Saturday, November 15, 2008
Coming back soon
It has taken a lot more of my time and energy that I thought it would to finish writing my dissertation. If all goes well, that will soon be over, and I am looking forward to returning to this blog and posting regularly. In the meantime, I have been saving all the notes from seminars I attended, and I will post them as soon as possible. Sadly, I was unable to attend all of those seminars. Blame it on the writing too! Exciting topics in are coming up, possibly as early as the first week of December.
Thursday, August 14, 2008
End of summer
The summer is almost over. I have not been posting as much as I would have like to. Currently I am trying to finish up my degree by December of this year. This poses interesting challenges. The first submission of my dissertation is due in the second week of October, but I still have experiments running until at least the third week of September. I have a set of backup experiments that will not be done until the first week of October. This means it will be extremely hectic while I try to write up my dissertation and do research at the same time.
For this blog that means that there will be almost no posting of original articles like I had planned. I have several articles in the pipeline, including one that would explain the title of this blog "The Hypersensitive Response."
The good news is that the Fall semester will start in a couple of weeks, which means that weekly seminar will return. I am still planning to attend every last one of those and post summaries on this blog as I have in the past. So stay tuned!
For this blog that means that there will be almost no posting of original articles like I had planned. I have several articles in the pipeline, including one that would explain the title of this blog "The Hypersensitive Response."
The good news is that the Fall semester will start in a couple of weeks, which means that weekly seminar will return. I am still planning to attend every last one of those and post summaries on this blog as I have in the past. So stay tuned!
Saturday, July 26, 2008
Women and Cultural Diversity
Today, I attended my first committee meeting, and a lively event it was. I officially joined the "Joint Committee on Women in Plant Pathology and Cultural Diversity." That is a mouthful, isn't it? And indeed, a good deal of the discussion concerned the name and scope of the committee.
The committee finds its roots in two committees of the past. One was the Committee of Women in Plant Pathology, the goal of which (among other things) was to enhance the opportunities of women in the field, whose representation in APS leadership was not a true reflection of their composition of the organization. As you can imagine, women in plant pathology have faced similar problems as women in science, or women in society in general. The committee for Cultural Diversity had similar goals, although their target audience was minorities. The two committees came to realize that their respective programs served both target groups, and decided to join.
A large part of the discussion today was focused on the fact that the majority of the attendees of the meeting were, in fact, women. Culturally diverse women, to be exact, but largely women. Period. There was at least one person who was of the opinion that the overwhelming majority of women signified the downfall of the cultural diversity aspect of the committee.
There were 2 men there at the start of the meeting, a few more came trickling in as the meeting progressed.
One of the discussion points was that it is possible that the name of the committee is off-putting to men who want to join (even culturally diverse ones). If so, should the name be changed? In the end we decided to put the issue up for vote. Six new names were suggested for the committee, and APS members will be able to decide which one of the 7 names (the old one and 6 new ones) will prevail. The discussion is scheduled to continue on the APSnet discussion boards, which are open to APS members only by clicking on the "Interactive" link.
More importantly though, the point was made that the group might be losing track of its goals, and those might need to be redefined. No specific plan was made to address that issue, but I have high hopes that the committee will find a way to do that.
The committee finds its roots in two committees of the past. One was the Committee of Women in Plant Pathology, the goal of which (among other things) was to enhance the opportunities of women in the field, whose representation in APS leadership was not a true reflection of their composition of the organization. As you can imagine, women in plant pathology have faced similar problems as women in science, or women in society in general. The committee for Cultural Diversity had similar goals, although their target audience was minorities. The two committees came to realize that their respective programs served both target groups, and decided to join.
A large part of the discussion today was focused on the fact that the majority of the attendees of the meeting were, in fact, women. Culturally diverse women, to be exact, but largely women. Period. There was at least one person who was of the opinion that the overwhelming majority of women signified the downfall of the cultural diversity aspect of the committee.
There were 2 men there at the start of the meeting, a few more came trickling in as the meeting progressed.
One of the discussion points was that it is possible that the name of the committee is off-putting to men who want to join (even culturally diverse ones). If so, should the name be changed? In the end we decided to put the issue up for vote. Six new names were suggested for the committee, and APS members will be able to decide which one of the 7 names (the old one and 6 new ones) will prevail. The discussion is scheduled to continue on the APSnet discussion boards, which are open to APS members only by clicking on the "Interactive" link.
More importantly though, the point was made that the group might be losing track of its goals, and those might need to be redefined. No specific plan was made to address that issue, but I have high hopes that the committee will find a way to do that.
APS Centennial Meeting
The American Phytopathological Society (APS) annual meeting started today July 26, 2008. It is a very special meeting, since it is the centennial meeting, and I'm very excited to be here. This is the first APS meeting I've had the pleasure to attend. I'm hoping to write regularly about the happenings at the meeting, so stay tuned! Hopefully, I'll also get a chance to put in some pictures over time, although I haven't taken a single one yet, I've been too involved with the goings on.
Tuesday, April 29, 2008
Recent posts from fungal genomes
Attention:
Two recent posts at the Fungal Genomes and Comparative Genomics blog:
1. Research on the causal agent of Sudden Oak Death, Phytophtora ramorum.
2. A project of the J. Craig Venter Institute aims to sequence the genome of Rhizoctonia solani, a soil pathogen that affects a number of crops. This is the direct link to the project page.
Two recent posts at the Fungal Genomes and Comparative Genomics blog:
1. Research on the causal agent of Sudden Oak Death, Phytophtora ramorum.
2. A project of the J. Craig Venter Institute aims to sequence the genome of Rhizoctonia solani, a soil pathogen that affects a number of crops. This is the direct link to the project page.
Thursday, April 24, 2008
Xylella fastidiosa
The seminar disclaimer applies to this post.
The topic of seminar this week was: "Xylella fastidiosa: pathogenicity, host specificity, and disease management." The talk was given by Don Hopkins, faculty member of the University of Florida Institute for Agricultural Sciences Mid-Florida Research & Education Center (UF/IFAS-MREC)
Xylella fastidiosa is a bacterium that used to be classified as fastidious, because it was considered to be unculturable. Currently, methods do exist for growing X. fastidiosa.
X. fastidiosa causes economic losses in grape (Pierce's disease), citrus (citrus variegated chlorosis, CVC), almond, coffee, peach, and plum. It is also responsible for decline of many urban shade trees and shrubs. There appear to be 3 subspecies with different host-specificities, which is what part of Dr. Hopkin's research is focused on. He isolated X. fastidiosa from different plant species, and inoculated other plant species with those isolates. He found that isolates were most pathogenic on the plant species they were isolated from, but some isolates could cause disease on several plant species.
The disease
Picture credit.
The bacterium is spread by the glassy-winged sharpshooter, and infects the plant xylem, clogging it, and thereby slowing down the transpiration stream. The vascular obstruction causes symptoms of water stress. Bacterial toxins have also been proposed to be responsible for chlorosis and scorching symptoms, and growth regulators cold be the source of flattened dark green leaves, and shortened internodes which are among the symptoms of infected plants.
Research questions
Picture credit.
One of the questions Dr. Hopkins was trying to answer was whether the virulence of the bacterium is related to the rate of colonization of the xylem vessels, or the movement of the bacterium within the xylem. He found that the ability of X. fastidiosa to colonize the plant systemically as opposed to staying locally at the site of initial infection, determined virulence and host specificity. Since the entire genome of Xylella fastidiosa has been sequenced, researchers can use the hints provided by research results to look for specific genes that are likely involved in pathogenicity and virulence.
Disease management
Because there both the bacterium and the insect vector have a wide host range, and there are a number of plant hosts that show little or no symptoms, it is difficult to sustain efforts to exclude either X. fastidiosa or the sharpshooter. Systemic insecticides, especially within the confines of a vineyard, can to some extent be used to control the insect vector, but is made more difficult by the fact that there are so many plant hosts. Elimination of inoculum sources is another strategy, and involves removal of infected trees.
One approach in the grape industry in California involves application of the soil-applied systemic insecticide Admire in May, monitoring the vineyards, and removal of infected trees.
Plant resistance is of little value in grape culture, where the genotypes of the crop are of immense importance to the quality of the wine. Transgenic resistance does show some promise, and currently there are some field trial underway with grape vines that have be genetically altered to include a lytic peptide gene.
Of major interest is current research that involves the use of a weekly virulent strain of X. fastidiosa obtained from elderberry, which appears to offer cross-protection in the field. Very young plants are inoculated with this strain early on with this mild strain. In one experiment, plants are still healthy more than 10 years after the initial inoculation. Further experiments to test this biological control agent are being conducted in several different states. Interestingly, the treatment is more effective if the initial inoculation is performed with a highly diluted bacterial suspension. The procedure is currently in the patent process. So far there is no data to support the idea that the sharpshooter spreads the biocontrol agent, but this is hard to test, because the protecting strain maintains very low numbers in the plant, and is often hard to detect.
Future research
Current and future experiments focus on the testing of the effectiveness of cross-protection on other grape genotypes, expansion of testing in commercial vineyards in different areas, and the use of X. fastidiosa strains to control other diseases. Data is being collected to submit to the EPA, commercial interest is being evaluated, and experiments are performed to get more data on the efficacy of the treatment.
Further reading
Almeida, R. No year. Xylella fastidiosa-A scientific and community internet resource on plant diseases caused by the bacterium Xylella fastidiosa. Online at: http://www.cnr.berkeley.edu/xylella/
Mizell, R.F., Andersen, P.C., Tipping, C. and Brodbeck, B. 2008. Xylella fastidiosa diseases and their leafhopper vector. Document ENY-683 (INA174) Department of Entomology and Nematology, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida. Online at: http://edis.ifas.ufl.edu/in174
The topic of seminar this week was: "Xylella fastidiosa: pathogenicity, host specificity, and disease management." The talk was given by Don Hopkins, faculty member of the University of Florida Institute for Agricultural Sciences Mid-Florida Research & Education Center (UF/IFAS-MREC)
Xylella fastidiosa is a bacterium that used to be classified as fastidious, because it was considered to be unculturable. Currently, methods do exist for growing X. fastidiosa.
X. fastidiosa causes economic losses in grape (Pierce's disease), citrus (citrus variegated chlorosis, CVC), almond, coffee, peach, and plum. It is also responsible for decline of many urban shade trees and shrubs. There appear to be 3 subspecies with different host-specificities, which is what part of Dr. Hopkin's research is focused on. He isolated X. fastidiosa from different plant species, and inoculated other plant species with those isolates. He found that isolates were most pathogenic on the plant species they were isolated from, but some isolates could cause disease on several plant species.
The disease
Picture credit.The bacterium is spread by the glassy-winged sharpshooter, and infects the plant xylem, clogging it, and thereby slowing down the transpiration stream. The vascular obstruction causes symptoms of water stress. Bacterial toxins have also been proposed to be responsible for chlorosis and scorching symptoms, and growth regulators cold be the source of flattened dark green leaves, and shortened internodes which are among the symptoms of infected plants.
Research questions
Picture credit.One of the questions Dr. Hopkins was trying to answer was whether the virulence of the bacterium is related to the rate of colonization of the xylem vessels, or the movement of the bacterium within the xylem. He found that the ability of X. fastidiosa to colonize the plant systemically as opposed to staying locally at the site of initial infection, determined virulence and host specificity. Since the entire genome of Xylella fastidiosa has been sequenced, researchers can use the hints provided by research results to look for specific genes that are likely involved in pathogenicity and virulence.
Disease management
Because there both the bacterium and the insect vector have a wide host range, and there are a number of plant hosts that show little or no symptoms, it is difficult to sustain efforts to exclude either X. fastidiosa or the sharpshooter. Systemic insecticides, especially within the confines of a vineyard, can to some extent be used to control the insect vector, but is made more difficult by the fact that there are so many plant hosts. Elimination of inoculum sources is another strategy, and involves removal of infected trees.
One approach in the grape industry in California involves application of the soil-applied systemic insecticide Admire in May, monitoring the vineyards, and removal of infected trees.
Plant resistance is of little value in grape culture, where the genotypes of the crop are of immense importance to the quality of the wine. Transgenic resistance does show some promise, and currently there are some field trial underway with grape vines that have be genetically altered to include a lytic peptide gene.
Of major interest is current research that involves the use of a weekly virulent strain of X. fastidiosa obtained from elderberry, which appears to offer cross-protection in the field. Very young plants are inoculated with this strain early on with this mild strain. In one experiment, plants are still healthy more than 10 years after the initial inoculation. Further experiments to test this biological control agent are being conducted in several different states. Interestingly, the treatment is more effective if the initial inoculation is performed with a highly diluted bacterial suspension. The procedure is currently in the patent process. So far there is no data to support the idea that the sharpshooter spreads the biocontrol agent, but this is hard to test, because the protecting strain maintains very low numbers in the plant, and is often hard to detect.
Future research
Current and future experiments focus on the testing of the effectiveness of cross-protection on other grape genotypes, expansion of testing in commercial vineyards in different areas, and the use of X. fastidiosa strains to control other diseases. Data is being collected to submit to the EPA, commercial interest is being evaluated, and experiments are performed to get more data on the efficacy of the treatment.
Further reading
Almeida, R. No year. Xylella fastidiosa-A scientific and community internet resource on plant diseases caused by the bacterium Xylella fastidiosa. Online at: http://www.cnr.berkeley.edu/xylella/
Mizell, R.F., Andersen, P.C., Tipping, C. and Brodbeck, B. 2008. Xylella fastidiosa diseases and their leafhopper vector. Document ENY-683 (INA174) Department of Entomology and Nematology, Florida Cooperative Extension Service, Institute of Food and Agricultural Sciences, University of Florida. Online at: http://edis.ifas.ufl.edu/in174
Tuesday, April 15, 2008
Liver cancer on citrus
The seminar disclaimer applies to this post.
Seminar was canceled two weeks ago. Last week’s seminar was presented by Mike Irey from the United States Sugar Corporation and Southern Gardens. Southern Gardens is the 3rd largest orange grower in Florida, with 21,000 total grove acreage, all planted with oranges. Over the years more than 21% of the acreage has been lost as a result of citrus canker and the citrus canker eradication effort.
However, if citrus canker was a hemorrhoid, citrus greening (also called huanglongbing, HLB) is the liver cancer of citrus
The disease
Picture credit.
HLB is a bacterial disease, caused by one of the two fastidious (up to now unculturable) bacteria Candidatus Liberibacter asiaticus or Candidatus Liberibacter africanus, the first one of which was found in Florida in 2005. The disease is vectored (spread) by the Asian citrus psyllid, an insect that doesn’t cause any major problems on citrus by itself. When 6 trees in Southern Gardens were identified to have HLB in October 2005, immediate inspection of all groves followed, and a control program to manage the vector, the Asian citrus psyllid was put into place.
Picture credit.
The initial HLB symptoms are misleadingly unimpressive, looking somewhat like nutritional deficiencies. Some leaves, usually near the center of the citrus tree show some mottling, but the trees themselves do not decline until much later. The spread of HLB has been quite dramatic over the years. It was first identified in Florida in 2005. In April 2006, 12 counties had positively identified trees, in January 2007 that was 14 counties, by June of 2007 there were 24 counties, and as of February 2008 all 30 citrus-producing countries had trees with HLB. The disease spreads very fast.
Impact
Crop losses include the immediate loss of removed trees, but also gradual tree decline and reduced production, fruit drop, reduced size of the fruit, and possibly juice quality issues, although the latter is still controversial. A small study with 10 pairs of trees comparing yields from symptomatic trees with non-symptomatic trees of approximately the same height, measured a 56% yield reduction in the symptomatic trees. This may be an over-estimate, but it is still a number to keep in mind.
Southern Gardens and US Sugar Corporation test samples from growers by polymerase chain reaction (PCR). They find that around 50-60% of the samples are positive. Some blocks of citrus have 80% of the trees infected, company-wide around 10% of the trees have HLB. Almost 300,000 trees (~1800 acres) have been removed so far, at a cost of more than 6 million dollars (roughly 1 million for tree removal, 2 million for tree replacement, 3 million for lost production). The costs of managing HLB disease has skyrocketed because of the ongoing tree removal, the increased insecticide applications, and currently 44 full-time scouts are employed, constantly surveying the groves in search of newly symptomatic trees.
Grower reactions have varied from doing nothing at all, to aggressive inoculum management, to abandoning groves all together. Those that wait for the silver bullet will likely be disappointed, as there will be no quick fix to the HLB problem.
Disease management
The main challenge is to make management decisions to deal with a disease when there is little knowledge, and a lot of data in the literature is anecdotal. In addition, the causal agent of HLB is a select agent, which complicates research.
Possible management options include:
- Vector control
- Tree removal
- Replanting disease-free material
- Disease-resistance plants (no know resistance to date)
Southern Gardens has opted for an open-door policy, opening their doors for hands-on training of scouts and managers, organizing grower meetings throughout the state, and field trials of experimental approaches.
Management of available inoculum through intensive surveys (full-time scouting) and aggressive removal of infected trees and control of the insect vector, have been the main focus of the approach so far.
The citrus industry has for a long time implemented an integrated pest management approach to control pests and diseases, using cultural practices, surveying, and careful weighing the necessity of chemical sprays. With the current intensive spray program to control the Asian citrus psyllid, the spray programs can no longer be considered IPM.
Management and administration costs have increased dramatically; disease testing for example, costs $6.50 per sample. If the psyllid is found in a nursery, the nursery managers risk have to worry about being assessed and quarantined, risking losses, and potentially even complete shutdown.
Even more troubling is that growers are becoming desperate, trying unproven methods. Often there is no data available from scientifically performed experiments with proper controls on products for which broad claims of efficacy are made. Meanwhile, the growers do not remove infected trees while they try out new products or approaches, risking further spread.
Long term strategies
At this point it is unclear what the best management strategy will turn out to be. One interesting observation to keep in mind in developing strategies is that it appears the disease is more prevalent at the edges of citrus blocks. Potential explanations are that the psyllid is coming from the outside, affecting the outer edges, or the psyllid is moving outward from the center of the block and is stopped by the lack of trees beyond the edge. Does it make sense to change the size and shape of blocks to reduce the edge/area ratio?
How effective are some of the alternative approaches and products that are currently available on the market? How can new strains be detected in a pathogen that is (up to now) unculturable? How does one optimize the PCR reaction used to detect the pathogen (where to set thresholds)? What time of the year is the best to sample? A particular tree may be negative if tested in one month, and positive in another. How effective (and economically feasible) is the strategy to intermingle citrus plants with guava plants, which seems to work in some countries? And can it still be considered a “citrus grove” if half the trees are guava?
Citrus greening is presenting new challenges to growers, nursery managers, plant pathologists, and lab technicians. A great deal of research is necessary to come up with answers.
Further reading
Halbert, Susan. Pest Alert. Florida Department of Agriculture and Consumer Services, Division of Plant Industry. http://www.doacs.state.fl.us/pi/chrp/greening/citrusgreeningalert.html
Langham, M.A.C. 2006. Citrus greening - The yellow dragon threatens Florida citrus. APSnet News and Views. http://www.apsnet.org/education/K-12PlantPathways/NewsViews/Archive/2006_04.html
Long, P. and Merzer, M. 2007. Florida citrus industry faces new peril. Miami Herald. Complete text online at Southern Gardens News and Press Releases: http://southerngardens.com/news/101607.html
Seminar was canceled two weeks ago. Last week’s seminar was presented by Mike Irey from the United States Sugar Corporation and Southern Gardens. Southern Gardens is the 3rd largest orange grower in Florida, with 21,000 total grove acreage, all planted with oranges. Over the years more than 21% of the acreage has been lost as a result of citrus canker and the citrus canker eradication effort.
However, if citrus canker was a hemorrhoid, citrus greening (also called huanglongbing, HLB) is the liver cancer of citrus
The disease
Picture credit.HLB is a bacterial disease, caused by one of the two fastidious (up to now unculturable) bacteria Candidatus Liberibacter asiaticus or Candidatus Liberibacter africanus, the first one of which was found in Florida in 2005. The disease is vectored (spread) by the Asian citrus psyllid, an insect that doesn’t cause any major problems on citrus by itself. When 6 trees in Southern Gardens were identified to have HLB in October 2005, immediate inspection of all groves followed, and a control program to manage the vector, the Asian citrus psyllid was put into place.
Picture credit.The initial HLB symptoms are misleadingly unimpressive, looking somewhat like nutritional deficiencies. Some leaves, usually near the center of the citrus tree show some mottling, but the trees themselves do not decline until much later. The spread of HLB has been quite dramatic over the years. It was first identified in Florida in 2005. In April 2006, 12 counties had positively identified trees, in January 2007 that was 14 counties, by June of 2007 there were 24 counties, and as of February 2008 all 30 citrus-producing countries had trees with HLB. The disease spreads very fast.
Impact
Crop losses include the immediate loss of removed trees, but also gradual tree decline and reduced production, fruit drop, reduced size of the fruit, and possibly juice quality issues, although the latter is still controversial. A small study with 10 pairs of trees comparing yields from symptomatic trees with non-symptomatic trees of approximately the same height, measured a 56% yield reduction in the symptomatic trees. This may be an over-estimate, but it is still a number to keep in mind.
Southern Gardens and US Sugar Corporation test samples from growers by polymerase chain reaction (PCR). They find that around 50-60% of the samples are positive. Some blocks of citrus have 80% of the trees infected, company-wide around 10% of the trees have HLB. Almost 300,000 trees (~1800 acres) have been removed so far, at a cost of more than 6 million dollars (roughly 1 million for tree removal, 2 million for tree replacement, 3 million for lost production). The costs of managing HLB disease has skyrocketed because of the ongoing tree removal, the increased insecticide applications, and currently 44 full-time scouts are employed, constantly surveying the groves in search of newly symptomatic trees.
Grower reactions have varied from doing nothing at all, to aggressive inoculum management, to abandoning groves all together. Those that wait for the silver bullet will likely be disappointed, as there will be no quick fix to the HLB problem.
Disease management
The main challenge is to make management decisions to deal with a disease when there is little knowledge, and a lot of data in the literature is anecdotal. In addition, the causal agent of HLB is a select agent, which complicates research.
Possible management options include:
- Vector control
- Tree removal
- Replanting disease-free material
- Disease-resistance plants (no know resistance to date)
Southern Gardens has opted for an open-door policy, opening their doors for hands-on training of scouts and managers, organizing grower meetings throughout the state, and field trials of experimental approaches.
Management of available inoculum through intensive surveys (full-time scouting) and aggressive removal of infected trees and control of the insect vector, have been the main focus of the approach so far.
The citrus industry has for a long time implemented an integrated pest management approach to control pests and diseases, using cultural practices, surveying, and careful weighing the necessity of chemical sprays. With the current intensive spray program to control the Asian citrus psyllid, the spray programs can no longer be considered IPM.
Management and administration costs have increased dramatically; disease testing for example, costs $6.50 per sample. If the psyllid is found in a nursery, the nursery managers risk have to worry about being assessed and quarantined, risking losses, and potentially even complete shutdown.
Even more troubling is that growers are becoming desperate, trying unproven methods. Often there is no data available from scientifically performed experiments with proper controls on products for which broad claims of efficacy are made. Meanwhile, the growers do not remove infected trees while they try out new products or approaches, risking further spread.
Long term strategies
At this point it is unclear what the best management strategy will turn out to be. One interesting observation to keep in mind in developing strategies is that it appears the disease is more prevalent at the edges of citrus blocks. Potential explanations are that the psyllid is coming from the outside, affecting the outer edges, or the psyllid is moving outward from the center of the block and is stopped by the lack of trees beyond the edge. Does it make sense to change the size and shape of blocks to reduce the edge/area ratio?
How effective are some of the alternative approaches and products that are currently available on the market? How can new strains be detected in a pathogen that is (up to now) unculturable? How does one optimize the PCR reaction used to detect the pathogen (where to set thresholds)? What time of the year is the best to sample? A particular tree may be negative if tested in one month, and positive in another. How effective (and economically feasible) is the strategy to intermingle citrus plants with guava plants, which seems to work in some countries? And can it still be considered a “citrus grove” if half the trees are guava?
Citrus greening is presenting new challenges to growers, nursery managers, plant pathologists, and lab technicians. A great deal of research is necessary to come up with answers.
Further reading
Halbert, Susan. Pest Alert. Florida Department of Agriculture and Consumer Services, Division of Plant Industry. http://www.doacs.state.fl.us/pi/chrp/greening/citrusgreeningalert.html
Langham, M.A.C. 2006. Citrus greening - The yellow dragon threatens Florida citrus. APSnet News and Views. http://www.apsnet.org/education/K-12PlantPathways/NewsViews/Archive/2006_04.html
Long, P. and Merzer, M. 2007. Florida citrus industry faces new peril. Miami Herald. Complete text online at Southern Gardens News and Press Releases: http://southerngardens.com/news/101607.html
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