Exploring the oral bacterial flora: current status and future directions

Oral Diseases (2010) 16 , 136–145 Objective: The oral cavity forms an indispensable part of the human microbiome, for its unique and diverse microflora distributed within various niches. While majority of these organisms exhibit commensalism, shifts in bacterial community dynamics cause pathological changes within oral cavity and distant sites. The aim of this review was to appraise the current and emerging methods of detecting bacteria of the oral cavity paying particular attention to the cultivation independent methods. Design: Literature pertaining to cultivation based and cultivation independent methods of oral bacterial identification was reviewed. Methods: The specific advantages and disadvantages of cultivation based, microscopic, immunological and metagenomic identification methods were appraised. Results: Because of their fastidious and exacting growth requirements, cultivation based studies grossly underestimate the extent of bacterial diversity in these polymicrobial infections. Culture independent methods deemed more sensitive in identifying difficult to culture and novel bacterial species. Conclusion: Apart from characterizing potentially novel bacterial species, the nucleic acid sequence data analyzed using various bioinformatics protocols have revealed that there are in excess of 700 bacterial species inhabiting the mouth. Moreover, the latest pyrosequencing based methods have further broadened the extent of bacterial diversity in oral niches.     

The two single nucleotide polymorphisms in the H37/RBM5 tumour suppressor gene at 3p21.3 correlated with different subtypes of non-small cell lung cancers

Allele loss and genetic alteration in chromosome 3p, particularly in 3p21.3 region, are the most frequent and the earliest genomic abnormalities found in lung cancer. Multiple 3p21.3 genes exhibit various degrees of tumour suppression activity suggesting that 3p21.3 genes may function as an integrated tumour suppressor region through their diverse biological activities. We have previously demonstrated growth inhibitory effects and tumour suppression mechanism of the H37/RBM5 gene which is one of the 19 genes residing in the 370kb minimal overlap region at 3p21.3. In the current study, in an attempt to find, if any, mutations in the H37 coding region in lung cancer cells, we compared nucleotide sequences of the entire H37 gene in tumour versus adjacent normal tissues from 17 non-small cell lung cancer (NSCLC) patients. No mutations were detected; instead, we found the two silent single nucleotide polymorphisms (SNPs), C1138T and C2185T, within the coding region of the H37 gene. In addition, we found that specific allele types at these SNP positions are correlated with different histological subtypes of NSCLC; tumours containing heterozygous alleles (C+T) at these SNP positions are more likely to be associated with adenocarcinoma (AC), whereas, homozygous alleles (either C or T) are associated with squamous cell carcinoma (SCC) (p=0.0098). We postulate that, these two silent polymorphisms may be in linkage disequilibrium (LD) with a disease causative allele in the 3p21.3 tumour suppressor region which is packed with a large number of important genes affecting lung cancer development. In addition, because of prevalent loss of heterozygosity (LOH) detected at 3p21.3 which precedes lung cancer initiation, these SNPs may be developed into a marker screening for the high risk individuals.     

Expression of p21 ras oncoproteins in human cancers

The expression of proteins encoded by ras oncogenes was examined in 52 fresh human tumors of 19 different types using antibodies generated to different peptide domains of ras proteins of molecular weight 21,000 (p21). Proteins related to ras genes were detected in 90% of tested tumors. In 21% of tumors there were high levels of ras p21 of greater than 40% of the level in a Harvey murine sarcoma virus transformed cell line. Predominance of either cellular Ha-ras or other ras p21s was found in 20 and 14% of tumors, respectively, and predominance of p21 other than Ha-ras was frequent in breast cancers. Abnormal electrophoretic mobility of p21 was observed in two cancers, and a novel rapidly migrating ras p21 was found in a rare malignant fibrohistiocytoma.     

Evaluation of HER-2/neu gene amplification and overexpression: comparison of frequently used assay methods in a molecularly characterized cohort of breast cancer specimens.

PURPOSE: To compare and evaluate HER-2/neu clinical assay methods. MATERIALS AND METHODS: One hundred seventeen breast cancer specimens with known HER-2/neu amplification and overexpression status were assayed with four different immunohistochemical assays and two different fluorescence in situ hybridization (FISH) assays. RESULTS: The accuracy of the FISH assays for HER-2/neu gene amplification was high, 97.4% for the Vysis PathVision assay (Vysis, Inc, Downers Grove, IL) and 95.7% for the the Ventana INFORM assay (Ventana, Medical Systems, Inc, Tucson, AZ). The immunohistochemical assay with the highest accuracy for HER-2/neu overexpression was obtained with R60 polyclonal antibody (96.6%), followed by immunohistochemical assays performed with 10H8 monoclonal antibody (95.7%), the Ventana CB11 monoclonal antibody (89.7%), and the DAKO HercepTest (88.9%; Dako, Corp, Carpinteria, CA). Only the sensitivities, and therefore, overall accuracy, of the DAKO Herceptest and Ventana CB11 immunohistochemical assays were significantly different from the more sensitive FISH assay. CONCLUSION: Based on these findings, the FISH assays were highly accurate, with immunohistochemical assays performed with R60 and 10H8 nearly as accurate. The DAKO HercepTest and the Ventana CB11 immunohistochemical assay were statistically significantly different from the Vysis FISH assay in evaluating these previously molecularly characterized breast cancer specimens.     

Culture conditions affect the ability of ex vivo expanded peripheral blood progenitor cells to accelerate hematopoietic recovery

OBJECTIVE: The aim of this study was to evaluate the effect of various ex vivo expansion conditions on the cell products and their ability to accelerate hematopoietic recovery in patients undergoing stem cell transplantation. PATIENTS AND METHODS: Unselected peripheral blood progenitor cells (PBPCs) from 43 breast cancer patients were seeded into gas-permeable bags containing serum-free media, granulocyte colony-stimulating factor, stem cell factor, and pegylated megakaryocyte growth and development factor. Between 2 and 24 x 10(9) PBPCs were cultured at 1, 2, or 3 x 10(6) cells/mL for 9 to 14 days. The expanded PBPCs and cryopreserved PBPCs containing at least 5 x 10(6) CD34(+) cells/kg were infused following completion of high-dose chemotherapy. RESULTS: Increasing culture duration from 9 to 11-14 days significantly improved the expanded cell yield and fold expansion, whereas increasing PBPC seeding density above 10(6) cells/mL had the opposite effect. The expanded cell dose was the only culture variable that correlated significantly with the time to neutrophil recovery (r = -0.66; p = 0.0001). Study patients had significantly faster neutrophil (p < 0.0001) and platelet (p = 0.001) recovery, reduced red cell transfusions (p = 0.01), and shorter hospital stays (p < 0.0001) than historical controls. The most clinically efficacious expanded cell product was seeded with 10(10) PBPCs at 10(6) cells/mL, then cultured for 11 days. The six patients in that cohort experienced 2.8 +/- 1 days of absolute neutropenia and had neutrophil recovery 5.7 +/- 0.8 days post-transplant; none had a neutropenic fever or required intravenous antibiotics. CONCLUSION: Unselected PBPCs expanded ex vivo significantly impact hematopoietic recovery following high-dose therapy. Optimization of the expansion conditions enhances the efficacy of this cell product.     

Review article: Identifying occupational violence patient risk factors and risk assessment tools in the emergency department: A scoping review

Occupational violence (OV) is a daily risk for ED staff. It contributes to staff stress, sick leave, turn‐over and burn‐out, and limits the capacity of staff to provide unimpeded quality care to patients and their families. Many factors contribute to incidents of OV; however, early detection of such risk factors could pre‐empt incidences of OV during ED episodes of care. A five‐stage methodological framework for scoping reviews was used to identify, summarise and synthesise OV risk factors from five key databases. A validated tool was used to appraise the quality of included studies. Independent evaluation by the reviewers was used throughout. Patient factors were extracted and described from 24 methodologically and geographically diverse papers. Methodological quality for these studies varied from moderate to high. A total of 34 OV risk factors were identified. Although there was variation in, and differences between, staff‐perceived and objective (documented) OV risk factors, patient risk factors can be categorised into three main groups: clinical presentation, behaviours and past history. Five existing ED OV risk assessment tools were identified, with limited supporting evidence for each. The results support the development of a reliable and validated OV risk assessment tool to be initiated at triage.     

A polyclonal CD4+ and CD8+ lymphocytosis in a patient doubly infected with HTLV-I and HIV-1: a clinical and molecular analysis

HTLV-I is associated with adult T-cell leukemia/lymphoma (ATL) characterized by monoclonal expansions of CD4+ T-lymphocytes. In this report we describe a histologically benign, polyclonal HTLV-I infection in a patient exhibiting both an absolute CD4+ and CD8+ lymphocytosis. Three T-cell lines containing integrated HTLV-I proviral copies established from this patient were initially polyclonal, but with time all grew out the same two clones as determined by analysis of their T-cell antigen receptor beta chain gene rearrangements. The patient subsequently developed pulmonary and nasopharyngeal nodules containing HTLV-I infected cells. Restriction analysis of the patient's HTLV-I provirus revealed no differences from prototype HTLV-I and the tax gene was normally expressed in vivo and in vitro. The patient's T-lymphocytosis and HTLV-I+ pulmonary tract nodules were put into a complete clinical remission by treatment with alkylating agents and steroids. Subsequently, the patient developed a severe immunodeficiency state and expired. Retrospective serologic and gene amplification assays for HIV-1 demonstrated that he had been doubly infected from the time of presentation. Postmortem analysis by polymerase chain reaction revealed the presence of both HTLV-I and HIV-1 in lymphatic tissues and the testes; HIV-1 was also detected in brain tissue.     

Expression of protooncogene c-myb in normal human hematopoietic cells

Expression of the protooncogene, c-myb, in various subpopulations of normal human hematopoietic cells was characterized. Cells expressing the immature cell surface marker, CD34 (My10), were isolated by immune adherence with the "panning" technique or immunomagnetic microspheres and were shown to be strongly positive for c-myb protein expression in an immunoperoxidase assay. The CD34+ progenitor cell population was further separated into myeloid plus erythroid progenitors (CD34+, CD10-) v B-lymphoid precursors (coexpressing CD34 and CD10) by two-color FACS. Both CD34+ progenitor cell subsets strongly expressed c-myb protein by the immunoperoxidase assay. A flow cytometric assay was then developed which permitted simultaneous detection of a cell-surface antigen (to characterize lineage and stage of maturation) and the nuclear oncoprotein. This assay confirmed that CD34+ cells were strongly positive for c-myb expression and also allowed quantitative comparisons of c-myb expression in selected populations of other normal hematopoietic cells. Most human bone marrow cells appear to express some level of c-myb protein, although the CD34+ progenitor cell population expresses the highest amount.