Bacterial Pathogens Related to Chronic Suppurative Otitis Media in Individuals With Cleft Palate: Bacteriological Culture and Polymerase Chain Reaction

Objective: To characterize the microbial etiology of chronic suppurative otitis media comparing the methods of classical bacteriological culture and polymerase chain reaction.Design/Setting/Patients: Bacteriological analysis by classical culture and by molecular polymerase chain reaction of 35 effusion otitis samples from patients with cleft lip and palate attending the Hospital for Rehabilitation of Craniofacial Anomalies of the University of Sao Paulo, Bauru, Brazil.Interventions: Collection of clinical samples of otitis by effusion through the external auditory tube.Main Outcome Measure: Otolaryngologic diagnosis of chronic suppurative otitis media.Results: Positive cultures were obtained from 83% of patients. Among the 31 bacterial lineages the following were isolated. In order of decreasing frequency: Pseudomonas aeruginosa (54.9%), Staphylococcus aureus (25.9%), and Enterococcus faecalis (19.2%). No anaerobes were isolated by culture. The polymerase chain reaction was positive for one or more bacteria investigated in 97.1% of samples. Anaerobe lineages were detected by the polymerase chain reaction method, such as Fusobacterium nucleatum, Bacteroides fragilis, and Peptostreptococcus anaerobius.Conclusions: Patients with cleft lip and palate with chronic suppurative otitis media presented high frequency of bacterial infection in the middle ear. The classical bacteriological culture did not detect strict anaerobes, whose presence was identified by the polymerase chain reaction method.

Evaluation of hsp65 Nested PCR-Restriction Analysis (PRA) for Diagnosing Tuberculosis in a High Burden Country

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Obsessive-compulsive symptom dimensions in a population-based, cross-sectional sample of school-aged children

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Família Enterobacteriaceae, Acinetobacter baumannii e Pseudomonados na microbiota bucal de pacientes mantidos em unidades de terapia intensiva

Enteric organisms, pseudomonads and other opportunistic microorganisms in the oral microbiota have been linked to serious infections in patients hospitalized in intensive care units (ICU). The present study evaluated the presence of family Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii in the mouth of patients in ICU, correlating it with oral and systemic conditions. Data on health, socioeconomic status, medication use, drug addiction, medical and family histories of patients held for more than 72 hours in the ICU with a diagnosis of severe infection or that developed this condition after entry in said unit were obtained. Fifty patients provided clinical samples of supragingival and subgingival biofilms, saliva and oral mucous membranes were collected, as well as respiratory secretions from patients with pneumonia, blood and urine for sepsis. The presence of target microorganisms was carried out by polymerase chain reaction (PCR) and by culture using selective media. The Chi-square and Mann-Whitney tests were used for statistical analysis, and the significance level was 5%. The intraoral clinical conditions of the patients were poor. The family Enterobacteriaceae was the most prevalent, affecting 39.5% of the supragingival biofilm samples of patients attended in ICU and 18.6% of patients in the control group, besides the rods were the only group found in extraoral samples.

Enterococcus spp. em espécimes clínicos de pacientes atendidos em unidades de terapia intensiva

The relationship between the occurrence of enterococci in the oral microbiota and serious infections in patients hospitalized in intensive care units (ICU) has been established. This study evaluated the presence of Enterococcus faecalis and other species of this genus in the mouths of patients on ICU, correlating it with oral and systemic conditions. Data on health and socioeconomic, medication use, medical and family history of patients maintained for 72 hours in the ICU, diagnosed with severe infection or who have developed this condition after the entry to the unit were obtained. Fifty patients provided intraoral and extraoral clinical samples for analysis (above and subgingival biofilm, saliva and buccal mucosa, followed by obtaining samples of respiratory secretions for patients with pneumonia, and blood and urine for sepsis). The presence of target microorganisms was performed by polymerase chain reaction (PCR) and culture using selective media. The chi-square and Mann-Whitney tests were used for statistical analysis, and the significance level was 5%. The intraoral clinical conditions of the patients showed poor. E. faecalis was significantly more frequent microorganism, followed by E. faecium. The use of broadspectrum antimicrobial action was associated with the presence of these opportunistic microorganisms. These bacteria were more frequent in patients with periodontitis or gingivitis. The results showed that enterococci associated with serious infectious processes may originate from resident microbiota of patients and its prevalence is not elevated in healthy individuals.

Opportunistic microorganisms in patients with head and neck trauma

The use of antimicrobial agents has facilitated the dissemination of multi-resistant microorganisms, compromising dental and medical treatment. The aim of this study was to evaluate the distribution of different opportunistic microbial species in patients who suffered head and neck trauma, under temporary maintenance in nosocomial environment, particularly intensive care units, on the occurrence of such microorganisms in the oral cavity of the patients. It was selected 38 patients subjected to head and neck traumas. After emergency surgical procedures, clinical samples of saliva, sub and supragingival biofilms and mucosal surfaces were collected at two different moments: just after stabilization of the patient and soon after patients’ release from medical units. The presence of opportunistic and superinfecting microorganisms was evaluated by culture on selective and non-selective media, and the presence of the family Enterobacteriaceae, as well as genera Enterococcus, Pseudomonas, and Staphylococcus was assessed by PCR. It was found that the use of antimicrobials, even for short periods of time was sufficient to facilitate colonization by microorganisms of the families Enterobacteriaceae and Pseudomonadaceae, as well as yeasts and enterococci. These results support the concept that medical and dental teams should make a periodically change of antimicrobials used in treatment protocols in hospital for head and neck trauma patients, in order to minimize dissemination of opportunistic or superinfecting microorganisms.

Epidemiological aspects of tuberculosis in children and adolescents in Rio de Janeiro

Objective: To describe the epidemiological aspects of childhood tuberculosis (TB) in a Brazilian reference hospital. Methods: This was a retrospective study (1999-2008) of 473 subjects (0-14 year olds) with confirmed TB, or with clinical improvement by the fourth month of treatment under the unit's care, including the review of medical records, monitoring reports and notifications by the TB unit. Results: Among 473 TB cases included in the study, positive tuberculin skin test was observed in 52%, history of contact with a patient with pulmonary tuberculosis in 66%, mostly intra-household, and with the father/stepfather most commonly involved; and disseminated TB in 22%. The result of HIV testing was obtained in 265 (56%) cases, being positive in 45 (17%). The diagnosis of TB was confirmed in 31% of cases, most frequently in children older than 5 years, with negative tuberculin skin test, and in disseminated forms. Of the 65 cultures positive for TB performed in the study, drug sensitivity testing to anti-TB drugs was done in 30 (46%) clinical samples, among which 10 (33%) were resistant to one or more anti-TB drugs, and 2 (0.8%) were multi-drug-resistant. Among patients with confirmed pulmonary TB, 31% did not meet the criteria for starting anti-TB treatment according to the scores of the Ministry of Health (<= 25 points). Conclusion: The high proportion of drug-resistant TB and co-infection with HIV identified in this study highlight the necessity to carry out additional studies in order to evaluate the impact of TB control activities on childhood TB.

Use of the polymerase chain reaction to detect Mycobacterium leprae in urine

Leprosy is an infectious disease caused by Mycobacterium leprae. The polymerase chain reaction (PCR) has been applied to detect M. leprae in different clinical samples and urine seems to be attractive for this purpose. PCR was used to improve the sensitivity for diagnosing leprosy by amplifying a 151-bp PCR fragment of the M. leprae pra gene (PCR-Pra) in urine samples. Seventy-three leprosy patients (39 males and 34 females, 14 to 78 years old) were selected for leprosy diagnosis at a reference laboratory in Maringa, PR, Brazil. Of these, 36 were under anti-leprosy multidrug therapy with dapsone and rifampicin for tuberculoid (TT) and dapsone, rifampicin and clofazimine for borderline (BB) and lepromatous (LL) forms. The control group contained 50 healthy individuals without any clinical history of leprosy. DNA isolated from leprosy patients' urine samples was successfully amplified by PCR-Pra in 46.6% (34/73) of the cases. The positivity of PCR-Pra for patients with the TT form was 75% for both patients under treatment and non-treated patients (P = 0.1306). In patients with the LL form, PCR-Pra positivity was 52 and 30% for patients under treatment and non-treated patients, respectively (P = 0.2386). PCR-Pra showed a statistically significant difference in detecting M. leprae between the TT and LL forms of leprosy in patients under treatment (P = 0.0033). Although the current study showed that the proposed PCR-Pra has some limitations in the detection of M. leprae, this method has the potential to be a useful tool for leprosy diagnosis mainly in TT leprosy where the AFB slit-skin smear is always negative.

Resistance to EGF receptor inhibitors in glioblastoma mediated by phosphorylation of the PTEN tumor suppressor at tyrosine 240

Glioblastoma multiforme (GBM) is the most aggressive of the astrocytic malignancies and the most common intracranial tumor in adults. Although the epidermal growth factor receptor (EGFR) is overexpressed and/or mutated in at least 50% of GBM cases and is required for tumor maintenance in animal models, EGFR inhibitors have thus far failed to deliver significant responses in GBM patients. One inherent resistance mechanism in GBM is the coactivation of multiple receptor tyrosine kinases, which generates redundancy in activation of phosphoinositide-3'-kinase (PI3K) signaling. Here we demonstrate that the phosphatase and tensin homolog deleted on chromosome 10 (PTEN) tumor suppressor is frequently phosphorylated at a conserved tyrosine residue, Y240, in GBM clinical samples. Phosphorylation of Y240 is associated with shortened overall survival and resistance to EGFR inhibitor therapy in GBM patients and plays an active role in mediating resistance to EGFR inhibition in vitro. Y240 phosphorylation can be mediated by both fibroblast growth factor receptors and SRC family kinases (SFKs) but does not affect the ability of PTEN to antagonize PI3K signaling. These findings show that, in addition to genetic loss and mutation of PTEN, its modulation by tyrosine phosphorylation has important implications for the development and treatment of GBM.

Long noncoding intronic RNAs are differentially expressed in primary and metastatic pancreatic cancer

Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is known by its aggressiveness and lack of effective therapeutic options. Thus, improvement in current knowledge of molecular changes associated with pancreatic cancer is urgently needed to explore novel venues of diagnostics and treatment of this dismal disease. While there is mounting evidence that long noncoding RNAs (lncRNAs) transcribed from intronic and intergenic regions of the human genome may play different roles in the regulation of gene expression in normal and cancer cells, their expression pattern and biological relevance in pancreatic cancer is currently unknown. In the present work we investigated the relative abundance of a collection of lncRNAs in patients' pancreatic tissue samples aiming at identifying gene expression profiles correlated to pancreatic cancer and metastasis. Methods Custom 3,355-element spotted cDNA microarray interrogating protein-coding genes and putative lncRNA were used to obtain expression profiles from 38 clinical samples of tumor and non-tumor pancreatic tissues. Bioinformatics analyses were performed to characterize structure and conservation of lncRNAs expressed in pancreatic tissues, as well as to identify expression signatures correlated to tissue histology. Strand-specific reverse transcription followed by PCR and qRT-PCR were employed to determine strandedness of lncRNAs and to validate microarray results, respectively. Results We show that subsets of intronic/intergenic lncRNAs are expressed across tumor and non-tumor pancreatic tissue samples. Enrichment of promoter-associated chromatin marks and over-representation of conserved DNA elements and stable secondary structure predictions suggest that these transcripts are generated from independent transcriptional units and that at least a fraction is under evolutionary selection, and thus potentially functional. Statistically significant expression signatures comprising protein-coding mRNAs and lncRNAs that correlate to PDAC or to pancreatic cancer metastasis were identified. Interestingly, loci harboring intronic lncRNAs differentially expressed in PDAC metastases were enriched in genes associated to the MAPK pathway. Orientation-specific RT-PCR documented that intronic transcripts are expressed in sense, antisense or both orientations relative to protein-coding mRNAs. Differential expression of a subset of intronic lncRNAs (PPP3CB, MAP3K14 and DAPK1 loci) in metastatic samples was confirmed by Real-Time PCR. Conclusion Our findings reveal sets of intronic lncRNAs expressed in pancreatic tissues whose abundance is correlated to PDAC or metastasis, thus pointing to the potential relevance of this class of transcripts in biological processes related to malignant transformation and metastasis in pancreatic cancer.

High-throughput sequencing of small RNA transcriptomes reveals critical biological features targeted by microRNAs in cell models used for squamous cell cancer research

Abstract Background The implication of post-transcriptional regulation by microRNAs in molecular mechanisms underlying cancer disease is well documented. However, their interference at the cellular level is not fully explored. Functional in vitro studies are fundamental for the comprehension of their role; nevertheless results are highly dependable on the adopted cellular model. Next generation small RNA transcriptomic sequencing data of a tumor cell line and keratinocytes derived from primary culture was generated in order to characterize the microRNA content of these systems, thus helping in their understanding. Both constitute cell models for functional studies of microRNAs in head and neck squamous cell carcinoma (HNSCC), a smoking-related cancer. Known microRNAs were quantified and analyzed in the context of gene regulation. New microRNAs were investigated using similarity and structural search, ab initio classification, and prediction of the location of mature microRNAs within would-be precursor sequences. Results were compared with small RNA transcriptomic sequences from HNSCC samples in order to access the applicability of these cell models for cancer phenotype comprehension and for novel molecule discovery. Results Ten miRNAs represented over 70% of the mature molecules present in each of the cell types. The most expressed molecules were miR-21, miR-24 and miR-205, Accordingly; miR-21 and miR-205 have been previously shown to play a role in epithelial cell biology. Although miR-21 has been implicated in cancer development, and evaluated as a biomarker in HNSCC progression, no significant expression differences were seen between cell types. We demonstrate that differentially expressed mature miRNAs target cell differentiation and apoptosis related biological processes, indicating that they might represent, with acceptable accuracy, the genetic context from which they derive. Most miRNAs identified in the cancer cell line and in keratinocytes were present in tumor samples and cancer-free samples, respectively, with miR-21, miR-24 and miR-205 still among the most prevalent molecules at all instances. Thirteen miRNA-like structures, containing reads identified by the deep sequencing, were predicted from putative miRNA precursor sequences. Strong evidences suggest that one of them could be a new miRNA. This molecule was mostly expressed in the tumor cell line and HNSCC samples indicating a possible biological function in cancer. Conclusions Critical biological features of cells must be fully understood before they can be chosen as models for functional studies. Expression levels of miRNAs relate to cell type and tissue context. This study provides insights on miRNA content of two cell models used for cancer research. Pathways commonly deregulated in HNSCC might be targeted by most expressed and also by differentially expressed miRNAs. Results indicate that the use of cell models for cancer research demands careful assessment of underlying molecular characteristics for proper data interpretation. Additionally, one new miRNA-like molecule with a potential role in cancer was identified in the cell lines and clinical samples.

Development of muliplexed analytical methods based on bioluminescent whole-cell biosensors

The subject of this Ph.D. research thesis is the development and application of multiplexed analytical methods based on bioluminescent whole-cell biosensors. One of the main goals of analytical chemistry is multianalyte testing in which two or more analytes are measured simultaneously in a single assay. The advantages of multianalyte testing are work simplification, high throughput, and reduction in the overall cost per test. The availability of multiplexed portable analytical systems is of particular interest for on-field analysis of clinical, environmental or food samples as well as for the drug discovery process. To allow highly sensitive and selective analysis, these devices should combine biospecific molecular recognition with ultrasensitive detection systems. To address the current need for rapid, highly sensitive and inexpensive devices for obtaining more data from each sample,genetically engineered whole-cell biosensors as biospecific recognition element were combined with ultrasensitive bioluminescence detection techniques. Genetically engineered cell-based sensing systems were obtained by introducing into bacterial, yeast or mammalian cells a vector expressing a reporter protein whose expression is controlled by regulatory proteins and promoter sequences. The regulatory protein is able to recognize the presence of the analyte (e.g., compounds with hormone-like activity, heavy metals…) and to consequently activate the expression of the reporter protein that can be readily measured and directly related to the analyte bioavailable concentration in the sample. Bioluminescence represents the ideal detection principle for miniaturized analytical devices and multiplexed assays thanks to high detectability in small sample volumes allowing an accurate signal localization and quantification. In the first chapter of this dissertation is discussed the obtainment of improved bioluminescent proteins emitting at different wavelenghts, in term of increased thermostability, enhanced emission decay kinetic and spectral resolution. The second chapter is mainly focused on the use of these proteins in the development of whole-cell based assay with improved analytical performance. In particular since the main drawback of whole-cell biosensors is the high variability of their analyte specific response mainly caused by variations in cell viability due to aspecific effects of the sample’s matrix, an additional bioluminescent reporter has been introduced to correct the analytical response thus increasing the robustness of the bioassays. The feasibility of using a combination of two or more bioluminescent proteins for obtaining biosensors with internal signal correction or for the simultaneous detection of multiple analytes has been demonstrated by developing a dual reporter yeast based biosensor for androgenic activity measurement and a triple reporter mammalian cell-based biosensor for the simultaneous monitoring of two CYP450 enzymes activation, involved in cholesterol degradation, with the use of two spectrally resolved intracellular luciferases and a secreted luciferase as a control for cells viability. In the third chapter is presented the development of a portable multianalyte detection system. In order to develop a portable system that can be used also outside the laboratory environment even by non skilled personnel, cells have been immobilized into a new biocompatible and transparent polymeric matrix within a modified clear bottom black 384 -well microtiter plate to obtain a bioluminescent cell array. The cell array was placed in contact with a portable charge-coupled device (CCD) light sensor able to localize and quantify the luminescent signal produced by different bioluminescent whole-cell biosensors. This multiplexed biosensing platform containing whole-cell biosensors was successfully used to measure the overall toxicity of a given sample as well as to obtain dose response curves for heavy metals and to detect hormonal activity in clinical samples (PCT/IB2010/050625: “Portable device based on immobilized cells for the detection of analytes.” Michelini E, Roda A, Dolci LS, Mezzanotte L, Cevenini L , 2010). At the end of the dissertation some future development steps are also discussed in order to develop a point of care (POCT) device that combine portability, minimum sample pre-treatment and highly sensitive multiplexed assays in a short assay time. In this POCT perspective, field-flow fractionation (FFF) techniques, in particular gravitational variant (GrFFF) that exploit the earth gravitational field to structure the separation, have been investigated for cells fractionation, characterization and isolation. Thanks to the simplicity of its equipment, amenable to miniaturization, the GrFFF techniques appears to be particularly suited for its implementation in POCT devices and may be used as pre-analytical integrated module to be applied directly to drive target analytes of raw samples to the modules where biospecifc recognition reactions based on ultrasensitive bioluminescence detection occurs, providing an increase in overall analytical output.

Entwicklung und Überprüfung objektiver Testverfahren zur Messung von Angstbewältigungsdispositionen

Für die Entwicklung objektiver Testverfahren zur Messung von Angstbewältigungsdispositionen, d.h. von Tests, deren Meßprinzip für die Probanden nicht durchschaubar ist, wurde das Dot-Probe-Paradigma verwendet. Mit diesem Paradigma läßt sich das Aufmerksamkeitsverhalten gegenüber bedrohlichem Material messen. Es wurde angenommen, daß dieses Paradigma besonders gut für eine objektive Messung der Angstbewältigungsdispositionen Vigilanz und kognitive Vermeidung geeignet ist, da Vigilanz durch verstärkte Aufnahme und Verarbeitung bedrohungsbezogener Information gekennzeichnet ist, während sich kognitive Vermeidung in der Abwendung der Aufmerksamkeit von diesen Reizen zeigt. In drei Studien wurde für verschiedene Versionen des Dot-Probe-Paradigmas überprüft, ob die für den Einsatz als Testinstrument in der Persönlichkeitsdiagnostik notwendigen Gütekriterien erfüllt sind. Dabei wurde festgestellt, daß das Dot-Probe-Paradigma sowohl bei Verwendung von Wörtern als auch von Bildern als Stimuli für klinisch unauffällige Testpersonen keine reliable Messung ermöglicht. Die erhobenen Werte waren weder über eine Woche hinweg stabil, noch waren sie intern konsistent. Infolge der ungenügenden Reliabilität fanden sich in den Studien nur unsystematische Befunde zum Zusammenhang zwischen dem Aufmerksamkeitsverhalten im Dot-Probe-Paradigma und verschiedenen Fragebogenmaßen. Darüber hinaus vermag die mangelnde Reliabilität auch die in der Literatur berichteten inkonsistenten Befunde bei der Untersuchung nicht-klinischer Stichproben mit diesem Paradigma zu erklären. Mögliche Gründe für die mangelnde Reliabilität der Messung werden diskutiert.

Experimentelle Diagnostik angstbezogener Informationsverarbeitung bei Kindern im Grundschulalter

Ziel war die Entwicklung und Erprobung von Varianten des emotionalen Strooptests zur Analyse angstbezogener Aufmerksamkeitsprozesse bei Grundschulkindern. Dabei wurde überprüft, ob dieses kognitiv-experimentelle Verfahren zukünftig als objektives Testverfahren zur Diagnostik von Ängstlichkeit im Kindesalter geeignet ist. Ausgangspunkt waren zahlreiche Befunde für die Gruppe Erwachsener, wonach die Zuwendung auf bedrohliche Situationsmerkmalen für Ängstliche charakteristisch ist. Für das Kindesalter liegen hierzu nur wenige Studien mit zudem inkonsistenten Befundmuster vor. In insgesamt drei Studien wurde der emotionale Strooptest für das Grundschulalter adaptiert, indem Bilder bzw. altersentsprechendes Wortmaterial als Stimuli eingesetzt wurden. An den Studien nahmen nicht-klinische, nicht-ausgelesene Stichproben mit Kindern der zweiten bis vierten Grundschulklassen teil. Sowohl Ängstlichkeit als auch Zustandsangst der Kinder wurden jeweils über Selbst- und Fremdeinschätzungen (Eltern, Klassenlehrer, Versuchsleiter) erhoben. Die Ergebnisse sprechen für eine nur unzureichende Reliabilität emotionaler Interferenzeffekte. Auch ergaben sich (möglichenfalls infolge) keine substantiellen Hinweise auf differentielle angstbezogene Interferenzeffekte. Die Befunde sprechen vielmehr dafür, dass alle Kinder unabhängig von der Ängstlichkeit höhere Benennungszeiten für bedrohliche Stimuli im Vergleich zur Kontrollbedingung mit neutralen oder freundlichen Stimuli zeigten, wobei zugleich methodische Einflussfaktoren des Strooptests von Relevanz waren. Die Diskussion konzentriert sich auf entwicklungspsychologische Überlegungen sowie mögliche Bedingungen emotionaler Interferenzeffekte unter kritischer Berücksichtigung der Reliabilität emotionaler Stroopinterferenz.

Quantitative differential proteomics for analysis of posttranslational modifications of proteins

In this work we developed a new and convenient method for high resolution IEF of proteins, which we termed: “daisy chain”. Usually an IEF is accomplished with IPG strips of a desired pH range. For high resolution focusing we are using strips with pH range, which covers only one or two pH units. Thereby the pro-teins, which have isoelectrical point outside of this pH range, are lost. We evalu-ated commercially available IPG strips with consecutive or overlapping pH ranges and connected them serially acidic to basic end, to construct in this way a high resolution IEF-system. For the first time, we showed that a high resolution IEF is possible in such a system and that results were by no means worse than those obtained when the same sample was analyzed on individual single IPGs. The great advantage of our system is that amount of sample used in serial IPG IEF is explicitly lower than when same sample was analyzed on individual single IPGs. This method was subsequently successfully applied to valuable clinical samples from cancer patients and to mitochondrial preparations related to a European project in gerontology. We thus developed a suite of experimental strategies, which adequately address complex biological situations, in particular on the level of protein expression.