gene, whose counterparts in other gram-positive bacteria, including Bacillus and Lactococcus, encode functions involved in protein post-export. In this study, we constructed a PrsA-deficient derivative of S. mutans and demonstrated that the prsA mutant displayed an altered cell wall/membrane protein profile as well as cell-surface-related phenotypes, including auto-aggregation, increased surface hydrophobicity and abnormal biofilm formation. Further analysis revealed that the disruption of the prsA gene resulted in reduced insoluble glucan production by cell surface localized glucosyltransferases, and mutacin as well as cell surface-display of a heterologous expressed GFP fusion to the cell surface protein SpaP. Our study suggested that PrsA in S. mutans encodes functions similar to those identified in Bacillus, and so is likely to be involved in protein post-export.

Evaluation of a nonthermal plasma needle to eliminate ex vivo biofilms in root canals of extracted human teeth

AIM

To evaluate the efficacy of a nonthermal plasma (NTP) at atmospheric pressure on ex vivo biofilm in root canals of extracted teeth.

METHODOLOGY

Intracanal contents from three teeth with root canal infections were collected, pooled and grown in thirty-five microCT-mapped root canals of extracted and instrumented human teeth. One group of teeth was treated with NTP, another with 6% NaOCl and one set was left untreated. The intracanal contents from twenty-seven teeth (nine teeth in each group) were plated on agar and colony forming units were determined. Parametric test of one-way analysis of variance (anova) was used to analyse statistical significance. The remaining teeth were cut open, stained with LIVE/DEAD(®) and examined with confocal laser scanning microscopy.

RESULTS

The untreated root canals were covered with biofilm of varying thickness. Treatment with nonthermal plasma decreased the number of viable bacteria in biofilms by one order of magnitude, whilst the NaOCl control achieved a reduction of more than four magnitudes. Both the NTP and the NaOCl treatment results were significantly different from the negative control (P < 0.05).

CONCLUSION

The nonthermal plasma displayed antimicrobial activity against endodontic biofilms in root canals, but was not as effective as the use of 6% NaOCl.