Single-tube nested PCR assay with in-house DNA extraction for Mycobacterium tuberculosis detection in blood and urine

Abstract: INTRODUCTION : Molecular analyses are auxiliary tools for detecting Koch's bacilli in clinical specimens from patients with suspected tuberculosis (TB). However, there are still no efficient diagnostic tests that combine high sensitivity and specificity and yield rapid results in the detection of TB. This study evaluated single-tube nested polymerase chain reaction (STNPCR) as a molecular diagnostic test with low risk of cross contamination for detecting Mycobacterium tuberculosis in clinical samples. METHODS: Mycobacterium tuberculosis deoxyribonucleic acid (DNA) was detected in blood and urine samples by STNPCR followed by agarose gel electrophoresis. In this system, reaction tubes were not opened between the two stages of PCR (simple and nested). RESULTS: STNPCR demonstrated good accuracy in clinical samples with no cross contamination between microtubes. Sensitivity in blood and urine, analyzed in parallel, was 35%-62% for pulmonary and 41%-72% for extrapulmonary TB. The specificity of STNPCR was 100% in most analyses, depending on the type of clinical sample (blood or urine) and clinical form of disease (pulmonary or extrapulmonary). CONCLUSIONS: STNPCR was effective in detecting TB, especially the extrapulmonary form for which sensitivity was higher, and had the advantage of less invasive sample collection from patients for whom a spontaneous sputum sample was unavailable. With low risk of cross contamination, the STNPCR can be used as an adjunct to conventional methods for diagnosing TB.

Valorization of grape pomace through hot compressed water extraction/hydrolysis

The world energy consumption is expected to increase strongly in coming years, because of the emerging economies. Biomass is the only renewable carbon resource that is abundant enough to be used as a source of energy Grape pomace is one of the most abundant agro-industrial residues in the world, being a good biomass resource. The aim of this work is the valorization of grape pomace from white grapes (WWGP) and from red grapes (RWGP), through the extraction of phenolic compounds with antioxidant activity, as well as through the extraction/hydrolysis of carbohydrates, using subcritical water, or hot compressed water (HCW). The main focus of this work is the optimization of the process for WWGP, while for RWGP only one set of parameters were tested. The temperatures used were 170, 190 and 210 °C for WWGP, and 180 °C for RWGP. The water flow rates were 5 and 10 mL/min, and the pressure was always kept at 100 bar. Before performing HCW assays, both residues were characterized, revealing that WWGP is very rich in free sugars (around 40%) essentially glucose and fructose, while RWGP has higher contents of structural sugars, lignin, lipids and protein. For WWGP the best results were achieved at 210 °C and 10 mL/min: higher yield in water soluble compounds (69 wt.%), phenolics extraction (26.2 mg/g) and carbohydrates recovery (49.3 wt.% relative to the existing 57.8%). For RWGP the conditions were not optimized (180 °C and 5 mL/min), and the values of the yield in water soluble compounds (25 wt.%), phenolics extraction (19.5 mg/g) and carbohydrates recovery (11.4 wt.% relative to the existing 33.5%) were much lower. The antioxidant activity of the HCW extracts from each assay was determined, the best result being obtained for WWGP, namely for extracts obtained at 210 °C (EC50=20.8 μg/mL; EC50 = half maximum effective concentration; EC50 = 22.1 μg/mL for RWGP, at 180 ºC).

Extraction of Trypanosoma cruzi DNA from food: a contribution to the elucidation of acute Chagas disease outbreaks

Abstract: INTRODUCTION: Before 2004, the occurrence of acute Chagas disease (ACD) by oral transmission associated with food was scarcely known or investigated. Originally sporadic and circumstantial, ACD occurrences have now become frequent in the Amazon region, with recently related outbreaks spreading to several Brazilian states. These cases are associated with the consumption of açai juice by waste reservoir animals or insect vectors infected with Trypanosoma cruzi in endemic areas. Although guidelines for processing the fruit to minimize contamination through microorganisms and parasites exist, açai-based products must be assessed for quality, for which the demand for appropriate methodologies must be met. METHODS: Dilutions ranging from 5 to 1,000 T. cruzi CL Brener cells were mixed with 2mL of acai juice. Four Extraction of T. cruzi DNA methods were used on the fruit, and the cetyltrimethyl ammonium bromide (CTAB) method was selected according to JRC, 2005. RESULTS: DNA extraction by the CTAB method yielded satisfactory results with regard to purity and concentration for use in PCR. Overall, the methods employed proved that not only extraction efficiency but also high sensitivity in amplification was important. CONCLUSIONS: The method for T. cruzi detection in food is a powerful tool in the epidemiological investigation of outbreaks as it turns epidemiological evidence into supporting data that serve to confirm T. cruzi infection in the foods. It also facilitates food quality control and assessment of good manufacturing practices involving acai-based products.

Semantic relations extraction from unstructured information for domain ontologies enrichment

Based in internet growth, through semantic web, together with communication speed improvement and fast development of storage device sizes, data and information volume rises considerably every day. Because of this, in the last few years there has been a growing interest in structures for formal representation with suitable characteristics, such as the possibility to organize data and information, as well as the reuse of its contents aimed for the generation of new knowledge. Controlled Vocabulary, specifically Ontologies, present themselves in the lead as one of such structures of representation with high potential. Not only allow for data representation, as well as the reuse of such data for knowledge extraction, coupled with its subsequent storage through not so complex formalisms. However, for the purpose of assuring that ontology knowledge is always up to date, they need maintenance. Ontology Learning is an area which studies the details of update and maintenance of ontologies. It is worth noting that relevant literature already presents first results on automatic maintenance of ontologies, but still in a very early stage. Human-based processes are still the current way to update and maintain an ontology, which turns this into a cumbersome task. The generation of new knowledge aimed for ontology growth can be done based in Data Mining techniques, which is an area that studies techniques for data processing, pattern discovery and knowledge extraction in IT systems. This work aims at proposing a novel semi-automatic method for knowledge extraction from unstructured data sources, using Data Mining techniques, namely through pattern discovery, focused in improving the precision of concept and its semantic relations present in an ontology. In order to verify the applicability of the proposed method, a proof of concept was developed, presenting its results, which were applied in building and construction sector.

An agent based architecture to support monitoring in plug and produce manufacturing systems using knowledge extraction

In recent years a set of production paradigms were proposed in order to capacitate manufacturers to meet the new market requirements, such as the shift in demand for highly customized products resulting in a shorter product life cycle, rather than the traditional mass production standardized consumables. These new paradigms advocate solutions capable of facing these requirements, empowering manufacturing systems with a high capacity to adapt along with elevated flexibility and robustness in order to deal with disturbances, like unexpected orders or malfunctions. Evolvable Production Systems propose a solution based on the usage of modularity and self-organization with a fine granularity level, supporting pluggability and in this way allowing companies to add and/or remove components during execution without any extra re-programming effort. However, current monitoring software was not designed to fully support these characteristics, being commonly based on centralized SCADA systems, incapable of re-adapting during execution to the unexpected plugging/unplugging of devices nor changes in the entire system’s topology. Considering these aspects, the work developed for this thesis encompasses a fully distributed agent-based architecture, capable of performing knowledge extraction at different levels of abstraction without sacrificing the capacity to add and/or remove monitoring entities, responsible for data extraction and analysis, during runtime.

Engineering of fatty acid production and secretion in Saccharomyces cerevisiae

Tese de Doutoramento em Ciências - Especialidade em Biologia

Search for photonic signatures of gauge-mediated supersymmetry in 8 TeV pp collisions with the ATLAS detector

A search is presented for photonic signatures motivated by generalised models of gauge-mediated supersymmetry breaking. This search makes use of 20.3 fb−1 of proton-proton collision data at s√=8 TeV recorded by the ATLAS detector at the LHC, and explores models dominated by both strong and electroweak production of supersymmetric partner states. Four experimental signatures incorporating an isolated photon and significant missing transverse momentum are explored. These signatures include events with an additional photon, lepton, b-quark jet, or jet activity not associated with any specific underlying quark flavor. No significant excess of events is observed above the Standard Model prediction and model-dependent 95% confidence-level exclusion limits are set.

Galanin-mediated behavioural hyperalgesia from the dorsomedial nucleus of the hypothalamus involves two independent descending pronociceptive pathways

Activation of the dorsomedial nucleus of the hypothalamus (DMH) by galanin (GAL) induces behavioural hyperalgesia. Since DMH neurones do not project directly to the spinal cord, we hypothesized that the medullary dorsal reticular nucleus (DRt), a pronociceptive region projecting to the spinal dorsal horn (SDH) and/or the serotoninergic raphe-spinal pathway acting on the spinal 5-HT3 receptor (5HT3R) could relay descending nociceptive facilitation induced by GAL in the DMH. Heat-evoked paw-withdrawal latency (PWL) and activity of SDH neurones were assessed in monoarthritic (ARTH) and control (SHAM) animals after pharmacological manipulations of the DMH, DRt and spinal cord. The results showed that GAL in the DMH and glutamate in the DRt lead to behavioural hyperalgesia in both SHAM and ARTH animals, which is accompanied particularly by an increase in heat-evoked responses of wide-dynamic range neurons, a group of nociceptive SDH neurones. Facilitation of pain behaviour induced by GAL in the DMH was reversed by lidocaine in the DRt and by ondansetron, a 5HT3R antagonist, in the spinal cord. However, the hyperalgesia induced by glutamate in the DRt was not blocked by spinal ondansetron. In addition, in ARTH but not SHAM animals PWL was increased after lidocaine in the DRt and ondansetron in the spinal cord. Our data demonstrate that GAL in the DMH activates two independent descending facilitatory pathways: (i) one relays in the DRt and (ii) the other one involves 5-HT neurones acting on spinal 5HT3Rs. In experimental ARTH, the tonic pain-facilitatory action is increased in both of these descending pathways.

Extraction and characterization of polysaccharides from non-traditional Brazilian Amazon sources

[Excerpt] Cupuassu (Theobroma grandiflorum), tucumã (Astrocaryum aculeatum), peach palm (Bactris gasipaes) and abricó (American Mammea L.) are exotic fruits found in the Brazilian Amazon rainforest. All of them are well known by the native populations, and for centuries the pulps have been used in the production of juices, deserts, jams, syrups, and alcoholic beverages, among others. Additionally, the fruit seeds have been used as animal feed, fertilizers or to plant new seedlings, but a great part of these seeds are usually discarded. (...)

Biological extraction of bromelain from pineapple byproducts

[Excerpt] Isolation and purification of valuable compounds are very important processes to valorize agro-food byproducts. Currently, protein extraction and development of environmentally friendly technologies are industrially relevant topics [1]. Among the extracted proteins from byproducts proteases are a relevant group for industrial applications. These enzymes are a class of hydrolytic enzymes capable of cleaving the peptide bonds of proteins chains and are essential in physiological processes [2]. (...)

Bioethanol production by Saccharomyces cerevisiae, Pichia stipitis and Zymomonas mobilis from delignified coconut fibre mature and lignin extraction according to biorefinery concept

In search to increase the offer of liquid, clean, renewable and sustainable energy in the world energy matrix, the use of lignocellulosic materials (LCMs) for bioethanol production arises as a valuable alternative. The objective of this work was to analyze and compare the performance of Saccharomyces cerevisiae, Pichia stipitis and Zymomonas mobilis in the production of bioethanol from coconut fibre mature (CFM) using different strategies: simultaneous saccharification and fermentation (SSF) and semi-simultaneous saccharification and fermentation (SSSF). The CFM was pretreated by hydrothermal pretreatment catalyzed with sodium hydroxide (HPCSH). The pretreated CFM was characterized by X-ray diffractometry and SEM, and the lignin recovered in the liquid phase by FTIR and TGA. After the HPCSH pretreatment (2.5% (v/v) sodium hydroxide at 180 °C for 30 min), the cellulose content was 56.44%, while the hemicellulose and lignin were reduced 69.04% and 89.13%, respectively. Following pretreatment, the obtained cellulosic fraction was submitted to SSF and SSSF. Pichia stipitis allowed for the highest ethanol yield 90.18% in SSSF, 91.17% and 91.03% were obtained with Saccharomyces cerevisiae and Zymomonas mobilis, respectively. It may be concluded that the selection of the most efficient microorganism for the obtention of high bioethanol production yields from cellulose pretreated by HPCSH depends on the operational strategy used and this pretreatment is an interesting alternative for add value of coconut fibre mature compounds (lignin, phenolics) being in accordance with the biorefinery concept.

Production and extraction of polysaccharides and oligosaccharides and their use as new food additives

Polysaccharides and oligosaccharides can improve quality and enhance nutritional value of final food products due to their technological and nutritional features ranging from their capacity to improve texture to their effect as dietary fibers. For this reason, they are among the most studied ingredients in the food industry. The use of natural polysaccharides and oligosaccharides as food additives has been a reality since the food industry understood their potential technological and nutritional applications. Currently, the replacement of traditional ingredients and/or the synergy between traditional ingredients and polysaccharides and oligosaccharides are perceived as promising approaches by the food industry. Traditionally, polysaccharides have been used as thickening, emulsifying, and stabilizing agents, however, at this moment polysaccharides and oligosaccharides claim health and nutritional advantages, thus opening a new market of nutritional and functional foods. Indeed, their use as nutritional food ingredients enabled the food industry to develop a countless number of applications, e.g., fat replacers, prebiotics, dietary fiber, and antiulcer agents. Based on this, among the scientific community and food industry, in the last years many research studies and commercial products showed the possibility of using either new or already used sources (though with changed properties) of polysaccharides for the production of food additives with new and enhanced properties. The increasing interest in such products is clearly illustrated by the market figures and consumption trends. As an example, the sole market of hydrocolloids is estimated to reach $7 billion in 2018. Moreover, oligosaccharides can be found in more than 500 food products resulting in a significant daily consumption. A recent study from the Transparency Market Research on Prebiotic Ingredients Market reported that prebiotics' demand was worth $2.3 billion in 2012 and it is estimated to reach $4.5 billion in 2018, growing at a compound annual growth rate of 11.4% between 2012 and 2018. The entrance of this new generation of food additives in the market, often claiming health and nutritional benefits, imposes an impartial analysis by the legal authorities regarding the accomplishment of requirements that have been established for introducing novel ingredients/food, including new poly- and oligosaccharides. This chapter deals with the potential use of polysaccharides and oligosaccharides as food additives, as well as alternative sources of these compounds and their possible applications in food products. Moreover, the regulation process to introduce novel polysaccharides and oligosaccharides in the market as food additives and to assign them health claims is discussed.

Valorization of agro-industrial wastes towards the production of rhamnolipids

In this work, oil mill wastewater (OMW), a residue generated during olive oil extraction, was evaluated as an inducer of rhamnolipid production. Using a medium containing as sole ingredients corn steep liquor (10%, v/v), sugarcane molasses (10%, w/v) and OMW (25%, v/v), Pseudomonas aeruginosa #112 produced 4.5 and 5.1 g of rhamnolipid per liter in flasks and reactor, respectively, with critical micelle concentrations as low as 13 mg/l. Furthermore, in the medium supplemented with OMW, a higher proportion of more hydrophobic rhamnolipid congeners was observed comparing with the same medium without OMW. OMW is a hazardous waste which disposal represents a serious environmental problem; therefore, its valorization as a substrate for the production of added-value compounds such as rhamnolipids is of great interest. This is the first report of rhamnolipid production using a mixture of these three agro-industrial by-products, which can be useful for the sustainable production of rhamnolipids.

Laser assisted extraction of pacemaker and implantable defibrillator leads

OBJECTIVE: To analyze the results of laser-assisted extraction of permanent pacemaker and defibrillator leads. METHODS: We operated upon 36 patients, whose mean age was 54.2 years, and extracted 56 leads. The reasons for extracting the leads were as follows: infection in 19 patients, elective replacement in 13, and other causes in 4 patients. The mean time of catheter placement was 7.5±5.5 years. Forty-seven leads were from pacemakers, and 9 were from defibrillators. Thirty-eight leads were in use, 14 had been abandoned in the pacemaker pocket, and 4 had been abandoned inside the venous system. RESULTS: We successfully extracted 54 catheters, obtaining a 96.4% rate of success and an 82.1% rate for complete extraction. The 2 unsuccessful cases were due to the presence of calcium in the trajectory of the lead. The mean duration of laser light application was 123.0±104.5 s, using 5,215.2±4,924.0 pulses, in a total of 24.4±24.2 cycles of application. Thirty-four leads were extracted from the myocardium with countertraction after complete progression of the laser sheath, 12 leads came loose during the progression of the laser sheath, and the remaining 10 were extracted with other maneuvers. One patient experienced cardiac tamponade after extraction of the defibrillator lead, requiring open emergency surgery. CONCLUSION: The use of the excimer laser allowed extraction of the leads with a 96% rate of success; it was not effective in 2 patients who had calcification on the lead. One patient (2.8%) had a complication that required cardiac surgery on an emergency basis.

Effect of arginine vasopressin on the canine epicardial coronary artery: experiments on V1-receptor-mediated production of nitric oxide

OBJECTIVE: To determine whether arginine vasopressin releases endothelium-derived nitric oxide (EDNO) from the epicardial coronary artery. METHODS: We studied segments of canine left circumflex coronary arteries suspended in organ chambers to measure isometric force. The coronary artery segments were contracted with prostaglandin F2alpha (2 x 10-6M) and exposed to a unique, strong arginine vasopressin concentration (10-6M) or titrated concentrations (10-9 a 10-5 M). RESULTS: The unique dose of arginine vasopressin concentration (10-6M) induced transient, but significant (p<0.05), relaxation in arterial segments with endothelium, and an increase, not significant, in tension in arteries without endothelium. Endothelium-dependent relaxation to arginine vasopressin was inhibited by Ng-monomethyl-L-arginine (L-NMMA, 10-5M) or N G-nitro-L-arginine (L-NOARG) (10-4M), 2 inhibitors of nitric oxide synthesis from L-arginine. Exogenous L-arginine (10-4M), but not D-arginine (10-4M), reversed the inhibitory effect of L-NMMA on vasopressin-mediated vasorelaxation. Endothelium dependent relaxation to vasopressin was also reversibly inhibited by the vasopressin V1-receptor blocker d(CH2)5Try(Me) arginine vasopressin (10-6M) (n=6, P<0.05). CONCLUSION: Vasopressin acts through V1 endothelial receptors to stimulate nitric oxide release from L-arginine.