Juliana de Saldanha da Gama Fischer

Search engine processor: Filtering and organizing peptide spectrum matches

The search engine processor (SEPro) is a tool for filtering, organizing, sharing, and displaying peptide spectrum matches. It employs a novel three‐tier Bayesian approach that uses layers of spectrum, peptide, and protein logic to lead the data to converge to a single list of reliable protein identifications. SEPro is integrated into the PatternLab for proteomics environment, where an arsenal of tools for analyzing shotgun proteomic data is provided. By using the semi‐labeled decoy approach for benchmarking, we show that SEPro significantly outperforms a commercially available competitor.

PatternLab: From Mass Spectra to Label‐Free Differential Shotgun Proteomics

PatternLab for proteomics is a self‐contained computational environment for analyzing shotgun proteomic data. Recent improvements incorporate modules to facilitate the computational analysis, such as FastaDBXtractor for sequence database preparation and ProLuCID runner for simplifying and managing the protein identification search engine; modules for pushing the limits on proteomics standards, such as SEPro, which relies on a semi‐labeled decoy approach for increasing confidence in filtering and organizing peptide spectrum matches; and modules with novel features, such as SEProQ for enabling label‐free quantitation by extracted ion chromatograms according to a distributed normalized ion abundance factor approach (dNIAF). Existing modules were also improved, such as the TFold module for pinpointing differentially expressed proteins. These new modules are integrated into the previously described arsenal of tools for further data analysis. Here we provide detailed instructions for operating and understanding them. Curr. Protoc. Bioinform. 40:13.19.1‐13.19.18.

Long-term Outcome in Patients with Recurrent Malignant Glioma Treated with Perillyl Alcohol Inhalation

As you begin the journey to understand the Emotional Core Therapy process please keep in mind the scientific method. The scientific method is a process for creating models of the natural world that can be verified experimentally. The scientific method requires making observations, recording data, and analyzing data in a form that can be duplicated by other scientists. The subject of a scientific experiment has to be observable and reproducible. Observations may be made with the unaided eye or any other apparatus suitable for detecting the desired phenomenon. The apparatus for making a scientific observation has to be comprised of well-known scientific principles. The scientific method requires that theories be testable. If a theory cannot be tested, it cannot be a scientific theory. The scientific method requires and relies on direct evidence. This means evidence that can be directly observed and tested. Scientific experiments are designed to be repeated by other scientists and to demonstrate unequivocally the point they are trying to prove by controlling all the factors that could influence the results. Source (Scientificpsychic.com/Scientific Method) Here are the four steps to the scientific method and the Emotional Core Therapy process. 1). Observation made both visually and with scientific equipment Stress affects both the mind and body. There exists a cause and effect relationship with stress. Oftentimes this stress can be uncomfortable for humans. 2) Formulation of a hypothesis to explain the phenomenon in the form of a causal mechanism/method/approach. Many psychology methods (REBT, CBT, ACT, DBT, etc.), religious approaches (Buddhism, 12 steps, etc.), and educational programs (Smart Recovery) have attempted to fully and completely explain via a model, how this cause and effect relationship with stress occurs. Up until this point in time, we have not had a model in the world that can successfully depict how this stress occurs each and every time. To their credit, many of these methods partially work and have contributed greatly to humanity. See Wiki.com for information on all the psychology methods and techniques mentioned in this book. With the invention/discovery of Emotional Core Therapy (ECT) we now have a psychology method that accurately can depict this causal relationship between stress and humans through my Eight Step Emotional Core Therapy Flowchart. With ECT, we now have a psychology approach that identifies and treats the root cause of psychological stress. The root cause is the temporary arousal of one of the four true emotions (joy, grief, fear, and relief). ECT also shares and borrows many psychological techniques from the aforementionedMethods: Adult male Wistar rats (225-275 g) were selected randomly and divided into 10 groups. All groups underwent stereotaxic surgery and in order to induce dependency, morphine was administered subcutaneously) Sc) at an interval of 12 hours for nine continuous days. On the ninth day of the experiment, animals received vehicle or CBX (100, 400, 600 μg/10μl/ rat, ICV) or MFQ (50, 100 and 200 μg/10μl/rat, ICV) after the last saline or morphine (Sc) injection. Morphine withdrawal symptoms were precipitated by naloxone hydrochloride 10 min after the treatments. The withdrawal signs including: jumping, rearing, genital grooming, abdomen writhing, wet dog shake and stool weight, were recorded for 60 minutes.D to the effect of thoracotomy on respiratory and circulatory systems, the anesthetic technique, one lung ventilation (OLV) is applied. With the consistent improvement and widespread application of double lumen endobronchial tube and novel endobronchial blockers, OLV is more popular for surgical performance. However, there are some issues of OLV, such as the dismatching of ventilation perfusion ratio, hypoxemia, SpO2 and increase of Pmax, which limited the use of OLV. Recently, many studies have been done in the advancement of safety of OLV and on the prevention and treatment of hypoxemia. This review briefly introduces the progress of OLV and discusses the function of OLV in anesthesia.BACKGROUND Treatment of patients with chronic conditions requiring hospitalization requires patient acceptance and cooperation and adoption of coping strategies. Inappropriate coping strategies such as substance abuse are concerning in the course of treatment. This study sought to explore the association of coping strategies with suicidal behavior in substance abusers and non substance abuser patients with chronic pulmonary diseases namely asthma and chronic obstructive pulmonary disease (COPD). MATERIALS AND METHODS This comparative study was performed on 100 patients with asthma and COPD selected via convenience sampling. Subjects with and without substance abuse were separated into two groups of 50 patients each. Ways of Coping Questionnaire of Lazarus (WOCQ) and Suicide Behavior Questionnaire-Revised (SBQ-R) were completed by them. Five Persian speaking patients rated this questionnaire to be easily understandable in the pre-test stage. Cronbachs alpha was calculated to measure the internal consistency. RESULTS The mean (±standard deviation) age of participants was 40 (±14) years; 58% of individuals were men; 62% had chosen problem-focused coping. The most abused substances were cigarettes (78%) and opium (42%); 6% of substance abusers had thought about suicide five times or more in the past year; 5% of substance abusers had seriously attempted suicide. Tendency to commit suicide was greater in men, substance abusers and participants who had chosen emotion-focused coping strategies, based on a regression model. Average score of suicide tendency was significantly higher in substance abusers (B=2.196, P =0.007). CONCLUSION Chronic disease is a crisis and patients need to acquire appropriate coping strategies to deal with it, especially in substance abusers and suicidal patients. Precise recognition of coping strategies in chronic pulmonary patients with substance abuse is necessary via a team cooperation among psychiatrics, psychologists and an internal physician in hospitals because medical treatment alone is not sufficient in such cases.N oxide is a colorless and virtually odorless gas with a faint, sweet smell. It is a safe and effective tool used in dental clinics to reduce anxiety, produce analgesia, and cause the depression of the central nervous system (CNS), leading to the sensation of euphoria with little effect on the respiratory system. It also enhances effective communication between the patient and their healthcare provider. The decision to use nitrous oxide/oxygen must take into consideration the alternative behavioral guidance modalities, the patient’s dental needs, the effect on the quality of dental care, the patient’s emotional development, and the patient’s physical considerations.AIM This retrospective study aimed to evaluate the long-term response and toxicity of recurrent malignant glioma patients to inhalation chemotherapy with perillyl alcohol (POH). PATIENTS AND METHODS The cohort included 117 men and 81 women with primary glioblastoma multiforme (GBM; n=154), grade III astrocytoma (AA; n=26) and anaplastic oligodendroglioma (AO; n=5). POH inhalation schedule 4-times daily started with 66.7 mg/dose; 266 mg/day and escalated up to 133.4 mg/dose; 533.6 mg/day. Clinical toxicity and overall survival following treatment were compared with tumor size, topography, extent of peritumoral edema and histological classification. RESULTS Adhesion to the protocol was high (>95%), POH (533.6 mg/daily) occasionally caused nose soreness but rarely nosebleed. Tumor size, peritumoral edema and the oligodendroglial component influenced response to treatment. CONCLUSION After 4 years under exclusive POH treatment, 19% of patients still remain in clinical remission. Long-term POH inhalation chemotherapy is a safe and non-invasive strategy efficient for recurrent malignant glioma.

Chemo-resistant protein expression pattern of glioblastoma cells (A172) to perillyl alcohol

Glioblastoma multiform (GBM) is by far the most malignant glioma. We have introduced a new treatment for GBMs that comprises the inhalation of a naturally occurring terpene with chemotherapeutic properties known as perillyl alcohol (POH). Clinical trial results on recurrent GBM patients showed that POH extends the average life by more than eight months, temporarily slows tumor growth, and in some cases even decreases tumor size. After approximately seven months, the tumor continues to grow and leads to a dismal prognosis. To investigate how these tumors become resistant to POH, we generated an A172 human glioblastoma cell culture tolerant to 0.06 mM of POH (A172r). We used Multidimensional Protein Identification Technology (MudPIT) to compare the protein expression profile of A172r cells to the established glioblastoma A172 cell line. Our results include a list of identified proteins unique to either the resistant or the nonresistant cell line. These proteins are related to cellular growth, negative apoptosis regulation, Ras pathway, and other key cellular functions that could be connected to the underlying mechanisms of resistance.

Proteomic profiling of the influence of iron availability on Cryptococcus gattii

Iron is essential and ubiquitous in living organisms. The competition for this micronutrient between the host and its pathogens has been related to disease establishment. Cryptococcus gattii is an encapsulated yeast that causes cryptococcosis mainly in immunocompetent individuals. In this study, we analyzed the proteomic profile of the C. gattii R265 Vancouver Island isolate under iron-depleted and -repleted conditions by multidimensional protein identification technology (MudPIT) and by 2D-GE. Proteins and key mechanisms affected by alteration of iron levels such as capsule production, cAMP-signaling pathway, response to stress, and metabolic pathways related to mitochondrial function were identified. Our results also show both proteomic methodologies employed to be complementary.

a Time-Based and intratumoral Proteomic assessment of a recurrent glioblastoma Multiforme

Tumors consist of cells in different stages of transformation with molecular and cellular heterogeneity. By far, heterogeneity is the hallmark of glioblastoma multiforme (GBM), the most malignant and aggressive type of glioma. Most proteomic studies aim in comparing tumors from different patients, but here we dive into exploring the intratumoral proteome diversity of a single GBM. For this, we profiled tumor fragments from the profound region of the same patient’s GBM but obtained from two surgeries a year’s time apart. Our analysis also included GBM‘s fragments from different anatomical regions. Our quantitative proteomic strategy employed 4-plex iTRAQ peptide labeling followed by a four-step strong cation chromatographic separation; each fraction was then analyzed by reversed-phase nano-chromatography coupled on-line with an Orbitrap-Velos mass spectrometer. Unsupervised clustering grouped the proteomic profiles into four major distinct groups and showed that most changes were related to the tumor’s anatomical region. Nevertheless, we report differentially abundant proteins from GBM’s fragments of the same region but obtained 1 year apart. We discuss several key proteins (e.g., S100A9) and enriched pathways linked with GBM such as the Ras pathway, RHO GTPases activate PKNs, and those related to apoptosis, to name a few. As far as we know, this is the only report that compares GBM fragments proteomic profiles from the same patient. Ultimately, our results fuel the forefront of scientific discussion on the importance in exploring the richness of subproteomes within a single tissue sample for a better understanding of the disease, as each tumor is unique.

Efeito do álcool perílico na expressão gênica de células de adenocarcinoma de pulmão humano

OBJECTIVE: To study the effect of perillyl alcohol on the gene expression of human pulmonary adenocarcinoma cells. METHODS: Pulmonary adenocarcinoma cells were incubated with perillyl alcohol in dilutions ranging from 0.03% to 0.0003% for 48 hours. Alterations were observed in the cell morphology, and cell viability was quantified using [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assays. Protein synthesis of samples previously targeted with S35 was analyzed using electrophoresis on a polyacrylamide gel. Expression of the proteins p53 and p44/42 was determined using the Western blot method. RESULTS: After 48 hours of incubation, greater nsumbers of morphological alterations were observed in cells treated with the 0.03% perillyl alcohol dilution than in those treated with perillyl alcohol diluted to 0.003% or further. Treatment with perillyl alcohol dilutions of 0.03%, 0.003% and 0.0003% inhibited cellular viability by 60.17% (p < 0.001), 15.62% (p < 0.001) and 11.53% (p < 0.05), respectively. The results show that 28-kDa, 42-kDa and 110-kDa proteins were induced. No statistically significant effect on p53 expression was observed. In comparison with the expression of a-tubulin, the 0.003% perillyl alcohol dilution induced an increase in p42 phosphorylation and a marked decrease in p44 phosphorylation. CONCLUSION: The results suggest that there are other, previously undescribed, metabolic pathways for perillyl alcohol effects in human pulmonary adenocarcinoma cells.

Marcadores séricos e espectrometria de massa no diagnóstico do câncer

This manuscript reviews mass spectrometry methods and limitations for analisys of biological fluids in the search for biomarkers that can aid medical diagnosis. Currently, mass spectrometry has the ability to discriminate differentially expressed molecular patterns among cancer patients and control subjects. Results in the literature point mass spectrometry as having a major role in the future of medical diagnosis.

Proteomic assessment of colorectal cancers and respective resection margins from patients of the Amazon state of Brazil

Colorectal cancer (CRC) is the third most common type of cancer in the world with a low survival rate and therapeutic efficiency. Tumor surgery implies the removal of an apparently non-tumorous tissue around the tumor in an attempt to reduce recurrence chances; this tissue is referred to as the resection margin. Our analysis employed an 8-plex iTRAQ to label four adenocarcinoma biopsies and their corresponding resection margins at 5cm; our results disclose fifty-six proteins as being differentially abundant. These proteins are mainly involved in energetic metabolism (e.g. S100 calcium binding protein A11), cell migration (e.g. transgelin), formation of the cytoskeleton (e.g. profilin 1) and degradation of extracellular matrix (e.g. carbonic anhydrase 2). A gene ontology enrichment analysis revealed several proteins related to adhesion, invasion, metastasis, death, and recognition cell. Taken together, our results highlight proteins related to invasion, cell proliferation, and linked to the metastasis of colorectal cancer in tumor tissue. Finally, we argue that the expression patterns revealed in our comparison helps shed light on the development of more effective surgical strategies and add to the comprehension of this disease. BIOLOGICAL SIGNIFICANCE Colorectal cancer (CRC) is the third most common type of cancer in the world with a low survival rate and therapeutic efficiency. Tumor surgery implies the removal of an apparently non-tumorous tissue around the tumor in an attempt to reduce recurrence chances; this tissue is also referred to as the resection margin. In this regard, resection margins pose as a treasure trove for investigating the molecular characteristics of the tumorigenesis process. While most studies focus on comparing cancer versus control tissue, this study contrasts the proteomic profiles of colorectal cancer biopsies with their corresponding resection margin at 5cm apart. Our analysis employed an 8-plex iTRAQ labeling and a 4-step offline MudPIT online with a Velos. A gene ontology enrichment analysis revealed several proteins related to adhesion, invasion, metastasis, death, and recognition cell.

Considerations about gastric cancer proteomics.

The frequency of molecular studies aimed to analyze promoter methylation of tumor suppressor genes and global proteomics in gastric carcinogenesis is increasing. Nonetheless, only a few considered the different types of stomach cells, the tumor location and the influence of Helicobacter pylori and Epstein Barr virus infection (EBV). Molecular differences relating to anatomical and histological tumor areas were also recently described. The authors propose a molecular classification of gastric cancer, dividing it into four subtypes: tumors positive for EBV; microsatellite unstable tumors; genomically stable tumors and tumors with chromosomal instability. RESUMO A frequência de estudos moleculares visando a analisar os promotores de metilação de genes supressores de tumor e proteômica globais na carcinogênese gástrica está aumentando. No entanto, apenas alguns consideraram os diferentes tipos de células do estômago, a localização do tumor e a influência da infecção por Helicobacter pylori e pelo vírus Epstein-Barr (EBV). Diferenças moleculares relacionadas com áreas tumorais anatômicas e histológicas também foram recentemente descritas. Os autores propõem uma classificação molecular de câncer gástrico, dividindo-o em quatro subtipos: tumores positivos para o EBV; tumores microssatélite instáveis; tumores genomicamente estáveis ​​e tumores com instabilidade cromossômica.