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Papers by Douglas Cancherini

Research paper thumbnail of PROCEEDINGS Open Access The role of exon shuffling in shaping protein-protein interaction networks

Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function ... more Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results: We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners) in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multipl...

Research paper thumbnail of ATP-sensitive K+ channels in renal mitochondria

American journal of physiology. Renal physiology, 2003

Isolated kidney mitochondria swell when incubated in hyposmotic solutions containing K+ salts in ... more Isolated kidney mitochondria swell when incubated in hyposmotic solutions containing K+ salts in a manner inhibited by ATP, ADP, 5-hydroxydecanoate, and glibenclamide and stimulated by GTP and diazoxide. These results suggest the existence of ATP-sensitive K+ channels in these mitochondria, similar to those previously described in heart, liver, and brain. Renal mitochondrial ATP-sensitive K+ uptake rates are approximately 140 nmol.min-1.mg protein-1. This K+ transport results in a slight increase in respiration and decrease in the inner membrane potential. In addition, the activation of ATP-inhibited K+ uptake using diazoxide leads to a decrease of ATP hydrolysis through the reverse activity of the F0F1 ATP synthase when respiration is inhibited. In conclusion, we characterize an ATP-sensitive K+ transport pathway in kidney mitochondria that affects volume, respiration, and membrane potential and may have a role in the prevention of mitochondrial ATP hydrolysis.

Research paper thumbnail of Evolutionary history of exon shuffling

Research paper thumbnail of The role of exon shuffling in shaping protein-protein interaction networks

BMC Genomics, 2010

Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function ... more Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results: We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners) in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains), selfinteracting (able to interact with another copy of themselves) and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions: Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

Research paper thumbnail of Ischemic Preconditioning of Renal Tissue: Identification of Early Up-Regulated Genes

Nephron, 2003

Given the important effects of ischemic preconditioning (IPC) in minimizing tissue damage induced... more Given the important effects of ischemic preconditioning (IPC) in minimizing tissue damage induced by sustained ischemia in several tissues, this study evaluated the effect of IPC in preserving renal function and identified up-regulated genes after 30 min of preconditioning. IPC induced by 2, 3 and 4 min of ischemia, intercalated by 5 min of reperfusion, induced a measurable protection of renal function and morphology. The improved functional and histological parameters occurred in parallel with up-regulation of 39 genes, as evaluated by subtractive hybridization; for 13 of them we could show, by RNAse protection assay, a significant increase in mRNA levels. These genes code for chaperones/chaperonins and cytoskeleton proteins that could be involved in preservation of protein folding and cellular structures after sustained ischemia; proteins related to oxidative metabolism that might be relevant for cellular use of alternate sources of energy or for faster recovery of ATP levels in this condition, and proteins that are putative scavengers of oxidant products. Summarizing, ischemic preconditioning induced up-regulation of genes that code proteins whose functional roles suggest their involvement in the tolerance of the preconditioned tissue to sustained ischemia.

Research paper thumbnail of Pharmacological and physiological stimuli do not promote Ca2+-sensitive K+ channel activity in isolated heart mitochondria

Cardiovascular Research, 2007

Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channe... more Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channels that are activated by Ca 2+ , inner mitochondrial membrane depolarization and drugs such as NS-1619. NS-1619 is cardioprotective, leading to the assumption that this effect is related to the opening of mitoK Ca channels. Here, we show several weaknesses in this hypothesis. Methods: Isolated mitochondria from rat hearts were tested for evidence of mitoK Ca activity by analyzing functional parameters in K + -rich and K + -free media. Results: NS-1619 promoted mitochondrial depolarization both in K + -rich and K + -free media. Respiratory rate increments were also seen in the presence of NS-1619 for both media. In parallel, NS-1619 promoted respiratory inhibition, as evidenced by respiratory measurements in state 3. Mitochondrial volume measurements conducted using light scattering showed that NS-1619 led to swelling, in a manner unaltered by inhibitors of mitoK Ca channels, antagonists of adenosine triphosphate-sensitive potassium channels or inhibitors of the permeability transition. Swelling was also maintained when K + in the media was substituted with tetraethylammonium (TEA + ), which is not transported by any known K + carrier. Electron microscopy experiments gave support to the idea that NS-1619-induced mitochondrial swelling took place in the absence of K + . In addition to testing the pharmacological effects of NS-1619, we attempted, unsuccessfully, to promote mitoK Ca activity by altering Ca 2+ concentrations in the medium and inducing mitochondrial uncoupling. Conclusion: Our data indicate that NS-1619 promotes non-selective permeabilization of the inner mitochondrial membrane to ions, in addition to partial respiratory inhibition. Furthermore, we found no specific K + transport in isolated heart mitochondria compatible with mitoK Ca opening, whether by pharmacological or physiological stimuli. Our results indicate that NS-1619 has extensive mitochondrial effects unrelated to mitoK Ca and suggest that tissue protection mediated by NS-1619 may occur through mechanisms other than activation of these channels.

Research paper thumbnail of Pharmacological and physiological stimuli do not promote Ca2+-sensitive K+ channel activity in isolated heart mitochondria

Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channe... more Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channels that are activated by Ca 2+ , inner mitochondrial membrane depolarization and drugs such as NS-1619. NS-1619 is cardioprotective, leading to the assumption that this effect is related to the opening of mitoK Ca channels. Here, we show several weaknesses in this hypothesis. Methods: Isolated mitochondria from rat hearts were tested for evidence of mitoK Ca activity by analyzing functional parameters in K + -rich and K + -free media. Results: NS-1619 promoted mitochondrial depolarization both in K + -rich and K + -free media. Respiratory rate increments were also seen in the presence of NS-1619 for both media. In parallel, NS-1619 promoted respiratory inhibition, as evidenced by respiratory measurements in state 3. Mitochondrial volume measurements conducted using light scattering showed that NS-1619 led to swelling, in a manner unaltered by inhibitors of mitoK Ca channels, antagonists of adenosine triphosphate-sensitive potassium channels or inhibitors of the permeability transition. Swelling was also maintained when K + in the media was substituted with tetraethylammonium (TEA + ), which is not transported by any known K + carrier. Electron microscopy experiments gave support to the idea that NS-1619-induced mitochondrial swelling took place in the absence of K + . In addition to testing the pharmacological effects of NS-1619, we attempted, unsuccessfully, to promote mitoK Ca activity by altering Ca 2+ concentrations in the medium and inducing mitochondrial uncoupling. Conclusion: Our data indicate that NS-1619 promotes non-selective permeabilization of the inner mitochondrial membrane to ions, in addition to partial respiratory inhibition. Furthermore, we found no specific K + transport in isolated heart mitochondria compatible with mitoK Ca opening, whether by pharmacological or physiological stimuli. Our results indicate that NS-1619 has extensive mitochondrial effects unrelated to mitoK Ca and suggest that tissue protection mediated by NS-1619 may occur through mechanisms other than activation of these channels.

Research paper thumbnail of PROCEEDINGS Open Access The role of exon shuffling in shaping protein-protein interaction networks

Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function ... more Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results: We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners) in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multipl...

Research paper thumbnail of ATP-sensitive K+ channels in renal mitochondria

American journal of physiology. Renal physiology, 2003

Isolated kidney mitochondria swell when incubated in hyposmotic solutions containing K+ salts in ... more Isolated kidney mitochondria swell when incubated in hyposmotic solutions containing K+ salts in a manner inhibited by ATP, ADP, 5-hydroxydecanoate, and glibenclamide and stimulated by GTP and diazoxide. These results suggest the existence of ATP-sensitive K+ channels in these mitochondria, similar to those previously described in heart, liver, and brain. Renal mitochondrial ATP-sensitive K+ uptake rates are approximately 140 nmol.min-1.mg protein-1. This K+ transport results in a slight increase in respiration and decrease in the inner membrane potential. In addition, the activation of ATP-inhibited K+ uptake using diazoxide leads to a decrease of ATP hydrolysis through the reverse activity of the F0F1 ATP synthase when respiration is inhibited. In conclusion, we characterize an ATP-sensitive K+ transport pathway in kidney mitochondria that affects volume, respiration, and membrane potential and may have a role in the prevention of mitochondrial ATP hydrolysis.

Research paper thumbnail of Evolutionary history of exon shuffling

Research paper thumbnail of The role of exon shuffling in shaping protein-protein interaction networks

BMC Genomics, 2010

Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function ... more Background: Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions. Exon shuffling, intron-mediated recombination of exons from existing genes, is known to have been a major mechanism of domain shuffling in metazoans. Thus, we hypothesized that exon shuffling could have a significant influence in shaping the topology of PPI networks. Results: We tested our hypothesis by compiling exon shuffling and PPI data from six eukaryotic species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Cryptococcus neoformans and Arabidopsis thaliana. For all four metazoan species, genes enriched in exon shuffling events presented on average higher vertex degree (number of interacting partners) in PPI networks. Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains), selfinteracting (able to interact with another copy of themselves) and abundant in the genomes presents a stronger signal for exon shuffling. Conclusions: Exon shuffling appears to have been a recurrent mechanism for the emergence of new PPIs along metazoan evolution. In metazoan genomes, exon shuffling also promoted the expansion of some protein domains. We speculate that their promiscuous and self-interacting properties may have been decisive for that expansion.

Research paper thumbnail of Ischemic Preconditioning of Renal Tissue: Identification of Early Up-Regulated Genes

Nephron, 2003

Given the important effects of ischemic preconditioning (IPC) in minimizing tissue damage induced... more Given the important effects of ischemic preconditioning (IPC) in minimizing tissue damage induced by sustained ischemia in several tissues, this study evaluated the effect of IPC in preserving renal function and identified up-regulated genes after 30 min of preconditioning. IPC induced by 2, 3 and 4 min of ischemia, intercalated by 5 min of reperfusion, induced a measurable protection of renal function and morphology. The improved functional and histological parameters occurred in parallel with up-regulation of 39 genes, as evaluated by subtractive hybridization; for 13 of them we could show, by RNAse protection assay, a significant increase in mRNA levels. These genes code for chaperones/chaperonins and cytoskeleton proteins that could be involved in preservation of protein folding and cellular structures after sustained ischemia; proteins related to oxidative metabolism that might be relevant for cellular use of alternate sources of energy or for faster recovery of ATP levels in this condition, and proteins that are putative scavengers of oxidant products. Summarizing, ischemic preconditioning induced up-regulation of genes that code proteins whose functional roles suggest their involvement in the tolerance of the preconditioned tissue to sustained ischemia.

Research paper thumbnail of Pharmacological and physiological stimuli do not promote Ca2+-sensitive K+ channel activity in isolated heart mitochondria

Cardiovascular Research, 2007

Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channe... more Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channels that are activated by Ca 2+ , inner mitochondrial membrane depolarization and drugs such as NS-1619. NS-1619 is cardioprotective, leading to the assumption that this effect is related to the opening of mitoK Ca channels. Here, we show several weaknesses in this hypothesis. Methods: Isolated mitochondria from rat hearts were tested for evidence of mitoK Ca activity by analyzing functional parameters in K + -rich and K + -free media. Results: NS-1619 promoted mitochondrial depolarization both in K + -rich and K + -free media. Respiratory rate increments were also seen in the presence of NS-1619 for both media. In parallel, NS-1619 promoted respiratory inhibition, as evidenced by respiratory measurements in state 3. Mitochondrial volume measurements conducted using light scattering showed that NS-1619 led to swelling, in a manner unaltered by inhibitors of mitoK Ca channels, antagonists of adenosine triphosphate-sensitive potassium channels or inhibitors of the permeability transition. Swelling was also maintained when K + in the media was substituted with tetraethylammonium (TEA + ), which is not transported by any known K + carrier. Electron microscopy experiments gave support to the idea that NS-1619-induced mitochondrial swelling took place in the absence of K + . In addition to testing the pharmacological effects of NS-1619, we attempted, unsuccessfully, to promote mitoK Ca activity by altering Ca 2+ concentrations in the medium and inducing mitochondrial uncoupling. Conclusion: Our data indicate that NS-1619 promotes non-selective permeabilization of the inner mitochondrial membrane to ions, in addition to partial respiratory inhibition. Furthermore, we found no specific K + transport in isolated heart mitochondria compatible with mitoK Ca opening, whether by pharmacological or physiological stimuli. Our results indicate that NS-1619 has extensive mitochondrial effects unrelated to mitoK Ca and suggest that tissue protection mediated by NS-1619 may occur through mechanisms other than activation of these channels.

Research paper thumbnail of Pharmacological and physiological stimuli do not promote Ca2+-sensitive K+ channel activity in isolated heart mitochondria

Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channe... more Objective: Mitochondrial calcium-activated K + (mitoK Ca ) channels have been described as channels that are activated by Ca 2+ , inner mitochondrial membrane depolarization and drugs such as NS-1619. NS-1619 is cardioprotective, leading to the assumption that this effect is related to the opening of mitoK Ca channels. Here, we show several weaknesses in this hypothesis. Methods: Isolated mitochondria from rat hearts were tested for evidence of mitoK Ca activity by analyzing functional parameters in K + -rich and K + -free media. Results: NS-1619 promoted mitochondrial depolarization both in K + -rich and K + -free media. Respiratory rate increments were also seen in the presence of NS-1619 for both media. In parallel, NS-1619 promoted respiratory inhibition, as evidenced by respiratory measurements in state 3. Mitochondrial volume measurements conducted using light scattering showed that NS-1619 led to swelling, in a manner unaltered by inhibitors of mitoK Ca channels, antagonists of adenosine triphosphate-sensitive potassium channels or inhibitors of the permeability transition. Swelling was also maintained when K + in the media was substituted with tetraethylammonium (TEA + ), which is not transported by any known K + carrier. Electron microscopy experiments gave support to the idea that NS-1619-induced mitochondrial swelling took place in the absence of K + . In addition to testing the pharmacological effects of NS-1619, we attempted, unsuccessfully, to promote mitoK Ca activity by altering Ca 2+ concentrations in the medium and inducing mitochondrial uncoupling. Conclusion: Our data indicate that NS-1619 promotes non-selective permeabilization of the inner mitochondrial membrane to ions, in addition to partial respiratory inhibition. Furthermore, we found no specific K + transport in isolated heart mitochondria compatible with mitoK Ca opening, whether by pharmacological or physiological stimuli. Our results indicate that NS-1619 has extensive mitochondrial effects unrelated to mitoK Ca and suggest that tissue protection mediated by NS-1619 may occur through mechanisms other than activation of these channels.