Difference between revisions of "Leishmania Major Articles"
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: This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome | : This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome | ||
:Citation for paper: | :Citation for paper: | ||
| − | ::Ivens, AC | + | ::Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RM, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Müller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schäfer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ. The genome of the kinetoplastid parasite, Leishmania major. Science, 2005 Jul 15. 309(5733):436-42. |
='''Microarray Articles'''= | ='''Microarray Articles'''= | ||
| − | 1.)[http://europepmc.org/abstract/MED/18638379/reload=0;jsessionid=UIW9RunP1XHUGCaWD7p4.48 ''Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy.''] | + | 1.[http://europepmc.org/abstract/MED/18510761 ''Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species.''] |
| + | *I typed in "Leishmania Major" in the organism field and "Array assay" in the technology field and filtered down my results. | ||
| + | *There were 11 results, 4 seemed relevant | ||
| + | *This experiment compared the gene expression profiles between between promastigote and amastigote developmental stages of Leishmania major and Leishmania infantum. | ||
| + | *Ten assays were performed. | ||
| + | * Rochette, A., Raymond F., Ubeda JM., Smith M., Messier N., Boisvert S., Rigault P., Corbeil J., Ouellette M., Papadopoulou B. Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics, (2008 May 29). '''9''':255. | ||
| + | *[http://www.biomedcentral.com/1471-2164/9/255#sec5 Link to article on Author's site] | ||
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| + | *[[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-10407/?query=rochette Link to Data on Array Express]] | ||
| + | : | ||
| + | *[[File:Leishmania.pdf]] | ||
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| + | <!--[http://europepmc.org/abstract/MED/18638379/reload=0;jsessionid=UIW9RunP1XHUGCaWD7p4.48 ''Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy.''] | ||
*I typed in "Leishmania Major" in the organism field and "Array assay" in the technology field and filtered down my results. | *I typed in "Leishmania Major" in the organism field and "Array assay" in the technology field and filtered down my results. | ||
*There were 11 results, 4 seemed relevant | *There were 11 results, 4 seemed relevant | ||
*Jean-Michel Ubeda, Danielle Légaré, Frédéric Raymond, Amin Ahmed Ouameur, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Michel J Tremblay, Martin Olivier, Barbara Papadopoulou and Marc Ouellette. (2008). Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biology 9:115. | *Jean-Michel Ubeda, Danielle Légaré, Frédéric Raymond, Amin Ahmed Ouameur, Sébastien Boisvert, Philippe Rigault, Jacques Corbeil, Michel J Tremblay, Martin Olivier, Barbara Papadopoulou and Marc Ouellette. (2008). Modulation of gene expression in drug resistant Leishmania is associated with gene amplification, gene deletion and chromosome aneuploidy. Genome Biology 9:115. | ||
| − | 3.) | + | |
| − | + | 3.)''[http://www.sciencedirect.com/science/article/pii/S0166685104000660 ''Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major]'' | |
*Searched Science Direct for keywords leishmania, and DNA microarray. There were 40 results on the first page, but the first hit was relevent. | *Searched Science Direct for keywords leishmania, and DNA microarray. There were 40 results on the first page, but the first hit was relevent. | ||
*Experiment: This was a microarray experiment comparing genes in leishmania in mice in different environments. The control parasites were initially grown in a neutral media, and the experimental parasites were initially grown in an acidic media where HEPES replaced 4-morpholinoethanesulfonic acid. | *Experiment: This was a microarray experiment comparing genes in leishmania in mice in different environments. The control parasites were initially grown in a neutral media, and the experimental parasites were initially grown in an acidic media where HEPES replaced 4-morpholinoethanesulfonic acid. | ||
*Replicates: Hybridization experiments were performed in triplets, so 3 biological replicates. | *Replicates: Hybridization experiments were performed in triplets, so 3 biological replicates. | ||
| − | *Natalia S Akopyants, Robin S Matlib, Elena N Bukanova, Matthew R Smeds, Bernard H Brownstein, Gary D Stormo, Stephen M Beverley, (2004) Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major, Molecular and Biochemical Parasitology, 136: 71-86. | + | *Citation: Natalia S Akopyants, Robin S Matlib, Elena N Bukanova, Matthew R Smeds, Bernard H Brownstein, Gary D Stormo, Stephen M Beverley, (2004) Expression profiling using random genomic DNA microarrays identifies differentially expressed genes associated with three major developmental stages of the protozoan parasite Leishmania major, Molecular and Biochemical Parasitology, 136: 71-86. |
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6.)[http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000476 ''Comparative Expression Profiling of Leishmania: Modulation in Gene Expression between Species and in Different Host Genetic Backgrounds''] | 6.)[http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000476 ''Comparative Expression Profiling of Leishmania: Modulation in Gene Expression between Species and in Different Host Genetic Backgrounds''] | ||
| + | Link for data download: [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2063/?keywords=&organism=Leishmania+major&array=&exptype%5B%5D=&exptype%5B%5D=%22array+assay%22 ''data download page''] | ||
*Opened browser and navigated to Array Express | *Opened browser and navigated to Array Express | ||
*Clicked Experiments tab on Array Express home page | *Clicked Experiments tab on Array Express home page | ||
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*This search yielded nine results | *This search yielded nine results | ||
*Approximately half seemed relevant | *Approximately half seemed relevant | ||
| + | *Depledge DP, Evans KJ, Ivens AC, Aziz N, Maroof A, et al. (2009) Comparative Expression Profiling of Leishmania: Modulation in Gene Expression between Species and in Different Host Genetic Backgrounds. PLoS Negl Trop Dis 3(7): e476. doi:10.1371/journal.pntd.0000476. | ||
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5.)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692916/pdf/11839181.pdf ''Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling''] - direct link:http://rstb.royalsocietypublishing.org/content/357/1417/47.full.pdf+html | 5.)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692916/pdf/11839181.pdf ''Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling''] - direct link:http://rstb.royalsocietypublishing.org/content/357/1417/47.full.pdf+html | ||
| − | + | * This article was found using PubMed. I searched related citations from the reference paper and got 132 results, this article was one of the top ones. It looked at the genome and which part may be involved in causing disease. I am not sure if the data will be accessible though. | |
| + | *Beverley SM, Akopyants NS, Goyard S, et al. (2002) Putting the Leishmania genome to work: functional genomics by transposon trapping and expression profiling. Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29;357(1417):47-53. | ||
| − | + | 4.)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592530/ ''Comparative genomic analysis of three Leishmania species that cause diverse human disease''] | |
| − | *Searched for genomic analysis and leishmania in PubMed. There were 59 results. Many papers were extremely specific, the 14th paper down was this one. It appeared to be a possible resource for information about the leishmania genome. | + | *Searched for genomic analysis and leishmania in PubMed. There were 59 results. Many papers were extremely specific, the 14th paper down was this one. It appeared to be a possible resource for information about the leishmania genome. |
| − | *Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, Quail MA, Peters N, Adlem E, Tivey A, Aslett M, Kerhornou A, Ivens A, Fraser A, Rajandream MA, Carver T, Norbertczak H, Chillingworth T, Hance Z, Jagels K, Moule S, Ormond D, Rutter S, Squares R, Whitehead S, Rabbinowitsch E, Arrowsmith C, White B, Thurston S, Bringaud F, Baldauf SL, Faulconbridge A, Jeffares D, Depledge DP, Oyola SO, Hilley JD, Brito LO, Tosi LR, Barrell B, Cruz AK, Mottram JC, Smith DF, Berriman M, (2007) Comparative genomic analysis of three Leishmania species that cause diverse human disease, National Genetics 7: 839-47 | + | *Experiment: This article does not seem to have a description of exactly what experiments were performed. I am not sure why it was chosen. |
| − | + | *Replicates: This article also does not seem to have any mention of replicates. | |
| − | + | *Citation: Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC, Quail MA, Peters N, Adlem E, Tivey A, Aslett M, Kerhornou A, Ivens A, Fraser A, Rajandream MA, Carver T, Norbertczak H, Chillingworth T, Hance Z, Jagels K, Moule S, Ormond D, Rutter S, Squares R, Whitehead S, Rabbinowitsch E, Arrowsmith C, White B, Thurston S, Bringaud F, Baldauf SL, Faulconbridge A, Jeffares D, Depledge DP, Oyola SO, Hilley JD, Brito LO, Tosi LR, Barrell B, Cruz AK, Mottram JC, Smith DF, Berriman M, (2007) Comparative genomic analysis of three Leishmania species that cause diverse human disease, National Genetics 7: 839-47. | |
:-Lena | :-Lena | ||
{{Leishmania Major Navigation}} | {{Leishmania Major Navigation}} | ||
Latest revision as of 18:36, 5 November 2013
[edit] Reference Genome Article
The Genome of the Kinetoplastid Parasite, Leishmania major (Reference Genome)
- This article was found via the PubMed database and the key terms used were "Leishmania Major [MeSH Terms] AND Genome [Title]"
- This search resulted in 30 articles, about 5 seemed relevant but this one was the first which had the entire genome
- Citation for paper:
- Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RM, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, Müller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Schäfer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ. The genome of the kinetoplastid parasite, Leishmania major. Science, 2005 Jul 15. 309(5733):436-42.
[edit] Microarray Articles
- I typed in "Leishmania Major" in the organism field and "Array assay" in the technology field and filtered down my results.
- There were 11 results, 4 seemed relevant
- This experiment compared the gene expression profiles between between promastigote and amastigote developmental stages of Leishmania major and Leishmania infantum.
- Ten assays were performed.
- Rochette, A., Raymond F., Ubeda JM., Smith M., Messier N., Boisvert S., Rigault P., Corbeil J., Ouellette M., Papadopoulou B. Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics, (2008 May 29). 9:255.
- Link to article on Author's site
