João Fernandes - Academia.edu (original) (raw)

Papers by João Fernandes

Research paper thumbnail of Diterpenes from Guarea trichilioides

Phytochemistry, 1996

Chemical investigation of the leaves of Guarea trichilioides afforded six diterpenoids, including... more Chemical investigation of the leaves of Guarea trichilioides afforded six diterpenoids, including four labdane and two clerodane derivatives. The following four are new: 3-oxolabd-8 (17), 12Z, 14-triene, 3α-hydroxylabd-8 (17), 12Z, 14-triene, 3β-hydroxylabd-8 (17), 12Z, ...

Research paper thumbnail of Polishable and Renewable DNA Hybridization Biosensors

Analytical Chemistry, 1998

Routine applications of DNA hybridization biosensors are often restricted by the need for regener... more Routine applications of DNA hybridization biosensors are often restricted by the need for regenerating the single-stranded (ss) probe for subsequent reuse. This note reports on a viable alternative to prolonged thermal or chemical regeneration schemes through the mechanical polishing of oligonucleotide-bulk-modified carbon composite electrodes. The surface of these biocomposite hybridization biosensors can be renewed rapidly and reproducibly by a simple extrusion/polishing protocol. The immobilized probe retains its hybridization activity on confinement in the interior of the carbon paste matrix, with the use of fresh surfaces erasing memory effects and restoring the original target response, to allow numerous hybridization/measurement cycles. We expect that such reusable nucleic acid modified composite electrodes can be designed for a wide variety of biosensing applications.

Research paper thumbnail of Interactions of antitumor drug daunomycin with DNA in solution and at the surface

Bioelectrochemistry and Bioenergetics, 1998

The interaction of the antitumor drug daunomycin with double-stranded ds calf thymus DNA was stud... more The interaction of the antitumor drug daunomycin with double-stranded ds calf thymus DNA was studied in solution and at the Ž . electrode surface by means of cyclic voltammetry and particularly by constant-current chronopotentiometric stripping analysis CPSA Ž . with the carbon paste electrodes CPE . As a result of intercalation of this drug between the base pairs in dsDNA, the CPSA daunomycin peak d decreased and a new more positive shoulder d appeared. This shoulder was attributed to the oxidation of the drug intercalated in b Ž . DNA. Under the same conditions almost no changes in the DNA peak G due to oxidation of guanine residues were observed. It was ox Ž . shown that daunomycin adheres strongly to the bare CPE resisting washing so that a daunomycin-modified electrode can be easily prepared. Daunomycin immobilized at CPE interacted with DNA on immersion of the modified electrode into the dsDNA solution, Ž showing a decrease of peak d and a well-separated peak d instead of the shoulder which resulted from the interaction of DNA with b . daunomycin in solution . When the DNA-modified CPE was immersed into a daunomycin solution the peak G increased in dependence ox on daunomycin concentration or on the time of interaction of daunomycin with dsDNA at the electrode surface. Such changes in peak G ox were observed only at submicromolar concentrations of daunomycin. At higher daunomycin concentrations or at longer interaction time intervals a daunomycin peak appeared, which was substantially smaller and more positive than the peak of free daunomycin. The increase of the DNA peak G was attributed to interaction of daunomycin from the side of the DNA double helix not contacting the electrode ox surface. Such binding may induce changes in the DNA structure including bending of the DNA molecule which may result in the increase of peak G . Our results thus suggest that the interaction of daunomycin with DNA anchored at the surface may significantly differ from ox that with DNA in solution. The prospects of using of electroanalytical methods in studies of DNA-drug interactions are discussed. q 1998 Elsevier Science S.A.

Research paper thumbnail of Mismatch-Sensitive Hybridization Detection by Peptide Nucleic Acids Immobilized on a Quartz Crystal Microbalance

Analytical Chemistry, 1997

A quartz crystal microbalance DNA hybridization biosensor, based on thiol-derivatized peptide nuc... more A quartz crystal microbalance DNA hybridization biosensor, based on thiol-derivatized peptide nucleic acid (PNA) probes, offers unusual in situ differentiation of single-base mismatches. A large excess of a single-base mismatch oligonucleotide has no effect on the frequency response of the target. Such remarkable distinction between perfect matches and mismatches is illustrated by the detection of a common mutation in the p53 gene. The greater specificity of the new mass-sensitive indicatorless hybridization device over those of analogous PNA-based carbon electrodes is attributed to the formation of a PNA monolayer and the use of a hydrophilic ethylene glycol linker. The improved specificity is coupled to very fast (3-5 min) hybridization in a low-ionic-strength medium.

Research paper thumbnail of Indicator-free electrochemical DNA hybridization biosensor

Analytica Chimica Acta, 1998

A new electrochemical hybridization biosensor protocol without an external indicator is described... more A new electrochemical hybridization biosensor protocol without an external indicator is described. The biosensor format involves the immobilization of inosine-substituted (guanine-free) probe onto the carbon paste transducer, and a direct chronopotentiometric detection of the duplex formation by the appearance of the guanine oxidation peak of the target. Such a use of the intrinsic DNA electrochemical response for monitoring hybridization events offers several advantages (over the common use of external indicators), including the appearance of a new peak, a¯at background, or simplicity. A 4 min short hybridization period allows a detection limit around 120 ng/ml. Performance characteristics of the sensor are described along with future prospects. #

Research paper thumbnail of Toxicity of sesame extracts to the symbiotic fungus of leaf-cutting ants

Bulletin of Entomological Research, 1990

Page 1. Bulletin of Entomological Research (1990) 80,349-352 349 Toxicity of sesame extracts to t... more Page 1. Bulletin of Entomological Research (1990) 80,349-352 349 Toxicity of sesame extracts to the symbiotic fungus of leaf-cutting ants Fernando Carlos Pagnocca Osvaldo Aulino da Silva Maria Jose Hebling-Beraldo Odair Correa Bueno ...

Research paper thumbnail of Dimethylchromene rotenoids from Tephrosia candida

Phytochemistry, 1997

The hexane and ethyl acetate extracts of roots of Tephrosia candida afforded a new rotenoid, 12ah... more The hexane and ethyl acetate extracts of roots of Tephrosia candida afforded a new rotenoid, 12ahydroxy-fl-toxicarol, together with a series of known ones, identified as: deguelin, c~-toxicarol, tephrosin, 6a, 12adehydrodeguelin, 12a-hydroxy-c~-toxicarol, 6a,12a-dehydro-c~-toxicarol and 6a,12a-dehydro-fl-toxicarol. The possibility of four of these rotenoids to be linear or angular is discussed on the basis of HMBC experiments. Angular rotenoids are very common, however the linear are restricted, and to the best of our knowledge only two linear dimethylchromene rotenoids are described in the literature. © 1997 Elsevier Science Ltd r 5r

Research paper thumbnail of Pyrano chalcones and a flavone from Neoraputia magnifica and their Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase-inhibitory activities

Phytochemistry, 2000

The fruits of Neoraptua magnifica var. magnifica afforded three new flavonoids: 2'-hydrox... more The fruits of Neoraptua magnifica var. magnifica afforded three new flavonoids: 2'-hydroxy-4,4',-dimethoxy-5',6'-(2'',2''-dimethylpyrano)chalcone, 2'-hydroxy-3,4,4'-trimethoxy-5',6'-(2'',2''-dimethylpyrano)chalcone, and 3',4'-methylenedioxy-5,7-dimethoxyflavone which were identified on the basis of spectroscopic methods. The known flavonoids 2'-hydroxy-3,4,4',5-tetramethoxy-5',6'-(2'',2''-dimethylpyrano)chalcone, 2'-hydroxy-3,4,4',5,6'-pentamethoxychalcone, 3',4'-methylenedioxy-5,6,7-trimethoxyflavone, 3',4'-methylenedioxy-5',5,6,7-tetramethoxyflavone, 3',4',5',5,7-pentamethoxyflavanone and 3',4',5'5,7-pentamethoxyflavone were also identified. The latter flavone was the most active as glyceraldehyde-3-phosphate dehydrogenase-inhibitor.

Research paper thumbnail of Limonoids from leaves of Khaya senegalensis

Phytochemistry, 1997

The leaves of Khaya senegalensis yielded two new limonoids. These compounds were identified on th... more The leaves of Khaya senegalensis yielded two new limonoids. These compounds were identified on the basis of spectroscopic analysis as methyl lct-acetoxy-3fl,6,8ct-trihydroxy-2ct-methoxy-2fl,1413-epoxy-[4.2.1 t°'3°.l ~'4]-tricyclomeliac-7-oate and methyl l~-acetoxy-6,8ct,14fl,30fl-tetrahydroxy-3-oxo [3.3.1 J0.2.1~,4]. tricyclomeliac-7-oate. Scopoletin, fl-quercitrin and rutin were also isolated.

Research paper thumbnail of Towards a catalog of aspect-oriented refactorings

In this paper, we present a collection of aspect-oriented refactorings covering both the extracti... more In this paper, we present a collection of aspect-oriented refactorings covering both the extraction of aspects from objectoriented legacy code and the subsequent tidying up of the resulting aspects. In some cases, this tidying up entails the replacement of the original implementation with a different, centralized design, made possible by modularization. The collection of refactorings includes the extraction of common code in various aspects into abstract superaspects. We review the traditional object-oriented code smells in the light of aspectorientation and propose some new smells for the detection of crosscutting concerns. In addition, we propose a new code smell that is specific to aspects.

Research paper thumbnail of Object-to-Aspect Refactorings for Feature Extraction

This report describes an experiment in using AspectJ to extract a feature from a Java code base i... more This report describes an experiment in using AspectJ to extract a feature from a Java code base in order to make it unpluggable. We describe issues and obstacles encountered while performing a series of code transformations and next present a collection of manual aspect-oriented refactorings, based on the experience gained in the process. These are described in detail and compounded with a self-contained example placing each refactoring in its proper context.

Research paper thumbnail of Towards a Catalogue of Refactorings and Code Smells for AspectJ

In this paper, we contribute to the characterisation of a programming style specific to aspect-or... more In this paper, we contribute to the characterisation of a programming style specific to aspect-oriented programming. For this purpose, we present a collection of refactorings for aspect-oriented source code, comprising refactorings to enable extraction to aspects of crosscutting concerns from object-oriented legacy code, the subsequent tidying up of the extracted aspects and factoring out of common code from similar aspects to superaspects. The second group of refactorings is documented in detail. In addition, we propose some new aspect-oriented code smells, including one smell that is specific to aspect modules. We also propose a reinterpretation of some of the traditional object-oriented code smells in the light of aspect-orientation, to detect the presence of crosscutting concerns.

Research paper thumbnail of Diterpenes from Guarea trichilioides

Phytochemistry, 1996

Chemical investigation of the leaves of Guarea trichilioides afforded six diterpenoids, including... more Chemical investigation of the leaves of Guarea trichilioides afforded six diterpenoids, including four labdane and two clerodane derivatives. The following four are new: 3-oxolabd-8 (17), 12Z, 14-triene, 3α-hydroxylabd-8 (17), 12Z, 14-triene, 3β-hydroxylabd-8 (17), 12Z, ...

Research paper thumbnail of Polishable and Renewable DNA Hybridization Biosensors

Analytical Chemistry, 1998

Routine applications of DNA hybridization biosensors are often restricted by the need for regener... more Routine applications of DNA hybridization biosensors are often restricted by the need for regenerating the single-stranded (ss) probe for subsequent reuse. This note reports on a viable alternative to prolonged thermal or chemical regeneration schemes through the mechanical polishing of oligonucleotide-bulk-modified carbon composite electrodes. The surface of these biocomposite hybridization biosensors can be renewed rapidly and reproducibly by a simple extrusion/polishing protocol. The immobilized probe retains its hybridization activity on confinement in the interior of the carbon paste matrix, with the use of fresh surfaces erasing memory effects and restoring the original target response, to allow numerous hybridization/measurement cycles. We expect that such reusable nucleic acid modified composite electrodes can be designed for a wide variety of biosensing applications.

Research paper thumbnail of Interactions of antitumor drug daunomycin with DNA in solution and at the surface

Bioelectrochemistry and Bioenergetics, 1998

The interaction of the antitumor drug daunomycin with double-stranded ds calf thymus DNA was stud... more The interaction of the antitumor drug daunomycin with double-stranded ds calf thymus DNA was studied in solution and at the Ž . electrode surface by means of cyclic voltammetry and particularly by constant-current chronopotentiometric stripping analysis CPSA Ž . with the carbon paste electrodes CPE . As a result of intercalation of this drug between the base pairs in dsDNA, the CPSA daunomycin peak d decreased and a new more positive shoulder d appeared. This shoulder was attributed to the oxidation of the drug intercalated in b Ž . DNA. Under the same conditions almost no changes in the DNA peak G due to oxidation of guanine residues were observed. It was ox Ž . shown that daunomycin adheres strongly to the bare CPE resisting washing so that a daunomycin-modified electrode can be easily prepared. Daunomycin immobilized at CPE interacted with DNA on immersion of the modified electrode into the dsDNA solution, Ž showing a decrease of peak d and a well-separated peak d instead of the shoulder which resulted from the interaction of DNA with b . daunomycin in solution . When the DNA-modified CPE was immersed into a daunomycin solution the peak G increased in dependence ox on daunomycin concentration or on the time of interaction of daunomycin with dsDNA at the electrode surface. Such changes in peak G ox were observed only at submicromolar concentrations of daunomycin. At higher daunomycin concentrations or at longer interaction time intervals a daunomycin peak appeared, which was substantially smaller and more positive than the peak of free daunomycin. The increase of the DNA peak G was attributed to interaction of daunomycin from the side of the DNA double helix not contacting the electrode ox surface. Such binding may induce changes in the DNA structure including bending of the DNA molecule which may result in the increase of peak G . Our results thus suggest that the interaction of daunomycin with DNA anchored at the surface may significantly differ from ox that with DNA in solution. The prospects of using of electroanalytical methods in studies of DNA-drug interactions are discussed. q 1998 Elsevier Science S.A.

Research paper thumbnail of Mismatch-Sensitive Hybridization Detection by Peptide Nucleic Acids Immobilized on a Quartz Crystal Microbalance

Analytical Chemistry, 1997

A quartz crystal microbalance DNA hybridization biosensor, based on thiol-derivatized peptide nuc... more A quartz crystal microbalance DNA hybridization biosensor, based on thiol-derivatized peptide nucleic acid (PNA) probes, offers unusual in situ differentiation of single-base mismatches. A large excess of a single-base mismatch oligonucleotide has no effect on the frequency response of the target. Such remarkable distinction between perfect matches and mismatches is illustrated by the detection of a common mutation in the p53 gene. The greater specificity of the new mass-sensitive indicatorless hybridization device over those of analogous PNA-based carbon electrodes is attributed to the formation of a PNA monolayer and the use of a hydrophilic ethylene glycol linker. The improved specificity is coupled to very fast (3-5 min) hybridization in a low-ionic-strength medium.

Research paper thumbnail of Indicator-free electrochemical DNA hybridization biosensor

Analytica Chimica Acta, 1998

A new electrochemical hybridization biosensor protocol without an external indicator is described... more A new electrochemical hybridization biosensor protocol without an external indicator is described. The biosensor format involves the immobilization of inosine-substituted (guanine-free) probe onto the carbon paste transducer, and a direct chronopotentiometric detection of the duplex formation by the appearance of the guanine oxidation peak of the target. Such a use of the intrinsic DNA electrochemical response for monitoring hybridization events offers several advantages (over the common use of external indicators), including the appearance of a new peak, a¯at background, or simplicity. A 4 min short hybridization period allows a detection limit around 120 ng/ml. Performance characteristics of the sensor are described along with future prospects. #

Research paper thumbnail of Toxicity of sesame extracts to the symbiotic fungus of leaf-cutting ants

Bulletin of Entomological Research, 1990

Page 1. Bulletin of Entomological Research (1990) 80,349-352 349 Toxicity of sesame extracts to t... more Page 1. Bulletin of Entomological Research (1990) 80,349-352 349 Toxicity of sesame extracts to the symbiotic fungus of leaf-cutting ants Fernando Carlos Pagnocca Osvaldo Aulino da Silva Maria Jose Hebling-Beraldo Odair Correa Bueno ...

Research paper thumbnail of Dimethylchromene rotenoids from Tephrosia candida

Phytochemistry, 1997

The hexane and ethyl acetate extracts of roots of Tephrosia candida afforded a new rotenoid, 12ah... more The hexane and ethyl acetate extracts of roots of Tephrosia candida afforded a new rotenoid, 12ahydroxy-fl-toxicarol, together with a series of known ones, identified as: deguelin, c~-toxicarol, tephrosin, 6a, 12adehydrodeguelin, 12a-hydroxy-c~-toxicarol, 6a,12a-dehydro-c~-toxicarol and 6a,12a-dehydro-fl-toxicarol. The possibility of four of these rotenoids to be linear or angular is discussed on the basis of HMBC experiments. Angular rotenoids are very common, however the linear are restricted, and to the best of our knowledge only two linear dimethylchromene rotenoids are described in the literature. © 1997 Elsevier Science Ltd r 5r

Research paper thumbnail of Pyrano chalcones and a flavone from Neoraputia magnifica and their Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase-inhibitory activities

Phytochemistry, 2000

The fruits of Neoraptua magnifica var. magnifica afforded three new flavonoids: 2'-hydrox... more The fruits of Neoraptua magnifica var. magnifica afforded three new flavonoids: 2'-hydroxy-4,4',-dimethoxy-5',6'-(2'',2''-dimethylpyrano)chalcone, 2'-hydroxy-3,4,4'-trimethoxy-5',6'-(2'',2''-dimethylpyrano)chalcone, and 3',4'-methylenedioxy-5,7-dimethoxyflavone which were identified on the basis of spectroscopic methods. The known flavonoids 2'-hydroxy-3,4,4',5-tetramethoxy-5',6'-(2'',2''-dimethylpyrano)chalcone, 2'-hydroxy-3,4,4',5,6'-pentamethoxychalcone, 3',4'-methylenedioxy-5,6,7-trimethoxyflavone, 3',4'-methylenedioxy-5',5,6,7-tetramethoxyflavone, 3',4',5',5,7-pentamethoxyflavanone and 3',4',5'5,7-pentamethoxyflavone were also identified. The latter flavone was the most active as glyceraldehyde-3-phosphate dehydrogenase-inhibitor.

Research paper thumbnail of Limonoids from leaves of Khaya senegalensis

Phytochemistry, 1997

The leaves of Khaya senegalensis yielded two new limonoids. These compounds were identified on th... more The leaves of Khaya senegalensis yielded two new limonoids. These compounds were identified on the basis of spectroscopic analysis as methyl lct-acetoxy-3fl,6,8ct-trihydroxy-2ct-methoxy-2fl,1413-epoxy-[4.2.1 t°'3°.l ~'4]-tricyclomeliac-7-oate and methyl l~-acetoxy-6,8ct,14fl,30fl-tetrahydroxy-3-oxo [3.3.1 J0.2.1~,4]. tricyclomeliac-7-oate. Scopoletin, fl-quercitrin and rutin were also isolated.

Research paper thumbnail of Towards a catalog of aspect-oriented refactorings

In this paper, we present a collection of aspect-oriented refactorings covering both the extracti... more In this paper, we present a collection of aspect-oriented refactorings covering both the extraction of aspects from objectoriented legacy code and the subsequent tidying up of the resulting aspects. In some cases, this tidying up entails the replacement of the original implementation with a different, centralized design, made possible by modularization. The collection of refactorings includes the extraction of common code in various aspects into abstract superaspects. We review the traditional object-oriented code smells in the light of aspectorientation and propose some new smells for the detection of crosscutting concerns. In addition, we propose a new code smell that is specific to aspects.

Research paper thumbnail of Object-to-Aspect Refactorings for Feature Extraction

This report describes an experiment in using AspectJ to extract a feature from a Java code base i... more This report describes an experiment in using AspectJ to extract a feature from a Java code base in order to make it unpluggable. We describe issues and obstacles encountered while performing a series of code transformations and next present a collection of manual aspect-oriented refactorings, based on the experience gained in the process. These are described in detail and compounded with a self-contained example placing each refactoring in its proper context.

Research paper thumbnail of Towards a Catalogue of Refactorings and Code Smells for AspectJ

In this paper, we contribute to the characterisation of a programming style specific to aspect-or... more In this paper, we contribute to the characterisation of a programming style specific to aspect-oriented programming. For this purpose, we present a collection of refactorings for aspect-oriented source code, comprising refactorings to enable extraction to aspects of crosscutting concerns from object-oriented legacy code, the subsequent tidying up of the extracted aspects and factoring out of common code from similar aspects to superaspects. The second group of refactorings is documented in detail. In addition, we propose some new aspect-oriented code smells, including one smell that is specific to aspect modules. We also propose a reinterpretation of some of the traditional object-oriented code smells in the light of aspect-orientation, to detect the presence of crosscutting concerns.