Extraction of polymeric galactoglucomannans from spruce wood by pressurized hot water

The major type of non-cellulosic polysaccharides (hemicelluloses) in softwoods, the partly acetylated galactoglucomannans (GGMs), which comprise about 15% of spruce wood, have attracted growing interest because of their potential to become high-value products with applications in many areas. The main objective of this work was to explore the possibilities to extract galactoglucomannans in native, polymeric form in high yield from spruce wood with pressurised hot-water, and to obtain a deeper understanding of the process chemistry involved. Spruce (Picea abies) chips and ground wood particles were extracted using an accelerated solvent extractor (ASE) in the temperature range 160 – 180°C. Detailed chemical analyses were done on both the water extracts and the wood residues. As much as 80 – 90% of the GGMs in spruce wood, i.e. about 13% based on the original wood, could be extracted from ground spruce wood with pure water at 170 – 180°C with an extraction time of 60 min. GGMs comprised about 75% of the extracted carbohydrates and about 60% of the total dissolved solids. Other substances in the water extracts were xylans, arabinogalactans, pectins, lignin and acetic acid. The yields from chips were only about 60% of that from ground wood. Both the GGMs and other non-cellulosic polysaccharides were extensively hydrolysed at severe extraction conditions when pH dropped to the level of 3.5. Addition of sodium bicarbonate increased the yields of polymeric GGMs at low additions, 2.5 – 5 mM, where the end pH remained around 3.9. However, at higher addition levels the yields decreased, mainly because the acetyl groups in GGMs were split off, leading to a low solubility of GGMs. Extraction with buffered water in the pH range 3.8 – 4.4 gave similar yields as with plain water, but gave a higher yield of polymeric GGMs. Moreover, at these pH levels the hydrolysis of acetyl groups in GGMs was significantly inhibited. It was concluded that hot-water extraction of polymeric GGMs in good yields (up to 8% of wood) demands appropriate control of pH, in a narrow range about 4. These results were supported by a study of hydrolysis of GGM at constant pH in the range of 3.8 – 4.2 where a kinetic model for degradation of GGM was developed. The influence of wood particle size on hot-water extraction was studied with particles in the range of 0.1 – 2 mm. The smallest particles (< 0.1 mm) gave 20 – 40% higher total yield than the coarsest particles (1.25 – 2 mm). The difference was greatest at short extraction times. The results indicated that extraction of GGMs and other polysaccharides is limited mainly by the mass transfer in the fibre wall, and for coarse wood particles also in the wood matrix. Spruce sapwood, heartwood and thermomechnical pulp were also compared, but only small differences in yields and composition of extracts were found. Two methods for isolation and purification of polymeric GGMs, i.e. membrane filtration and precipitation in ethanol-water, were compared. Filtration through a series of membranes with different pore sizes separated GGMs of different molar masses, from polymers to oligomers. Polysaccharides with molar mass higher than 4 kDa were precipitated in ethanol-water. GGMs comprised about 80% of the precipitated polysaccharides. Other polysaccharides were mainly arabinoglucuronoxylans and pectins. The ethanol-precipitated GGMs were by 13C NMR spectroscopy verified to be very similar to GGMs extracted from spruce wood in low yield at a much lower temperature, 90°C. The obtained large body of experimental data could be utilised for further kinetic and economic calculations to optimise technical hot-water extractionof softwoods.

Long-term nutrient load management and lake restoration: Case of Säkylän Pyhäjärvi (SW Finland)

Eutrophication caused by anthropogenic nutrient pollution has become one of the most severe threats to water bodies. Nutrients enter water bodies from atmospheric precipitation, industrial and domestic wastewaters and surface runoff from agricultural and forest areas. As point pollution has been significantly reduced in developed countries in recent decades, agricultural non-point sources have been increasingly identified as the largest source of nutrient loading in water bodies. In this study, Lake Säkylän Pyhäjärvi and its catchment are studied as an example of a long-term, voluntary-based, co-operative model of lake and catchment management. Lake Pyhäjärvi is located in the centre of an intensive agricultural area in southwestern Finland. More than 20 professional fishermen operate in the lake area, and the lake is used as a drinking water source and for various recreational activities. Lake Pyhäjärvi is a good example of a large and shallow lake that suffers from eutrophication and is subject to measures to improve this undesired state under changing conditions. Climate change is one of the most important challenges faced by Lake Pyhäjärvi and other water bodies. The results show that climatic variation affects the amounts of runoff and nutrient loading and their timing during the year. The findings from the study area concerning warm winters and their influences on nutrient loading are in accordance with the IPCC scenarios of future climate change. In addition to nutrient reduction measures, the restoration of food chains (biomanipulation) is a key method in water quality management. The food-web structure in Lake Pyhäjärvi has, however, become disturbed due to mild winters, short ice cover and low fish catch. Ice cover that enables winter seining is extremely important to the water quality and ecosystem of Lake Pyhäjärvi, as the vendace stock is one of the key factors affecting the food web and the state of the lake. New methods for the reduction of nutrient loading and the treatment of runoff waters from agriculture, such as sand filters, were tested in field conditions. The results confirm that the filter technique is an applicable method for nutrient reduction, but further development is needed. The ability of sand filters to absorb nutrients can be improved with nutrient binding compounds, such as lime. Long-term hydrological, chemical and biological research and monitoring data on Lake Pyhäjärvi and its catchment provide a basis for water protection measures and improve our understanding of the complicated physical, chemical and biological interactions between the terrestrial and aquatic realms. In addition to measurements carried out in field conditions, Lake Pyhäjärvi and its catchment were studied using various modelling methods. In the calibration and validation of models, long-term and wide-ranging time series data proved to be valuable. Collaboration between researchers, modellers and local water managers further improves the reliability and usefulness of models. Lake Pyhäjärvi and its catchment can also be regarded as a good research laboratory from the point of view of the Baltic Sea. The main problem in both of them is eutrophication caused by excess nutrients, and nutrient loading has to be reduced – especially from agriculture. Mitigation measures are also similar in both cases.

Growth and nutrient concentration in coffee root system under weed species competition

The effects of competition of six weed species on growth, nutrient concentration and nutrient content of coffee plant root system under greenhouse conditions were evaluated. Thirty days after coffee seedling transplantation into 12 L pots with soil level area of 6.5 dm². Weeds were transplanted or sowed in these pots, at densities of 0, 1, 2, 3, 4 and 5 plants per pot. The duration of competition (or weedy periods) from weed transplantation or emergence until plant harvesting, at the weed preflowering stage, were (in days): 77 (Bidens pilosa), 180 (Commelina diffusa), 82 (Leonurus sibiricus), 68 (Nicandra physaloides), 148 (Richardia brasiliensis) and 133 (Sida rhombifolia). Dry matter of coffee plants was linearly reduced with increasing B. pilosa and S. rhombifolia density, with pronounced effect of B. pilosa. C. diffusa was the only weed species whose increasing density in the pots did not diminish crop root dry matter. L. sibiricus, N. physaloides and R. brasiliensis reduced root dry matter of coffee plants by 75, 52 and 47%, respectively, as compared to the weed-free treatment, regardless of weed density. Under competition, even though weed species showed lower macronutrient concentration in the roots (except for P), they accumulated 4.2 (N), 12.3 (P), 4.3 (K), 5.5 (Ca), 7.6 (Mg) and 4.4 (S) times more nutrients in the roots than the coffee plants. Crop and weed nutrient concentration, as well as competition degrees greatly varied depending on both weed species and densities.

Weed control under integrated nutrient management systems in faba bean (Vicia faba) production in Egypt

Two field experiments were conducted in two successive seasons, 2005/2006 and 2006/2007, to determine whether management can improve faba bean competitiveness with weeds, thus helping to achieve its yield potential. The experiment included five treatments, composed of organic and mineral fertilizers, alone and mixed at different rates, along with a control and six weed control treatments, including oxadiargyl, prometryn, hand hoeing treatments alone or mixed with the herbicides, and a nonweeded treatment (control).The herbicide treatments were not superior to the two hand-hoeing treatments. Using compost favored growth and yield of faba bean more than of weeds. Adding fertilizer also improved most yield parameters. Application of compost alone or combined with 50 or 100% of the recommended NPK rate improved faba bean growth in terms of net assimilation rate, specific leaf area, and leaf weight ratio as components of relative growth rate. This improvement in growth resulted in increase of seed yield, yield components and protein of faba bean. Faba bean yield performance improved under interactive fertilizer effects and weed control treatments as growth improved, as a result of nutrient release from fertilizers and weed control.

Microwave-assisted solvent extraction and analysis of shikimic acid from plant tissues

A better method for determination of shikimate in plant tissues is needed to monitor exposure of plants to the herbicide glyphosate [N-(phosphonomethyl)glycine] and to screen the plant kingdom for high levels of this valuable phytochemical precursor to the pharmaceutical oseltamivir. A simple, rapid, and efficient method using microwave-assisted extraction (MWAE) with water as the extraction solvent was developed for the determination of shikimic acid in plant tissues. High performance liquid chromatography was used for the separation of shikimic acid, and chromatographic data were acquired using photodiode array detection. This MWAE technique was successful in recovering shikimic acid from a series of fortified plant tissues at more than 90% efficiency with an interference-free chromatogram. This allowed the use of lower amounts of reagents and organic solvents, reducing the use of toxic and/or hazardous chemicals, as compared to currently used methodologies. The method was used to determine the level of endogenous shikimic acid in several species of Brachiaria and sugarcane (Saccharum officinarum) and on B. decumbens and soybean (Glycine max) after treatment with glyphosate. The method was sensitive, rapid and reliable in all cases.

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.

Response of Dalbergia miscolobium Benth. seedlings, a cerrado tree species, to mineral nutrient supply

(Response of Dalbergia miscolobium Benth. seedlings, a cerrado tree species, to a mineral nutrient supply). The soil under the Brazilian cerrado vegetation is very poor in nutrients. The aim of this study was to investigate the effect of the addition of a nutrient solution in the early growth of D. miscolobium, a typical cerrado tree species, cultivated in cerrado soil. Seeds were germinated in Petri dishes and seven-day old seedlings were transfered to pots containing cerrado soil. These were supplied once a week with a normal, 1/2 or 1/10 strength nutrient solution. Four growth analysis were done over a period of 145 days from seed imbibition, in terms of dry mass, leaf area and carbohydrate and nitrogen contents. Other derived parameters were also analysed. The addition of a nutrient solution promoted early growth with a preferential separation of dry matter towards the tops; in the control seedlings (no nutrient addition) more dry matter accumulated in the root system. This suggests a preferential investment in root growth in poor soils such as the cerrado ones. Reliable evidence of this is given by the level of carbohydrate and protein which was higher in the roots than in the tops of plants growing in cerrado soil without the addition of nutrients.

Litterfall and litter nutrient content in two Brazilian Tropical Forests

Litterfall and transfer of nutrients was estimated in two tropical coastal forests of Brazil - the Atlantic and the Restinga Forests at Cardoso Island, São Paulo. Samples were collected monthly, from June 1990 to May 1991, using thirty 0.25 m2 traps. There were significant differences in litter production between the Atlantic Forest (6.3 t.ha-1.year-1) and the Restinga Forest (3.9 t.ha-1.year-1). Litterfall was continuous throughout the year with maximum in the beginning of the rainy season in both sites. The annual return of mineral elements through litter in the Atlantic Forest was (kg.ha-1): 101.8 N, 3.8 P, 20.3 K, 60.0 Ca, 18.0 Mg, and 14.6 S and in the Restinga Forest was: 27.5 N, 1.0 P, 6.5 K, 30.0 Ca, 10.9 Mg, and 6.6 S. The return, although small, is relevant due to the low fertility of the soils in those ecosystems, especially in Restinga. The Restinga Forest seems to be an ecosystem well adapted to oligotrophic conditions, lying among those presenting higher nutrient use efficiency.

Nutrient cycling disturbance in Atlantic Forest sites affected by air pollution coming from the industrial complex of Cubatão, Southeast Brazil

Several aspects of nutrient cycling were studied at two sites of Atlantic Forest, in São Paulo State, Southeast Brazil (23o46’ S; 46o18’ W), which exhibited different degrees of forest structure decline caused by the air pollution emitted by the industrial complex of Cubatão, being referred here as the most and least affected sites (MAS and LAS, respectively). These investigations were developed during 1984 - 1986, a period in which the most severe negative effects of air pollution could be observed. Concentrations and amounts of N, P, K, Ca, Mg and S in four ecosystem compartments (leaves, litter layer, soil and roots) and in rainfall, throughfall and litterfall are briefly presented. At each site, the content of mineral elements generally decreased from leaves to litterfall and litter layer on the forest floor. Soil surface layer (0 - 5 cm) in both sites was the richest in mineral elements. Soil fertility was greater at LAS. In general, nutrient amounts remaining in the compartments and cycling through the ecosystem were greater at LAS as well, which could be due to the higher complexity of the forest structure at this site. Rainfall contributed more to soil inputs of K, Ca, Mg and S than litterfall at both sites. The nutrient residence times in the litter layer were higher and the index of nutrient use efficiency was lower at the most affected site. It was concluded that nutrient cycling was disturbed by air pollution at both sites, but to a greater extent at MAS. The main consequences of the air pollution stress were detected in the flux of nutrients through litterfall and in the litter layer on the forest floor.

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.

Effects of nutrient impoverishment on phytoplankton biomass: a mesocosms experimental approach in a shallow eutrophic reservoir (Garças Pond), São Paulo, southeast Brazil

Nutrient impoverishment in mesocosms was carried out in a shallow eutrophic reservoir aiming to evaluate the nutrient removal technique as a method for eutrophication reduction. Garças Pond is located in the Parque Estadual das Fontes do Ipiranga Biological Reserve situated in the southeast region of the municipality of São Paulo. Three different treatments were designed, each consisting of two enclosures containing 360 liters of water each. Mesocosms were made of polyethylene bags and PVC pipes, and were attached to the lake bottom. Treatment dilutions followed Carlson's trophic state index modified by Toledo and collaborators, constituting the oligotrophic, mesotrophic, and eutrophic treatments. Ten abiotic and 9 biological samplings were carried out simultaneously. Trophic states previously calculated for the treatments were kept unaltered during the entire experiment period, except for the mesotrophic mesocosms in which TP reached oligotrophic concentrations on the 31st day of the experiment. In all three treatments a reduction of DO was observed during the study period. At the same time, NH4+ and free CO2 rose, indicating decomposition within the enclosures. Nutrient impoverishment caused P limitation in all three treatments during most of the experiment period. Reduction of algal density, chlorophyll a, and phaeophytin was observed in all treatments. Competition for nutrients led to changes in phytoplankton composition. Once isolated and diluted, the mesocosms' trophic state did not change. This led to the conclusion that isolation of the allochthonous sources of nutrients is the first step for the recovery of the Garças Pond.

Effectiveness of plant growth promoting rhizobacteria in facilitating lead and nutrient uptake by little seed canary grass

We investigated the effectiveness of Nitroxin inoculation on lead (Pb) and nutrient uptakes by little seed canary grass. The factors tested included inoculation (or not) with Nitroxin and different soil concentrations of Pb (0, 200, 400 and 800mgPbkg-1 soil). Increasing soil concentrations of Pb decreased stem, leaf and root dry weights. Shoot phosphorus concentrations increased in parallel with increasing soil Pb concentrations. Nitroxin inoculation did not alter the phosphorus concentration of the roots. The Pb translocation factor was >1 in inoculated treatments in the Pb soil concentration range of 200 to 400mgkg-1; the translocation factor for 800mgPbkg‑1 with no inoculation of Nitroxin was, however, <1. Our results indicated that the Pb bioaccumulation factor for little seed canary grass was <1, indicating that it is a Pb excluding plant.

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

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.