Metabolomics to Unveil and Understand Phenotypic Diversity between Pathogen Populations

RA Scheltema, 2010, The potential of metabolomics for <italic>Leishmania</italic> research in the post-genomics era., Parasitology, 9, 1291, 10.1017/S0031182009992022

R Breitling, 2006, Precision mapping of the metabolome., Trends Biotechnol, 24, 543, 10.1016/j.tibtech.2006.10.006

HW Murray, 2004, Progress in the treatment of a neglected infectious disease: visceral leishmaniasis., Expert Rev Anti Infect Ther, 2, 279, 10.1586/14787210.2.2.279

F Chappuis, 2007, Visceral leishmaniasis: what are the needs for diagnosis, treatment and control?, Nat Rev Microbiol, 5, 873, 10.1038/nrmicro1748

2007, WHO meeting on the guidelines and standard operating procedures for kala-azar elimination.

S Sundar, 2000, Failure of pentavalent antimony in visceral leishmaniasis in India: report from the center of the Indian epidemic., Clin Infect Dis, 31, 1104, 10.1086/318121

D Kumar, 2009, <italic>In vitro</italic> susceptibility of field isolates of <italic>Leishmania donovani</italic> to Miltefosine and amphotericin B: correlation with sodium antimony gluconate susceptibility and implications for treatment in areas of endemicity., Antimicrob Agents Chemother, 53, 835, 10.1128/AAC.01233-08

J Alvar, 2006, Chemotherapy in the treatment and control of leishmaniasis., Adv Parasitol, 61, 223, 10.1016/S0065-308X(05)61006-8

S Rijal, 2007, Antimonial treatment of visceral leishmaniasis: are current <italic>in vitro</italic> susceptibility assays adequate for prognosis of <italic>in vivo</italic> therapy outcome?, Microbes Infect, 9, 529, 10.1016/j.micinf.2007.01.009

KW Tintaya, 2004, Antigen genes for molecular epidemiology of leishmaniasis: polymorphism of cysteine proteinase B and surface metalloprotease glycoprotein 63 in the <italic>Leishmania donovani</italic> complex., J Infect Dis, 189, 1035, 10.1086/382049

T Laurent, 2007, Epidemiological dynamics of antimonial resistance in <italic>Leishmania donovani</italic>: Genotyping reveals a polyclonal population structure among naturally-resistant clinical isolates from Nepal., Infect Genet Evol, 7, 206, 10.1016/j.meegid.2006.08.005

N Van Meirvenne, 1975, Antigenic variation in syringe passaged populations of Trypanosoma (Trypanozoon) brucei. II. Comparative studies on two antigenic-type collections., Ann Soc Belg Med Trop, 55, 25

JC Mottram, 1992, A developmentally regulated cysteine proteinase gene of <italic>Leishmania mexicana</italic>., Mol Microbiol, 6, 1925, 10.1111/j.1365-2958.1992.tb01365.x

A Kamleh, 2008, Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography: a method with wide applicability to analysis of biomolecules., Rapid Commun Mass Spectrom, 22, 1912, 10.1002/rcm.3564

MA Kamleh, 2009, Towards a platform for the metabonomic profiling of different strains of <italic>Drosophila melanogaster</italic> using liquid chromatography-Fourier transform mass spectrometry., FEBS J, 276, 6798, 10.1111/j.1742-4658.2009.07397.x

MA Kamleh, 2009, Applications of mass spectrometry in metabolomic studies of animal model and invertebrate systems., Brief Funct Genomic Proteomic, 8, 28, 10.1093/bfgp/eln052

RA Scheltema, 2008, Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap., Proteomics, 8, 4647, 10.1002/pmic.200800314

JV Olsen, 2005, Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap., Mol Cell Proteomics, 4, 2010, 10.1074/mcp.T500030-MCP200

C Christin, 2008, Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms., Anal Chem, 80, 7012, 10.1021/ac800920h

W Windig, 2005, The use of the Durbin-Watson criterion for noise and background reduction of complex liquid chromatography/mass spectrometry data and a new algorithm to determine sample differences., Chemometr Intell Lab Syst, 77, 206, 10.1016/j.chemolab.2004.10.008

J Vandesompele, 2002, Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes., Genome Biol, 7, RESEARCH0034

VP Shah, 2000, Bioanalytical method validation—a revisit with a decade of progress., Pharm Res, 17, 1551, 10.1023/A:1007669411738

RA Scheltema, 2009, Simple data-reduction method for high-resolution LC-MS data in metabolomics., Bioanalysis, 1, 1551, 10.4155/bio.09.146

MA Doyle, 2009, LeishCyc: a biochemical pathways database for <italic>Leishmania major</italic>., BMC Syst Biol, 3, 57, 10.1186/1752-0509-3-57

E Fahy, 2007, LIPID MAPS online tools for lipid research., Nucleic Acids Res, 35, W606, 10.1093/nar/gkm324

BO Keller, 2008, Interferences and contaminants encountered in modern mass spectrometry., Anal Chim Acta, 627, 71, 10.1016/j.aca.2008.04.043

H Ogata, 1999, KEGG: Kyoto Encyclopedia of Genes and Genomes., Nucleic Acids Res, 27, 29, 10.1093/nar/27.1.29

DS Wishart, 2007, HMDB: the Human Metabolome Database., Nucleic Acids Res, 35, D521, 10.1093/nar/gkl923

A Scalbert, 2009, Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research., Metabolomics, 5, 435, 10.1007/s11306-009-0168-0

MB Eisen, 1998, Cluster analysis and display of genome-wide expression patterns., Proc Natl Acad Sci U S A, 95, 14863, 10.1073/pnas.95.25.14863

J Trygg, 2007, Chemometrics in metabonomics., J Proteome Res, 6, 469, 10.1021/pr060594q

F Hong, 2006, RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis., Bioinformatics, 22, 2825, 10.1093/bioinformatics/btl476

R Breitling, 2004, Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments., FEBS Lett, 573, 83, 10.1016/j.febslet.2004.07.055

R Breitling, 2005, Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data., J Bioinform Comput Biol, 3, 1171, 10.1142/S0219720005001442

MZ Alam, 2009, Multilocus microsatellite typing (MLMT) reveals genetic homogeneity of <italic>Leishmania donovani</italic> strains in the Indian subcontinent., Infect Genet Evol, 9, 24, 10.1016/j.meegid.2008.09.005

AK Chavali, 2008, Systems analysis of metabolism in the pathogenic trypanosomatid <italic>Leishmania major</italic>., Mol Syst Biol, 4, 177, 10.1038/msb.2008.15

HJ Atherton, 2006, A combined 1H-NMR spectroscopy- and mass spectrometry-based metabolomic study of the PPAR-alpha null mutant mouse defines profound systemic changes in metabolism linked to the metabolic syndrome., Physiol Genomics, 27, 178, 10.1152/physiolgenomics.00060.2006

WB Dunn, 2008, Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes., Phys Biol, 5, 011001, 10.1088/1478-3975/5/1/011001

HC Maltezou, 2010, Drug resistance in visceral leishmaniasis., J Biomed Biotechnol, 2010, 617521, 10.1155/2010/617521

K Zhang, 2007, Redirection of sphingolipid metabolism toward <italic>de novo</italic> synthesis of ethanolamine in <italic>Leishmania</italic>., EMBO J, 26, 1094, 10.1038/sj.emboj.7601565

K Zhang, 2010, Phospholipid and sphingolipid metabolism in <italic>Leishmania</italic>., Mol Biochem Parasitol, 170, 55, 10.1016/j.molbiopara.2009.12.004

M Rakotomanga, 2007, Miltefosine affects lipid metabolism in <italic>Leishmania donovani</italic> promastigotes., Antimicrob Agents Chemother, 51, 1425, 10.1128/AAC.01123-06

MK Wassef, 1985, Lipid analyses of isolated surface membranes of <italic>Leishmania donovani</italic> promastigotes., Lipids, 20, 108, 10.1007/BF02534216

CC HsuChen, 1973, Polyene antibiotic action on lecithin liposomes: effect of cholesterol and fatty acyl chains., Biochem Biophys Res Commun, 51, 972, 10.1016/0006-291X(73)90022-3

N Mbongo, 1998, Mechanism of amphotericin B resistance in <italic>Leishmania donovani</italic> promastigotes., Antimicrob Agents Chemother, 42, 352, 10.1128/AAC.42.2.352

G Barratt, 2009, Cellular transport and lipid interactions of miltefosine., Curr Drug Metab, 10, 247, 10.2174/138920009787846332

E Cauchetier, 2002, Characterisation of atovaquone resistance in <italic>Leishmania infantum</italic> promastigotes., Int J Parasitol, 32, 1043, 10.1016/S0020-7519(02)00065-6

M Basselin, 1998, Alterations in membrane fluidity, lipid metabolism, mitochondrial activity, and lipophosphoglycan expression in pentamidine-resistant <italic>Leishmania</italic>., Parasitol Res, 84, 78, 10.1007/s004360050361

M Basselin, 1997, Altered transport properties of pentamidine-resistant <italic>Leishmania donovani</italic> and <italic>L. amazonensis</italic> promastigotes., Parasitol Res, 83, 413, 10.1007/s004360050274

T Naderer, 2008, The <italic>Leishmania</italic>-macrophage interaction: a metabolic perspective., Cell Microbiol, 10, 301, 10.1111/j.1462-5822.2007.01096.x

FR Opperdoes, 2007, Metabolism of <italic>Leishmania</italic>: proven and predicted., Trends Parasitol, 23, 149, 10.1016/j.pt.2007.02.004

HP de Koning, 2005, Purine and pyrimidine transport in pathogenic protozoa: from biology to therapy., FEMS Microbiol Rev, 29, 987, 10.1016/j.femsre.2005.03.004

MA Basinger, 1981, Structural requirements for chelate antidotal efficacy in acute antimony(III) intoxication., Res Commun Chem Pathol Pharmacol, 32, 355

C Bern, 2006, Liposomal amphotericin B for the treatment of visceral leishmaniasis., Clin Infect Dis, 43, 917, 10.1086/507530