4-amine-2-mercaptopyrimidine modified silica gel applied in Cd(II) and Pb(II) extraction from an aqueous medium

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales

DNA-based studies have been one of the major interests in conservation biology of endangered species and in population genetics. As species and population genetic assessment requires a source of biological material, the sampling strategy can be overcome by non-destructive procedures for DNA isolation. An improved method for obtaining DNA from fish fins and scales with the use of an extraction buffer containing urea and further DNA purification with phenol-chloroform is described. The methodology combines the benefits of a non-destructive DNA sampling and its high efficiency. In addition, comparisons with other methodologies for isolating DNA from fish demonstrated that the present procedure also becomes a very attractive alternative to obtain large amounts of high-quality DNA for use in different molecular analyses. The DNA samples, isolated from different fish species, have been successfully used on random amplified polymorphic DNA (RAPD) experiments, as well as on amplification of specific ribosomal and mitochondrial DNA sequences. The present DNA extraction procedure represents an alternative for population approaches and genetic studies on rare or endangered taxa.

Improvement in RNA extraction from S. cerevisie by optimization in the autolysis and NH3 hydrolysis

The optimization of autolysis of Saccharomyces cerevisiae from brewery was studied aiming at the maximum ribonucleic acid extraction and yeast extract production. The best conditions for yeast autolysis was 55.2ºC, pH= 5.1 and 9.8% NaCl for 24h of processing, without the NH3 use. In these conditions, the RNA yield was 89.7%, resulting in 51.3% of dehydrated yeast extract with 57.9% protein. The use of 12.2% NH3 at 60ºC after autolysis (8h) and plasmolysis (8h) was not viable due to the reduction in the RNA yield from 89.7to78.4%. on the other hand, the thermal shock at 60ºC for 15 minutes prior to autolysis provided an increase in the yield from 89.7 to 91.4%. The autolysis, including NaCl plasmolysis in the optimized conditions was efficient, economic and with short time, thus usable for industrial purpose to obtain more valuable products such as yeast extract enriched in RNA and/or protein, for different applications.

Supercritical fluid extraction from fennel (Foeniculum vulgare): global yield, composition and kinetic data

Supercritical fluid extraction (SFE) from solids has proven to be technically feasible for almost any system; nonetheless, its economical viability has been proven for a restricted number of systems. A common practice is to compare the cost of manufacturing of vegetable extracts by a variety of techniques without deeply considering the huge differences in composition and functional properties among the various types of extracts obtained; under this circumstance, the cost of manufacturing do not favor SFE. Additionally, the influence of external parameters such as the agronomic conditions and the SFE system geometry are not considered. In the present work, these factors were studied for the system fennel seeds + CO2. The effects of the harvesting season and the degree of maturation on the global yields for the system fennel seeds + CO2 were analyzed at 300 bar and 40 degrees C. The effects of the pressure on the global yields were determined for the temperatures of 30 and 40 degrees C. Kinetics experiments were done for various ratios of bed height to bed diameter. Fennel extracts were also obtained by hydrodistillation and low-pressure solvent extraction. The chemical composition of the fennel extracts were determined by gas chromatography. The SFE maximum global yield (12.5%, dry basis) was obtained with dry harvested fennel seeds. Anethole and fenchone were the major constituents of the extract; the following fat acids palmitic (C16H32O2), palmitoleic stearic (C18H36O2), oleic (C18H34O2), linoleic (C18H32O2) and linolenic (C18H30O2) were also detected in the extracts. A relation between amounts of feed and solvent, bed height and diameter, and solvent flow rate was proposed. The models of Sovova, Goto et al. and Tan and Lion were capable of describing the mass transfer kinetics. (c) 2005 Elsevier B.V. All rights reserved.

Dynamic programming approach for road centerline extraction from digital images

This paper presents a dynamic programming approach for semi-automated road extraction from medium-and high-resolution images. This method is a modified version of a pre-existing dynamic programming method for road extraction from low-resolution images. The basic assumption of this pre-existing method is that roads manifest as lines in low-resolution images (pixel footprint> 2 m) and as such can be modeled and extracted as linear features. On the other hand, roads manifest as ribbon features in medium- and high-resolution images (pixel footprint ≤ 2 m) and, as a result, the focus of road extraction becomes the road centerlines. The original method can not accurately extract road centerlines from medium- and high- resolution images. In view of this, we propose a modification of the merit function of the original approach, which is carried out by a constraint function embedding road edge properties. Experimental results demonstrated the modified algorithm's potential in extracting road centerlines from medium- and high-resolution images.

Building roof contour extraction from LiDAR data

This paper proposes a method for the automatic extraction of building roof contours from a LiDAR-derived digital surface model (DSM). The method is based on two steps. First, to detect aboveground objects (buildings, trees, etc.), the DSM is segmented through a recursive splitting technique followed by a region merging process. Vectorization and polygonization are used to obtain polyline representations of the detected aboveground objects. Second, building roof contours are identified from among the aboveground objects by optimizing a Markov-random-field-based energy function that embodies roof contour attributes and spatial constraints. Preliminary results have shown that the proposed methodology works properly.

RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies

Abstract Background The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp. Results Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86–100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp. Conclusion All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.

Applying design of experiments (DOE) to flavonoid extraction from Passiflora alata and P. edulis

The Passifloraceae family is extensively used in native Brazilian folk medicine to treat a wide variety of diseases. The problem of flavonoid extraction from Passiflora was treated by application of design of experiments (DOE), as an experiment with mixture including one categorical process variable. The components of the binary mixture were: ethanol (component A) and water (component B); the categorical process variable: extraction method (factor C) was varied at two levels: (+1) maceration and (-1) percolation. ANOVA suggested a cubic model for P. edulis extraction and a quadratic model for P. alata.These results indicate that the proportion of components A and B in the mixture is the main factor involved in significantly increasing flavonoid extraction. In regard to the extraction methods, no important differences were observed, which indicates that these two traditional extraction methods could be effectively used to extract flavonoids from both medicinal plants. The evaluation of antioxidant activity of the extract by ORAC method showed that P. edulis displays twice as much antioxidant activity as P. alata. Considering that maceration is a simple, rapid and environmentally friendly extraction method, in this study, the optimized conditions for flavonoid extraction from these Passiflora species is maceration with 75% ethanol for P. edulis and 50% ethanol for P. alata.

Multicentre validation study of nucleic acids extraction from FFPE tissues

In most pathology laboratories worldwide, formalin-fixed paraffin embedded (FFPE) samples are the only tissue specimens available for routine diagnostics. Although commercial kits for diagnostic molecular pathology testing are becoming available, most of the current diagnostic tests are laboratory-based assays. Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, participating to the European FP6 program IMPACTS (www.impactsnetwork.eu), isolated nucleic acids from four diagnostic FFPE tissues using their routine methods, followed by quality assessment. The DNA-extraction protocols ranged from homemade protocols to commercial kits. Except for one homemade protocol, the majority gave comparable results in terms of the quality of the extracted DNA measured by the ability to amplify differently sized control gene fragments by PCR. For array-applications or tests that require an accurately determined DNA-input, we recommend using silica based adsorption columns for DNA recovery. For RNA extractions, the best results were obtained using chromatography column based commercial kits, which resulted in the highest quantity and best assayable RNA. Quality testing using RT-PCR gave successful amplification of 200 bp-250 bp PCR products from most tested tissues. Modifications of the proteinase-K digestion time led to better results, even when commercial kits were applied. The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories.