In 2008 we published the first set of guidelines for standardizing research in autophagy. Since t... more In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Archives internationales de physiologie, de biochimie et de biophysique
A gamma-guanidobutyrate ureahydrolase isolated from tench liver has been characterized. Some of i... more A gamma-guanidobutyrate ureahydrolase isolated from tench liver has been characterized. Some of its physicochemical properties like pH effect and thermal stability resemble those of arginases, however it shows some peculiarities that makes it different from arginases and other amidino hydrolases. Thus cation requirement is not as strong as in arginases, and the Km value for gamma-guanido-butyric acid (230 +/- 25 mM) is shifted to a lower value (45 +/- 5 mM) by 5 mM arginine. The possible regulatory role of arginine on gamma-guanidobutyrate ureahydrolase activity is discussed.
Archives internationales de physiologie, de biochimie et de biophysique
Rat liver plasma-membrane-bound arginase was investigated in order to obtain data regarding its p... more Rat liver plasma-membrane-bound arginase was investigated in order to obtain data regarding its physico-chemical properties. Arginase bound to plasma membrane presented a specific activity of 0.74 +/- 0.09 IU/mg for the fully-activated enzyme, the pH of maximum activity being 9.8. Maximum stability was recorded at two pH values, 7 and 10.5 respectively. Mn2+ activated the enzyme, while Cu2+ and Zn2+, and to a lesser extend Co2+, showed a strong inhibitory effect. Ca2+ and Mg2+ had no effect at the concentrations assayed. The influence of temperature was studied in the presence and in the absence of Mn2+. The enzyme was stable up to 65 degrees C in both cases. Membrane- bound arginase showed an activation energy of 11.5 +/- 1.4 Kcal/mol between 20 and 40 degrees C, and 13.3 +/- 2.5 Kcal/mol between 40 and 60 degrees C. The Q10 for the same temperature ranges were 1.78 and 1.9 respectively. The membrane-bound enzyme presented two different Michaelis constants, one with high affinity (2.05 +/- 0.73 mM) and the other with low affinity for arginine (130 +/- 27.2 mM). Solubilized arginase showed very similar values. Among all the structural analogous assayed, only L-canavanine proved to be substrate for arginase, with and L-arginine/L-canavanine hydrolysis ratio of 5.8 +/- 0.28. No reactivity was found between plasma-membrane-bound arginase and anti-rat liver arginase antibodies raised in rabbits.
Most laboratories interested in autophagy use different imaging software for managing and analyzi... more Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision ...
... The authors would like to thank Lidia Floria, Carmen Marcellán, Pilar Pina, Sara Serrano, and... more ... The authors would like to thank Lidia Floria, Carmen Marcellán, Pilar Pina, Sara Serrano, and Carolina Villalba, Superior Technicians of Pathological Anatomy, for their collaboration, and Dr. Javier Mateos, of the Service of ... Kong SL, Salto-Téllez M, Leong AP, Chan YH, Koay ES ...
Current topics in medicinal chemistry, Jan 10, 2015
The pathogenesis of neurodegenerative diseases involves altered activity of proteolytic systems a... more The pathogenesis of neurodegenerative diseases involves altered activity of proteolytic systems and accumulation of protein aggregates. Autophagy is an intracellular process in which damaged organelles and long-lived proteins are degraded and recycled for maintaining normal cellular homeostasis. Disruption of autophagic activity in neurons leads to modify the cellular homeostasis, causing deficient elimination of abnormal and toxic protein aggregates that promotes cellular stress and death. Therefore, induction of autophagy has been proposed as a reasonable strategy to help neurons to clear abnormal protein aggregates and survive. This review aims to give an overview of some of the main modulators of autophagy that are currently being studied as possible alternatives in the search of therapies that slow the progression of neurodegenerative diseases, which are incurable to date.
LRRK2 mutations have been described as a common cause of Parkinson's disease (PD) in patients... more LRRK2 mutations have been described as a common cause of Parkinson's disease (PD) in patients from northern Spain. Here we investigated the prevalence of these mutations in a cohort of Spanish PD patients (n = 96) from Extremadura, a region in southwestern Spain. To evaluate the rate of the G2019S and R1441G/C/H LRKK2 mutations in PD patients and healthy controls (n = 163). Here we show that the G2019S mutation is present at a low prevalence in our Spanish cohort, while the R1441G/C/H mutation, which has been reported to be common in northern Spain, was not observed in the PD patients or in the controls. LRRK2 mutations do not appear to be a common cause of Parkinson's disease in Extremadura, Spain.
A detailed understanding of the regulatory mechanisms of arginase in the cell will depend on the ... more A detailed understanding of the regulatory mechanisms of arginase in the cell will depend on the clarification of the origin of the two different molecular mass subunits and on the arrangements of them to constitute the native enzyme. Here, we show the immunological recognition of the 39.5 and 37.0 kDa subunits of arginase by antibodies against both subunits. We also find that the subunit stoichiometry (39.5 kDa: 37.0 kDa) present in purified arginase preparations as well as in fresh isolated microsomes and cytoplasm corresponds to 3:1, indicating high prevalence of a constant arrangement of the constitutive subunits of arginase. These findings represent evidence for a limited posttranscriptional or posttranslational modification of only a fraction of the synthesized arginase in liver.
Apoptosis signal-regulating kinase 1 (ASK1) is activated by various types of stress, including, e... more Apoptosis signal-regulating kinase 1 (ASK1) is activated by various types of stress, including, endoplasmic reticulum (ER) stress. ER stress-induced ASK1 activation could play an important role both in neuronal apoptosis and an autophagic response in the pathogenesis of several neurodegenerative diseases, including Parkinson's disease. The mechanism by which ASK1 executes apoptosis and/or autophagy under ER stress is still unclear. We have addressed this question using SH-SY5Y cells overexpressing wild-type (WT) ASK1. We show an important autophagic response and an acceleration of the paraquat (PQ)-induced autophagy with hallmarks as accumulation of autophagic vacuoles, activation of beclin-1, accumulation of LC3 II, p62 degradation, and mammalian target of rapamycin dephosphorylation. Inhibition of autophagy caused an exacerbation of the apoptosis induced by WT ASK1 overexpression with or without PQ. These data support the idea that the autophagic response could have a protector role. We found also an increase in the phosphorylation of the proteins such as IRE1 and eIF2α in response to both the overexpression of WT ASK1 and pesticide exposure. These data suggest that the WT ASK1 overexpression-induced autophagy is an event that occurs in parallel with ER stress activation. The importance of ER stress in the autophagy induced by ASK1 and/or PQ was confirmed with salubrinal, a selective inhibitor of eIF2α dephosphorylation. In conclusion, we report that PQ induces an early ER stress response that is correlated with the activation of autophagy as a protective response, which is accelerated in cells that overexpress WT ASK1. However, when the toxic stimuli remain, the cell eventually succumbs to apoptosis.
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since t... more In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Archives internationales de physiologie, de biochimie et de biophysique
A gamma-guanidobutyrate ureahydrolase isolated from tench liver has been characterized. Some of i... more A gamma-guanidobutyrate ureahydrolase isolated from tench liver has been characterized. Some of its physicochemical properties like pH effect and thermal stability resemble those of arginases, however it shows some peculiarities that makes it different from arginases and other amidino hydrolases. Thus cation requirement is not as strong as in arginases, and the Km value for gamma-guanido-butyric acid (230 +/- 25 mM) is shifted to a lower value (45 +/- 5 mM) by 5 mM arginine. The possible regulatory role of arginine on gamma-guanidobutyrate ureahydrolase activity is discussed.
Archives internationales de physiologie, de biochimie et de biophysique
Rat liver plasma-membrane-bound arginase was investigated in order to obtain data regarding its p... more Rat liver plasma-membrane-bound arginase was investigated in order to obtain data regarding its physico-chemical properties. Arginase bound to plasma membrane presented a specific activity of 0.74 +/- 0.09 IU/mg for the fully-activated enzyme, the pH of maximum activity being 9.8. Maximum stability was recorded at two pH values, 7 and 10.5 respectively. Mn2+ activated the enzyme, while Cu2+ and Zn2+, and to a lesser extend Co2+, showed a strong inhibitory effect. Ca2+ and Mg2+ had no effect at the concentrations assayed. The influence of temperature was studied in the presence and in the absence of Mn2+. The enzyme was stable up to 65 degrees C in both cases. Membrane- bound arginase showed an activation energy of 11.5 +/- 1.4 Kcal/mol between 20 and 40 degrees C, and 13.3 +/- 2.5 Kcal/mol between 40 and 60 degrees C. The Q10 for the same temperature ranges were 1.78 and 1.9 respectively. The membrane-bound enzyme presented two different Michaelis constants, one with high affinity (2.05 +/- 0.73 mM) and the other with low affinity for arginine (130 +/- 27.2 mM). Solubilized arginase showed very similar values. Among all the structural analogous assayed, only L-canavanine proved to be substrate for arginase, with and L-arginine/L-canavanine hydrolysis ratio of 5.8 +/- 0.28. No reactivity was found between plasma-membrane-bound arginase and anti-rat liver arginase antibodies raised in rabbits.
Most laboratories interested in autophagy use different imaging software for managing and analyzi... more Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision ...
... The authors would like to thank Lidia Floria, Carmen Marcellán, Pilar Pina, Sara Serrano, and... more ... The authors would like to thank Lidia Floria, Carmen Marcellán, Pilar Pina, Sara Serrano, and Carolina Villalba, Superior Technicians of Pathological Anatomy, for their collaboration, and Dr. Javier Mateos, of the Service of ... Kong SL, Salto-Téllez M, Leong AP, Chan YH, Koay ES ...
Current topics in medicinal chemistry, Jan 10, 2015
The pathogenesis of neurodegenerative diseases involves altered activity of proteolytic systems a... more The pathogenesis of neurodegenerative diseases involves altered activity of proteolytic systems and accumulation of protein aggregates. Autophagy is an intracellular process in which damaged organelles and long-lived proteins are degraded and recycled for maintaining normal cellular homeostasis. Disruption of autophagic activity in neurons leads to modify the cellular homeostasis, causing deficient elimination of abnormal and toxic protein aggregates that promotes cellular stress and death. Therefore, induction of autophagy has been proposed as a reasonable strategy to help neurons to clear abnormal protein aggregates and survive. This review aims to give an overview of some of the main modulators of autophagy that are currently being studied as possible alternatives in the search of therapies that slow the progression of neurodegenerative diseases, which are incurable to date.
LRRK2 mutations have been described as a common cause of Parkinson's disease (PD) in patients... more LRRK2 mutations have been described as a common cause of Parkinson's disease (PD) in patients from northern Spain. Here we investigated the prevalence of these mutations in a cohort of Spanish PD patients (n = 96) from Extremadura, a region in southwestern Spain. To evaluate the rate of the G2019S and R1441G/C/H LRKK2 mutations in PD patients and healthy controls (n = 163). Here we show that the G2019S mutation is present at a low prevalence in our Spanish cohort, while the R1441G/C/H mutation, which has been reported to be common in northern Spain, was not observed in the PD patients or in the controls. LRRK2 mutations do not appear to be a common cause of Parkinson's disease in Extremadura, Spain.
A detailed understanding of the regulatory mechanisms of arginase in the cell will depend on the ... more A detailed understanding of the regulatory mechanisms of arginase in the cell will depend on the clarification of the origin of the two different molecular mass subunits and on the arrangements of them to constitute the native enzyme. Here, we show the immunological recognition of the 39.5 and 37.0 kDa subunits of arginase by antibodies against both subunits. We also find that the subunit stoichiometry (39.5 kDa: 37.0 kDa) present in purified arginase preparations as well as in fresh isolated microsomes and cytoplasm corresponds to 3:1, indicating high prevalence of a constant arrangement of the constitutive subunits of arginase. These findings represent evidence for a limited posttranscriptional or posttranslational modification of only a fraction of the synthesized arginase in liver.
Apoptosis signal-regulating kinase 1 (ASK1) is activated by various types of stress, including, e... more Apoptosis signal-regulating kinase 1 (ASK1) is activated by various types of stress, including, endoplasmic reticulum (ER) stress. ER stress-induced ASK1 activation could play an important role both in neuronal apoptosis and an autophagic response in the pathogenesis of several neurodegenerative diseases, including Parkinson's disease. The mechanism by which ASK1 executes apoptosis and/or autophagy under ER stress is still unclear. We have addressed this question using SH-SY5Y cells overexpressing wild-type (WT) ASK1. We show an important autophagic response and an acceleration of the paraquat (PQ)-induced autophagy with hallmarks as accumulation of autophagic vacuoles, activation of beclin-1, accumulation of LC3 II, p62 degradation, and mammalian target of rapamycin dephosphorylation. Inhibition of autophagy caused an exacerbation of the apoptosis induced by WT ASK1 overexpression with or without PQ. These data support the idea that the autophagic response could have a protector role. We found also an increase in the phosphorylation of the proteins such as IRE1 and eIF2α in response to both the overexpression of WT ASK1 and pesticide exposure. These data suggest that the WT ASK1 overexpression-induced autophagy is an event that occurs in parallel with ER stress activation. The importance of ER stress in the autophagy induced by ASK1 and/or PQ was confirmed with salubrinal, a selective inhibitor of eIF2α dephosphorylation. In conclusion, we report that PQ induces an early ER stress response that is correlated with the activation of autophagy as a protective response, which is accelerated in cells that overexpress WT ASK1. However, when the toxic stimuli remain, the cell eventually succumbs to apoptosis.
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Papers by Jose M Fuentes