Optimization and validation of the solid-liquid extraction technique for determination of picloram in soils by high performance liquid chromatography

The objective of this study was to optimize and validate the solid-liquid extraction (ESL) technique for determination of picloram residues in soil samples. At the optimization stage, the optimal conditions for extraction of soil samples were determined using univariate analysis. Ratio soil/solution extraction, type and time of agitation, ionic strength and pH of extraction solution were evaluated. Based on the optimized parameters, the following method of extraction and analysis of picloram was developed: weigh 2.00 g of soil dried and sieved through a sieve mesh of 2.0 mm pore, add 20.0 mL of KCl concentration of 0.5 mol L-1, shake the bottle in the vortex for 10 seconds to form suspension and adjust to pH 7.00, with alkaline KOH 0.1 mol L-1. Homogenate the system in a shaker system for 60 minutes and then let it stand for 10 minutes. The bottles are centrifuged for 10 minutes at 3,500 rpm. After the settlement of the soil particles and cleaning of the supernatant extract, an aliquot is withdrawn and analyzed by high performance liquid chromatography. The optimized method was validated by determining the selectivity, linearity, detection and quantification limits, precision and accuracy. The ESL methodology was efficient for analysis of residues of the pesticides studied, with percentages of recovery above 90%. The limits of detection and quantification were 20.0 and 66.0 mg kg-1 soil for the PVA, and 40.0 and 132.0 mg kg-1 soil for the VLA. The coefficients of variation (CV) were equal to 2.32 and 2.69 for PVA and TH soils, respectively. The methodology resulted in low organic solvent consumption and cleaner extracts, as well as no purification steps for chromatographic analysis were required. The parameters evaluated in the validation process indicated that the ESL methodology is efficient for the extraction of picloram residues in soils, with low limits of detection and quantification.

Extraction and Simultaneous Determination of Glyphosate, AMPA and Compounds of the Shikimic Acid Pathway in Plants

This study has aimed to develop a method for simultaneous extraction and determination by liquid chromatography and mass spectrometry (LC-MS/MS) of glyphosate, aminomethylphosphonic acid (AMPA), shikimic acid, quinic acid, phenylalanine, tyrosine and tryptophan. For the joint analysis of these compounds the best conditions of ionization in mass spectrometry and for chromatographic separation of the compounds were selected. Calibration curves and linearity ranges were also determined for each compound. Different extraction systems of the compounds were tested from plant tissues collected from sugarcane (Saccharum officinarum) and eucalyptus (Eucalyptus urophylla platiphylla) plants two days after the glyphosate application at the dose of 720 g a.e. ha-1. The plant material was dried in a forced air circulation drying oven and in a lyophilizer, and subsequently the extractions with acidified water (pH 2.5), acetonitrile-water (50:50) [v/v] and methanol-water (50:50) [v/v] were tested. To verify the recovery of the compounds in the plant matrix with acidified water as an extracting solution, the samples were fortified with a solution containing the mixture of the different analytical standards present so that this one presented the same levels of 50 and 100 μg L-1 of each compound. All experiments were conducted with three replicates. The analytical method developed was efficient for compounds quantifications. The extraction from the samples dried in an oven and using acidified water allowed better extraction levels for all compounds. The recovery levels of the compounds in the fortified samples with known amounts of each compound for both plants samples were rather satisfactory.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

Chemical derivatization of galactoglucomannan for functional materials

In the framework of the biorefinery concept researchers aspire to optimize the utilization of plant materials, such as agricultural wastes and wood. For most of the known processes, the first steps in the valorisation of biomass are the extraction and purification of the individual components. The obtained raw products by means of a controlled separation can consecutively be modified to result in biofuels or biogas for energy production, but also in value-added products such as additives and important building blocks for the chemical and material industries. Considerable efforts are undertaken in order to substitute the use of oil-based starting materials or at least minimize their processing for the production of everyday goods. Wood is one of the raw materials, which have gained large attention in the last decades and its composition has been studied in detail. Nowadays, the extraction of water-soluble hemicelluloses from wood is well known and so for example xylan can be obtained from hardwoods and O-acetyl galactoglucomannans (GGMs) from softwoods. The aim of this work was to develop water-soluble amphiphilic materials of GGM and to assess their potential use as additives. Furthermore, GGM was also applied as a crosslinker in the synthesis of functional hydrogels for the removal of toxic metals and metalloid ions from aqueous solutions. The distinguished products were obtained by several chemical approaches and analysed by nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FTIR), size exclusion chromatography (SEC), thermal gravimetric analysis (TGA), scanning electron microscope SEM, among others. Bio-based surfactants were produced by applying GGM and different fatty acids as starting materials. On one hand, GGM-grafted-fatty acids were prepared by esterification and on the other hand, well-defined GGM-block-fatty acid derivatives were obtained by linking amino-functional fatty acids to the reducing end of GGM. The reaction conditions for the syntheses were optimized and the resultant amphiphilic GGM derivatives were evaluated concerning their ability to reduce the surface tension of water as surfactants. Furthermore, the block-structured derivatives were tested in respect to their applicability as additives for the surface modification of cellulosic materials. Besides the GGM surfactants with a bio-based hydrophilic and a bio-based hydrophobic part, also GGM block-structured derivatives with a synthetic hydrophobic tail, consisting of a polydimethylsiloxane chain, were prepared and assessed for the hydrophobization of surface of nanofibrillated cellulose films. In order to generate GGM block-structured derivatives containing a synthetic tail with distinguished physical and chemical properties, as well as a tailored chain length, a controlled polymerization method was used. Therefore, firstly an initiator group was introduced at the reducing end of the GGM and consecutively single electron transfer-living radical polymerization (SET-LRP) was performed by applying three different monomers in individual reactions. For the accomplishment of the synthesis and the analysis of the products, challenges related to the solubility of the reactants had to be overcome. Overall, a synthesis route for the production of GGM block-copolymers bearing different synthetic polymer chains was developed and several derivatives were obtained. Moreover, GGM with different molar masses were, after modification, used as a crosslinker in the synthesis of functional hydrogels. Hereby, a cationic monomer was used during the free radical polymerization and the resultant hydrogels were successfully tested for the removal of chromium and arsenic ions from aqueous solutions. The hydrogel synthesis was tailored and materials with distinguished physical properties, such as the swelling rate, were obtained after purification. The results generated in this work underline the potential of bio-based products and the urge to continue carrying out research in order to be able to use more green chemicals for the manufacturing of biorenewable and biodegradable daily products.

The position of the hyaline papilla and the genus concept of Cheilolejeunea (Spruce) Schiffn. (Lejeuneaceae)

In this paper, the genus concept of Cheilolejeunea is discussed and revalued based upon the concept of the real position of the hyaline papilla, as well as upon the definition of apical tooth of the lobule in the genus.

Extraction of genomic DNA from Melipona quadrifasciata (Hymenoptera: Apidae, Meliponinae)

The objective of the present study was to test three different procedures for DNA extraction of Melipona quadrifasciata based on existing methods for DNA extraction of Apis, plants and fungi. These methods differ in the concentrations of specific substances in the extraction buffer. The results demonstrate that the method used for Apis is not adequate for DNA extraction from M. quadrifasciata. On the other hand, with minor modifications this method and the methods for plants and fungi were adequate for DNA extraction of this stingless bee, both for adults and larvae

AQUAREL CONCEPT Aquatic resources for green energy realization

The AQUAREL project studied the availability and optional utilization methods for fish processing side streams and other aquatic biomaterial in the Republic of Karelia. Additionally processing aquatic biomaterial with manure and sewage sludge was studied. Based on the results, the most feasible option today is to process fish side streams to fish oil and dewatered oil-free residue and to use them for fish or animal feed production. However, it is necessary to highlight, that changes in e.g. economic environment, energy prices and demand may require re-evaluating the results and conclusions made in the project. Producing fish oil from fish processing side streams is an easy and relatively simple production process generating a valuable end product. The functionality of the process was confirmed in a pilot conducted in the project. The oil and solids are separated from the heated fish waste based on gravity. The fish oil separating on top of the separator unit is removed. Fish oil can as such be utilized for heating purposes, fish meal or animal feed production, but it can also be further processed to biodiesel. However, due to currently moderate energy prices in Russia, biodiesel production is not economically profitable. Even if the fish oil production process is not complicated, the operative management of small-scale fish oil production unit requires dedicated resources and separate facilities especially to meet hygiene requirements. Managing the side streams is not a core business for fish farmers. Efficient and economically profitable fish oil production requires a centralized production unit with bigger processing capacity. One fish processing unit needs to be designed to manage side streams collected from several fish farms. The optimum location for the processing unit is in the middle of the fish farms. Based on the transportation cost analysis in the Republic of Karelia, it is not economically efficient to transport bio-wastes for more than 100 km since the transportation costs start increasing substantially. Another issue to be considered is that collection of side streams, including the dead fish, from the fish farms should be organized on a daily basis in order to eliminate the need for storing the side streams at the farms. Based on AQUAREL project studies there are different public funding sources available for supporting and enabling profitable and environmentally sustainable utilization, research or development of fish processing side streams and other aquatic biomaterial. Different funding programmes can be utilized by companies, research organizations, authorities and non-governmental organizations.

Radioautographology: the proposal of a new concept

A new concept termed "radioautographology" is advocated. This term was synthesized from "radioautography" and "ology", expressing a new science derived from radioautography. The concept of radioautographology (RAGology) is that of a science whose objective is to localize radioactive substances in the biological structure of objects and to analyze and study the significance of these substances in the biological structure. On the other hand, the old term radioautography (RAG) is the technique used to demonstrate the pattern of localization of various radiolabeled compounds in specimens. The specimens used in biology and medicine are cells and tissues. They are fixed, sectioned and placed in contact with the radioautographic emulsions, which are exposed and developed to produce metallic silver grains. Such specimens are designated as radioautographs and the patterns of pictures made of silver grains are named radioautograms. The technicians who produce radioautographs are named radioautographers, while those who study RAGology are scientists and should be called radioautographologists. The science of RAGology can be divided into two parts, general RAGology and special RAGology, as most natural sciences usually can. General RAGology is the technology of RAG which consists of three fields of science, i.e., physics concerning radioactivity, histochemistry for the treatment of cells and tissues, and photochemistry dealing with the photographic emulsions. Special RAGology, on the other hand, consists of applications of general RAGology. The applications can be classified into several scientific fields, i.e., cellular and molecular biology, anatomy, histology, embryology, pathology and pharmacology. Studies carried out in our laboratory are summarized and reviewed. All the results obtained from such applications should be systematized as a new field of science in the future.

Use of a cysteine proteinase from Carica candamarcensis as a protective agent during DNA extraction

We describe the use of a plant cysteine proteinase isolated from latex of Carica candamarcensis as a protective agent during isolation of bacterial DNA following growth in culture of these cells. Between 100 to 720 units of proteinase (1 µg = 6 units) afforded good DNA protection when incubated with various kinds of microorganisms. Agarose gel electrophoresis showed that the resulting DNA was similar in size to DNA preparations obtained by treatment with proteinase K. The viability of the resulting material was checked by PCR amplification using species-specific primers. After standing at room temperature (25oC) for 35 days, the enzyme lost 10% of its initial activity. The enzyme stability and good yield of DNA suggest the use of this proteinase as an alternative to proteinase K.

Effects of the partial removal of wood hemicelluloses on the properties of kraft pulp

The objective of this work was to study the effects of partial removal of wood hemicelluloses on the properties of kraft pulp.The work was conducted by extracting hemicelluloses (1) by a softwood chip pretreatment process prior to kraft pulping, (2) by alkaline extraction from bleached birch kraft pulp, and (3) by enzymatic treatment, xylanase treatment in particular, of bleached birch kraft pulp. The qualitative and quantitative changes in fibers and paper properties were evaluated. In addition, the applicability of the extraction concepts and hemicellulose-extracted birch kraft pulp as a raw material in papermaking was evaluated in a pilot-scale papermaking environment. The results showed that each examined hemicellulose extraction method has its characteristic effects on fiber properties, seen as differences in both the physical and chemical nature of the fibers. A prehydrolysis process prior to the kraft pulping process offered reductions in cooking time, bleaching chemical consumption and produced fibers with low hemicellulose content that are more susceptible to mechanically induced damages and dislocations. Softwood chip pretreatment for hemicellulose recovery prior to cooking, whether acidic or alkaline, had an impact on the physical properties of the non-refined and refined pulp. In addition, all the pretreated pulps exhibited slower beating response than the unhydrolyzed reference pulp. Both alkaline extraction and enzymatic (xylanase) treatment of bleached birch kraft pulp fibers indicated very selective hemicellulose removal, particularly xylan removal. Furthermore, these two hemicellulose-extracted birch kraft pulps were utilized in a pilot-scale papermaking environment in order to evaluate the upscalability of the extraction concepts. Investigations made using pilot paper machine trials revealed that some amount of alkalineextracted birch kraft pulp, with a 24.9% reduction in the total amount of xylan, could be used in the papermaking stock as a mixture with non-extracted pulp when producing 75 g/m2 paper. For xylanase-treated fibers there were no reductions in the mechanical properties of the 180 g/m2 paper produced compared to paper made from the control pulp, although there was a 14.2% reduction in the total amount of xylan in the xylanase-treated pulp compared to the control birch kraft pulp. This work emphasized the importance of the hemicellulose extraction method in providing new solutions to create functional fibers and in providing a valuable hemicellulose co-product stream. The hemicellulose removal concept therefore plays an important role in the integrated forest biorefinery scenario, where the target is to the co-production of hemicellulose-extracted pulp and hemicellulose-based chemicals or fuels.

Photodynamic therapy: a new concept in medical treatment

A new concept in the therapy of both neoplastic and non-neoplastic diseases is discussed in this article. Photodynamic therapy (PDT) involves light activation, in the presence of molecular oxygen, of certain dyes that are taken up by the target tissue. These dyes are termed photosensitizers. The mechanism of interaction of the photosensitizers and light is discussed, along with the effects produced in the target tissue. The present status of clinical PDT is discussed along with the newer photosensitizers being used and their clinical roles. Despite the promising results from earlier clinical trials of PDT, considerable additional work is needed to bring this new modality of treatment into modern clinical practice. Improvements in the area of light source delivery, light dosimetry and the computation of models of treatment are necessary to standardize treatments and ensure proper treatment delivery. Finally, quality assurance issues in the treatment process should be introduced.

Insulin secretion, insulin sensitivity, and hepatic insulin extraction in first-degree relatives of type 2 diabetic patients

To identify early metabolic abnormalities in type 2 diabetes mellitus, we measured insulin secretion, sensitivity to insulin, and hepatic insulin extraction in 48 healthy normal glucose-tolerant Brazilians, first-degree relatives of type 2 diabetic patients (FH+). Each individual was matched for sex, age, weight, and body fat distribution with a person without history of type 2 diabetes (FH-). Both groups were submitted to a hyperglycemic clamp procedure (180 mg/dl). Insulin release was evaluated in its two phases. The first was calculated as the sum of plasma insulin at 2.5, 5.0, 7.5, and 10.0 min after the beginning of glucose infusion, and the second as the mean plasma insulin level in the third hour of the clamp procedure. Insulin sensitivity index (ISI) was the mean glucose infusion rate in the third hour of the clamp experiment divided by the mean plasma insulin concentration during the same period of time. Hepatic insulin extraction was determined under fasting conditions and in the third hour of the clamp procedure as the ratio between C-peptide and plasma insulin levels. FH+ individuals did not differ from FH- individuals in terms of the following parameters [median (range)]: a) first-phase insulin secretion, 174 (116-221) vs 207 (108-277) µU/ml, b) second-phase insulin secretion, 64 (41-86) vs 53 (37-83) µU/ml, and c) ISI, 14.8 (9.0-20.8) vs 16.8 (9.0-27.0) mg kg-1 min-1/µU ml-1. Hepatic insulin extraction in FH+ subjects was similar to that of FH- ones at basal conditions (median, 0.27 vs 0.27 ng/µU) and during glucose infusion (0.15 vs 0.15 ng/µU). Normal glucose-tolerant Brazilian FH+ individuals well-matched with FH- ones did not show defects of insulin secretion, insulin sensitivity, or hepatic insulin extraction as tested by hyperglycemic clamp procedures.

Antioxidant status of dog aqueous humor after extracapsular lens extraction

We determined the antioxidant status of the aqueous humor after extracapsular lens extraction in 14 mongrel dogs weighing about 10 kg. The animals were examined by slit lamp biomicroscopy, applanation tonometry and indirect ophthalmoscopy. One eye was submitted to conventional extracapsular lens extraction and the other was used as control. Samples of aqueous humor were obtained by anterior chamber paracentesis before and at days 1, 2, 3, 7 and 15 after surgery. Total antioxidant status was determined as the capacity of aqueous humor to inhibit free radical generation by 2,2-azobis(2-amidopropane) chlorine. Ascorbic acid concentration was measured by HPLC with UV detection. Protein content was determined with the biuret reagent. Statistical analysis was performed by ANOVA followed by the Tukey-Kramer test. Protein concentration increased from 0.61 to 22 mg/ml 24 h after surgery. These levels were maintained and returned to normal at day 7. Total antioxidant capacity was reduced from 50 to about 30 min until day 3 and at day 7 it was equal to control. Ascorbic acid levels were reduced from 252 to about 110 µM and then returned to control values at day 15. Considering the importance of ascorbic acid concentration in aqueous humor for the maintenance of the antioxidant status of the anterior segment of the eye, the decrease of antioxidant defenses suggests that the surgical procedures promote an oxidative stress condition in the eye.