@comment{{This file has been generated by bib2bib 1.97}}
@comment{{Command line: bib2bib ../bibli.bib -c 'subject:"plasmodium" or keywords:"plasmodium"' -ob tmp.bib}}
@article{Bozdech2004Antioxidant,
author = {Bozdech, Z. and Ginsburg, H.},
title = {Antioxidant defense in {P}lasmodium falciparum - data mining of the
transcriptome},
journal = {Malaria {J}ournal},
year = {2004},
volume = {3},
pages = {23},
number = {1},
abstract = {The intraerythrocytic malaria parasite is under constant oxidative
stress originating both from endogenous and exogenous processes.
{T}he parasite is endowed with a complete network of enzymes and
proteins that protect it from those threats, but also uses redox
activities to regulate enzyme activities. {I}n the present analysis,
the transcription of the genes coding for the antioxidant defense
elements are viewed in the time-frame of the intraerythrocytic cycle.
{T}ime-dependent transcription data were taken from the transcriptome
of the human malaria parasite {P}lasmodium falciparum. {W}hereas
for several processes the transcription of the many participating
genes is coordinated, in the present case there are some outstanding
deviations where gene products that utilize glutathione or thioredoxin
are transcribed before the genes coding for elements that control
the levels of those substrates are transcribed. {S}uch insights may
hint to novel, non-classical pathways that necessitate further investigations.},
doi = {10.1186/1475-2875-3-23},
pdf = {../local/Bozdech2004Antioxidant.pdf},
file = {Bozdech2004Antioxidant.pdf:local/Bozdech2004Antioxidant.pdf:PDF},
keywords = {microarray plasmodium},
owner = {vert},
url = {http://www.malariajournal.com/content/3/1/23}
}
@article{Bozdech2003Transcriptome,
author = {Bozdech, Z. and Llinas, M. and Pulliam, B. L. and Wong, E. D. and
Zhu, J. and DeRisi, J. L.},
title = {The {T}ranscriptome of the {I}ntraerythrocytic {D}evelopmental {C}ycle
of {P}lasmodium falciparum },
journal = {P{L}o{S} {B}iology},
year = {2003},
volume = {1},
pages = {e5},
number = {1},
abstract = {Plasmodium falciparum is the causative agent of the most burdensome
form of human malaria, affecting 200-300 million individuals per
year worldwide. {T}he recently sequenced genome of {P}. falciparum
revealed over 5,400 genes, of which 60{percnt} encode proteins of
unknown function. {I}nsights into the biochemical function and regulation
of these genes will provide the foundation for future drug and vaccine
development efforts toward eradication of this disease. {B}y analyzing
the complete asexual intraerythrocytic developmental cycle ({IDC})
transcriptome of the {HB}3 strain of {P}. falciparum, we demonstrate
that at least 60{percnt} of the genome is transcriptionally active
during this stage. {O}ur data demonstrate that this parasite has
evolved an extremely specialized mode of transcriptional regulation
that produces a continuous cascade of gene expression, beginning
with genes corresponding to general cellular processes, such as protein
synthesis, and ending with {P}lasmodium-specific functionalities,
such as genes involved in erythrocyte invasion. {T}he data reveal
that genes contiguous along the chromosomes are rarely coregulated,
while transcription from the plastid genome is highly coregulated
and likely polycistronic. {C}omparative genomic hybridization between
{HB}3 and the reference genome strain (3{D}7) was used to distinguish
between genes not expressed during the {IDC} and genes not detected
because of possible sequence variations. {G}enomic differences between
these strains were found almost exclusively in the highly antigenic
subtelomeric regions of chromosomes. {T}he simple cascade of gene
regulation that directs the asexual development of {P}. falciparum
is unprecedented in eukaryotic biology. {T}he transcriptome of the
{IDC} resembles a "just-in-time" manufacturing process whereby induction
of any given gene occurs once per cycle and only at a time when it
is required. {T}hese data provide to our knowledge the first comprehensive
view of the timing of transcription throughout the intraerythrocytic
development of {P}. falciparum and provide a resource for the identification
of new chemotherapeutic and vaccine candidates.},
comment = {(JP Vert) The paper that monitors the 48h cell cycle of P. falciparum},
doi = {10.1371/journal.pbio.0000005},
pdf = {../local/Bozdech2003Transcriptome.pdf},
file = {Bozdech2003Transcriptome.pdf:local/Bozdech2003Transcriptome.pdf:PDF},
keywords = {microarray plasmodium},
owner = {vert},
url = {http://dx.doi.org/10.1371/journal.pbio.0000005 }
}
@article{Bozdech2003Expression,
author = {Bozdech, Z. and Zhu, J. and Joachimiak, M. and Cohen, F. and Pulliam,
B. and DeRisi, J.},
title = {Expression profiling of the schizont and trophozoite stages of {P}lasmodium
falciparum with a long-oligonucleotide microarray},
journal = {Genome {B}iology},
year = {2003},
volume = {4},
pages = {R9},
number = {2},
abstract = {B{ACKGROUND}:{T}he worldwide persistence of drug-resistant {P}lasmodium
falciparum, the most lethal variety of human malaria, is a global
health concern. {T}he {P}. falciparum sequencing project has brought
new opportunities for identifying molecular targets for antimalarial
drug and vaccine development.{RESULTS}:{W}e developed a software
package, {A}rray{O}ligo{S}elector, to design an open reading frame
({ORF})-specific {DNA} microarray using the publicly available {P}.
falciparum genome sequence. {E}ach gene was represented by one or
more long 70 mer oligonucleotides selected on the basis of uniqueness
within the genome, exclusion of low-complexity sequence, balanced
base composition and proximity to the 3' end. {A} first-generation
microarray representing approximately 6,000 {ORF}s of the {P}. falciparum
genome was constructed. {A}rray performance was evaluated through
the use of control oligonucleotide sets with increasing levels of
introduced mutations, as well as traditional northern blotting. {U}sing
this array, we extensively characterized the gene-expression profile
of the intraerythrocytic trophozoite and schizont stages of {P}.
falciparum. {T}he results revealed extensive transcriptional regulation
of genes specialized for processes specific to these two stages.{CONCLUSIONS}:{DNA}
microarrays based on long oligonucleotides are powerful tools for
the functional annotation and exploration of the {P}. falciparum
genome. {E}xpression profiling of trophozoites and schizonts revealed
genes associated with stage-specific processes and may serve as the
basis for future drug targets and vaccine development.},
doi = {10.1186/gb-2003-4-2-r9},
pdf = {../local/Bozdech2003Expression.pdf},
file = {Bozdech2003Expression.pdf:local/Bozdech2003Expression.pdf:PDF},
keywords = {microarray plasmodium},
owner = {vert},
url = {http://genomebiology.com/2003/4/2/R9}
}
@article{Daily2007Distinct,
author = {Daily, J. P. and Scanfeld, D. and Pochet, N. and Le Roch, K. and
Plouffe, D. and Kamal, M. and Sarr, O. and Mboup, S. and Ndir, O.
and Wypi, D.j and Levasseur, K. and Thomas, E. and Tamayo, P. and
Dong, C. and Zhou, Y. and Lander, E. S. and Ndiaye, D. and Wirth,
D. and Winzeler, E. A. and Mesirov, J. P. and Regev, A.},
title = {Distinct physiological states of Plasmodium falciparum in malaria-infected
patients},
journal = {Nature},
year = {2007},
volume = {450},
pages = {1091--1095},
number = {7172},
month = {Dec},
abstract = {Infection with the malaria parasite Plasmodium falciparum leads to
widely different clinical conditions in children, ranging from mild
flu-like symptoms to coma and death. Despite the immense medical
implications, the genetic and molecular basis of this diversity remains
largely unknown. Studies of in vitro gene expression have found few
transcriptional differences between different parasite strains. Here
we present a large study of in vivo expression profiles of parasites
derived directly from blood samples from infected patients. The in
vivo expression profiles define three distinct transcriptional states.
The biological basis of these states can be interpreted by comparison
with an extensive compendium of expression data in the yeast Saccharomyces
cerevisiae. The three states in vivo closely resemble, first, active
growth based on glycolytic metabolism, second, a starvation response
accompanied by metabolism of alternative carbon sources, and third,
an environmental stress response. The glycolytic state is highly
similar to the known profile of the ring stage in vitro, but the
other states have not been observed in vitro. The results reveal
a previously unknown physiological diversity in the in vivo biology
of the malaria parasite, in particular evidence for a functional
mitochondrion in the asexual-stage parasite, and indicate in vivo
and in vitro studies to determine how this variation may affect disease
manifestations and treatment.},
doi = {10.1038/nature06311},
pdf = {../local/Daily2007Distinct.pdf},
file = {Daily2007Distinct.pdf:Daily2007Distinct.pdf:PDF},
institution = {Department of Immunology and Infectious Disease, [Harvard School
of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115,
USA.},
keywords = {plasmodium},
owner = {jp},
pii = {nature06311},
pmid = {18046333},
timestamp = {2009.04.28},
url = {http://dx.doi.org/10.1038/nature06311}
}
@article{Doolan2003Identification,
author = {Denise L Doolan and Scott Southwood and Daniel A Freilich and John
Sidney and Norma L Graber and Lori Shatney and Lolita Bebris and
Laurence Florens and Carlota Dobano and Adam A Witney and Ettore
Appella and Stephen L Hoffman and John R Yates and Daniel J Carucci
and Alessandro Sette},
title = {{I}dentification of {P}lasmodium falciparum antigens by antigenic
analysis of genomic and proteomic data.},
journal = {Proc. Natl. Acad. Sci. U. S. A.},
year = {2003},
volume = {100},
pages = {9952--9957},
number = {17},
month = {Aug},
abstract = {The recent explosion in genomic sequencing has made available a wealth
of data that can now be analyzed to identify protein antigens, potential
targets for vaccine development. Here we present, in the context
of Plasmodium falciparum, a strategy that rapidly identifies target
antigens from large and complex genomes. Sixteen antigenic proteins
recognized by volunteers immunized with radiation-attenuated P. falciparum
sporozoites, but not by mock immunized controls, were identified.
Several of these were more antigenic than previously identified and
well characterized P. falciparum-derived protein antigens. The data
suggest that immune responses to Plasmodium are dispersed on a relatively
large number of parasite antigens. These studies have implications
for our understanding of immunodominance and breadth of responses
to complex pathogens.},
doi = {10.1073/pnas.1633254100},
pdf = {../local/Doolan2003Identification.pdf},
file = {Doolan2003Identification.pdf:local/Doolan2003Identification.pdf:PDF},
keywords = {plasmodium},
pii = {1633254100},
pmid = {12886016},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1073/pnas.1633254100}
}
@article{Florens2002proteomic,
author = {Laurence Florens and Michael P Washburn and J. Dale Raine and Robert
M Anthony and Munira Grainger and J. David Haynes and J. Kathleen
Moch and Nemone Muster and John B Sacci and David L Tabb and Adam
A Witney and Dirk Wolters and Yimin Wu and Malcolm J Gardner and
Anthony A Holder and Robert E Sinden and John R Yates and Daniel
J Carucci},
title = {{A} proteomic view of the {P}lasmodium falciparum life cycle.},
journal = {Nature},
year = {2002},
volume = {419},
pages = {520--526},
number = {6906},
month = {Oct},
abstract = {The completion of the Plasmodium falciparum clone 3D7 genome provides
a basis on which to conduct comparative proteomics studies of this
human pathogen. Here, we applied a high-throughput proteomics approach
to identify new potential drug and vaccine targets and to better
understand the biology of this complex protozoan parasite. We characterized
four stages of the parasite life cycle (sporozoites, merozoites,
trophozoites and gametocytes) by multidimensional protein identification
technology. Functional profiling of over 2,400 proteins agreed with
the physiology of each stage. Unexpectedly, the antigenically variant
proteins of var and rif genes, defined as molecules on the surface
of infected erythrocytes, were also largely expressed in sporozoites.
The detection of chromosomal clusters encoding co-expressed proteins
suggested a potential mechanism for controlling gene expression.},
doi = {10.1038/nature01107},
pdf = {../local/Florens2002proteomic.pdf},
file = {Florens2002proteomic.pdf:local/Florens2002proteomic.pdf:PDF},
keywords = {plasmodium},
pii = {nature01107},
pmid = {12368862},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1038/nature01107}
}
@article{Fraunholz2005Systems,
author = {M. J. Fraunholz},
title = {{S}ystems biology in malaria research.},
journal = {Trends Parasitol.},
year = {2005},
volume = {21},
pages = {393--395},
number = {9},
month = {Sep},
abstract = {A recent publication of genome and expression analyses of the murine
parasites Plasmodium chabaudi chabaudi and Plasmodium berghei presents
the state of the art in Plasmodium systems biology. By integrating
genomics, transcriptomics and proteomics, the authors can classify
and annotate genes by their expression profiles and can even detect
evidence of posttranscriptional gene silencing in the murine malaria
species.},
doi = {10.1016/j.pt.2005.07.007},
pdf = {../local/Fraunholz2005Systems.pdf},
file = {Fraunholz2005Systems.pdf:Fraunholz2005Systems.pdf:PDF},
keywords = {plasmodium},
pii = {S1471-4922(05)00194-7},
pmid = {16043412},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1016/j.pt.2005.07.007}
}
@article{Gardner2002Genome,
author = {Malcolm J Gardner and Neil Hall and Eula Fung and Owen White and
Matthew Berriman and Richard W Hyman and Jane M Carlton and Arnab
Pain and Karen E Nelson and Sharen Bowman and Ian T Paulsen and Keith
James and Jonathan A Eisen and Kim Rutherford and Steven L Salzberg
and Alister Craig and Sue Kyes and Man-Suen Chan and Vishvanath Nene
and Shamira J Shallom and Bernard Suh and Jeremy Peterson and Sam
Angiuoli and Mihaela Pertea and Jonathan Allen and Jeremy Selengut
and Daniel Haft and Michael W Mather and Akhil B Vaidya and David
M A Martin and Alan H Fairlamb and Martin J Fraunholz and David S
Roos and Stuart A Ralph and Geoffrey I McFadden and Leda M Cummings
and G. Mani Subramanian and Chris Mungall and J. Craig Venter and
Daniel J Carucci and Stephen L Hoffman and Chris Newbold and Ronald
W Davis and Claire M Fraser and Bart Barrell},
title = {{G}enome sequence of the human malaria parasite {P}lasmodium falciparum.},
journal = {Nature},
year = {2002},
volume = {419},
pages = {498--511},
number = {6906},
month = {Oct},
abstract = {The parasite Plasmodium falciparum is responsible for hundreds of
millions of cases of malaria, and kills more than one million African
children annually. Here we report an analysis of the genome sequence
of P. falciparum clone 3D7. The 23-megabase nuclear genome consists
of 14 chromosomes, encodes about 5,300 genes, and is the most (A
+ T)-rich genome sequenced to date. Genes involved in antigenic variation
are concentrated in the subtelomeric regions of the chromosomes.
Compared to the genomes of free-living eukaryotic microbes, the genome
of this intracellular parasite encodes fewer enzymes and transporters,
but a large proportion of genes are devoted to immune evasion and
host-parasite interactions. Many nuclear-encoded proteins are targeted
to the apicoplast, an organelle involved in fatty-acid and isoprenoid
metabolism. The genome sequence provides the foundation for future
studies of this organism, and is being exploited in the search for
new drugs and vaccines to fight malaria.},
doi = {10.1038/nature01097},
pdf = {../local/Gardner2002Genome.pdf},
file = {Gardner2002Genome.pdf:local/Gardner2002Genome.pdf:PDF},
keywords = {plasmodium},
pii = {nature01097},
pmid = {12511928},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1038/nature01097}
}
@article{Hall2005comprehensive,
author = {Neil Hall and Marianna Karras and J. Dale Raine and Jane M Carlton
and Taco W A Kooij and Matthew Berriman and Laurence Florens and
Christoph S Janssen and Arnab Pain and Georges K Christophides and
Keith James and Kim Rutherford and Barbara Harris and David Harris
and Carol Churcher and Michael A Quail and Doug Ormond and Jon Doggett
and Holly E Trueman and Jacqui Mendoza and Shelby L Bidwell and Marie-Adele
Rajandream and Daniel J Carucci and John R Yates and Fotis C Kafatos
and Chris J Janse and Bart Barrell and C. Michael R Turner and Andrew
P Waters and Robert E Sinden},
title = {{A} comprehensive survey of the {P}lasmodium life cycle by genomic,
transcriptomic, and proteomic analyses.},
journal = {Science},
year = {2005},
volume = {307},
pages = {82--86},
number = {5706},
month = {Jan},
abstract = {Plasmodium berghei and Plasmodium chabaudi are widely used model malaria
species. Comparison of their genomes, integrated with proteomic and
microarray data, with the genomes of Plasmodium falciparum and Plasmodium
yoelii revealed a conserved core of 4500 Plasmodium genes in the
central regions of the 14 chromosomes and highlighted genes evolving
rapidly because of stage-specific selective pressures. Four strategies
for gene expression are apparent during the parasites' life cycle:
(i) housekeeping; (ii) host-related; (iii) strategy-specific related
to invasion, asexual replication, and sexual development; and (iv)
stage-specific. We observed posttranscriptional gene silencing through
translational repression of messenger RNA during sexual development,
and a 47-base 3' untranslated region motif is implicated in this
process.},
doi = {10.1126/science.1103717},
pdf = {../local/Hall2005comprehensive.pdf},
file = {Hall2005comprehensive.pdf:local/Hall2005comprehensive.pdf:PDF},
keywords = {plasmodium},
pii = {307/5706/82},
pmid = {15637271},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1126/science.1103717}
}
@article{Khan2005Proteome,
author = {Shahid M Khan and Blandine Franke-Fayard and Gunnar R Mair and Edwin
Lasonder and Chris J Janse and Matthias Mann and Andrew P Waters},
title = {{P}roteome analysis of separated male and female gametocytes reveals
novel sex-specific {P}lasmodium biology.},
journal = {Cell},
year = {2005},
volume = {121},
pages = {675--687},
number = {5},
month = {Jun},
abstract = {Gametocytes, the precursor cells of malaria-parasite gametes, circulate
in the blood and are responsible for transmission from host to mosquito
vector. The individual proteomes of male and female gametocytes were
analyzed using mass spectrometry, following separation by flow sorting
of transgenic parasites expressing green fluorescent protein, in
a sex-specific manner. Promoter tagging in transgenic parasites confirmed
the designation of stage and sex specificity of the proteins. The
male proteome contained 36\% (236 of 650) male-specific and the female
proteome 19\% (101 of 541) female-specific proteins, but they share
only 69 proteins, emphasizing the diverged features of the sexes.
Of all the malaria life-cycle stages analyzed, the male gametocyte
has the most distinct proteome, containing many proteins involved
in flagellar-based motility and rapid genome replication. By identification
of gender-specific protein kinases and phosphatases and using targeted
gene disruption of two kinases, new sex-specific regulatory pathways
were defined.},
doi = {10.1016/j.cell.2005.03.027},
pdf = {../local/Khan2005Proteome.pdf},
file = {Khan2005Proteome.pdf:local/Khan2005Proteome.pdf:PDF},
keywords = {plasmodium},
pii = {S0092-8674(05)00299-0},
pmid = {15935749},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1016/j.cell.2005.03.027}
}
@article{LaCount2005protein,
author = {Douglas J LaCount and Marissa Vignali and Rakesh Chettier and Amit
Phansalkar and Russell Bell and Jay R Hesselberth and Lori W Schoenfeld
and Irene Ota and Sudhir Sahasrabudhe and Cornelia Kurschner and
Stanley Fields and Robert E Hughes},
title = {{A} protein interaction network of the malaria parasite {P}lasmodium
falciparum.},
journal = {Nature},
year = {2005},
volume = {438},
pages = {103--107},
number = {7064},
month = {Nov},
abstract = {Plasmodium falciparum causes the most severe form of malaria and kills
up to 2.7 million people annually. Despite the global importance
of P. falciparum, the vast majority of its proteins have not been
characterized experimentally. Here we identify P. falciparum protein-protein
interactions using a high-throughput version of the yeast two-hybrid
assay that circumvents the difficulties in expressing P. falciparum
proteins in Saccharomyces cerevisiae. From more than 32,000 yeast
two-hybrid screens with P. falciparum protein fragments, we identified
2,846 unique interactions, most of which include at least one previously
uncharacterized protein. Informatic analyses of network connectivity,
coexpression of the genes encoding interacting fragments, and enrichment
of specific protein domains or Gene Ontology annotations were used
to identify groups of interacting proteins, including one implicated
in chromatin modification, transcription, messenger RNA stability
and ubiquitination, and another implicated in the invasion of host
cells. These data constitute the first extensive description of the
protein interaction network for this important human pathogen.},
doi = {10.1038/nature04104},
pdf = {../local/LaCount2005protein.pdf},
file = {LaCount2005protein.pdf:local/LaCount2005protein.pdf:PDF},
keywords = {plasmodium},
pii = {nature04104},
pmid = {16267556},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1038/nature04104}
}
@article{Lasonder2002Analysis,
author = {Edwin Lasonder and Yasushi Ishihama and Jens S Andersen and Adriaan
M W Vermunt and Arnab Pain and Robert W Sauerwein and Wijnand M C
Eling and Neil Hall and Andrew P Waters and Hendrik G Stunnenberg
and Matthias Mann},
title = {{A}nalysis of the {P}lasmodium falciparum proteome by high-accuracy
mass spectrometry.},
journal = {Nature},
year = {2002},
volume = {419},
pages = {537--542},
number = {6906},
month = {Oct},
abstract = {The annotated genomes of organisms define a 'blueprint' of their possible
gene products. Post-genome analyses attempt to confirm and modify
the annotation and impose a sense of the spatial, temporal and developmental
usage of genetic information by the organism. Here we describe a
large-scale, high-accuracy (average deviation less than 0.02 Da at
1,000 Da) mass spectrometric proteome analysis of selected stages
of the human malaria parasite Plasmodium falciparum. The analysis
revealed 1,289 proteins of which 714 proteins were identified in
asexual blood stages, 931 in gametocytes and 645 in gametes. The
last two groups provide insights into the biology of the sexual stages
of the parasite, and include conserved, stage-specific, secreted
and membrane-associated proteins. A subset of these proteins contain
domains that indicate a role in cell-cell interactions, and therefore
can be evaluated as potential components of a malaria vaccine formulation.
We also report a set of peptides with significant matches in the
parasite genome but not in the protein set predicted by computational
methods.},
doi = {10.1038/nature01111},
pdf = {../local/Lasonder2002Analysis.pdf},
file = {Lasonder2002Analysis.pdf:local/Lasonder2002Analysis.pdf:PDF},
keywords = {plasmodium},
pii = {nature01111},
pmid = {12368862},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1038/nature01111}
}
@article{LeRoch2003Discovery,
author = {Le Roch, K. G. and Zhou, Y. and Blair, P. L. and Grainger, M. and
Moch, J. K. and Haynes, J. D. and De la Vega, P. and Holder, A. A.
and Batalov, S. and Carucci, D. J. and Winzeler, E. A.},
title = {Discovery of Gene Function by Expression Profiling of the Malaria
Parasite Life Cycle},
journal = {Science},
year = {2003},
volume = {301},
pages = {1503-1508},
number = {5639},
abstract = {The completion of the genome sequence for {P}lasmodium falciparum,
the species responsible for most malaria human deaths, has the potential
to reveal hundreds of new drug targets and proteins involved in pathogenesis.
{H}owever, only approximately 35% of the genes code for proteins
with an identifiable function. {T}he absence of routine genetic tools
for studying {P}lasmodium parasites suggests that this number is
unlikely to change quickly if conventional serial methods are used
to characterize encoded proteins. {H}ere, we use a high-density oligonucleotide
array to generate expression profiles of human and mosquito stages
of the malaria parasite's life cycle. {G}enes with highly correlated
levels and temporal patterns of expression were often involved in
similar functions or cellular processes.},
doi = {10.1126/science.1087025},
pdf = {../local/LeRoch2003Discovery.pdf},
file = {LeRoch2003Discovery.pdf:LeRoch2003Discovery.pdf:PDF},
keywords = {microarray plasmodium},
owner = {vert},
url = {http://www.sciencemag.org/cgi/content/full/301/5639/1503}
}
@article{Llinas2006Comparative,
author = {Llin{\'a}s, M. and Bozdech, Z. and Wong, E. D. and Adai, A. T. and
DeRisi, J. L.},
title = {{C}omparative whole genome transcriptome analysis of three {P}lasmodium
falciparum strains.},
journal = {Nucleic Acids Res.},
year = {2006},
volume = {34},
pages = {1166--1173},
number = {4},
abstract = {Gene expression patterns have been demonstrated to be highly variable
between similar cell types, for example lab strains and wild strains
of Saccharomyces cerevisiae cultured under identical growth conditions
exhibit a wide range of expression differences. We have used a genome-wide
approach to characterize transcriptional differences between strains
of Plasmodium falciparum by characterizing the transcriptome of the
48 h intraerythrocytic developmental cycle (IDC) for two strains,
3D7 and Dd2 and compared these results to our prior work using the
HB3 strain. These three strains originate from geographically diverse
locations and possess distinct drug sensitivity phenotypes. Our goal
was to identify transcriptional differences related to phenotypic
properties of these strains including immune evasion and drug sensitivity.
We find that the highly streamlined transcriptome is remarkably well
conserved among all three strains, and differences in gene expression
occur mainly in genes coding for surface antigens involved in parasite-host
interactions. Our analysis also detects several transcripts that
are unique to individual strains as well as identifying large chromosomal
deletions and highly polymorphic regions across strains. The majority
of these genes are uncharacterized and have no homology to other
species. These tractable transcriptional differences provide important
phenotypes for these otherwise highly related strains of Plasmodium.},
doi = {10.1093/nar/gkj517},
keywords = {plasmodium},
pii = {34/4/1166},
pmid = {16493140},
timestamp = {2007.10.04},
url = {http://dx.doi.org/10.1093/nar/gkj517}
}
@article{Puijalon2004Malaria,
author = {O. Mercereau-Puijalon},
title = {Malaria research in the post-genomic era},
journal = {J. Soc. Biol.},
year = {2004},
volume = {198},
pages = {193--197},
number = {3},
abstract = {Genomic sequence determination of Plasmodium falciparum and other
species of the genus, as well as that of Anopheles gambiae, and human,
rat and mouse genome sequencing have completely changed the landscape
of fundamental research about malaria. These data should urgently
be exploited, in order to develop new tools to combat the disease:
new drugs, fine dissection of the cascade of events following infection
of the various vector species and vertebrate host, analysis of the
complex interaction leading to the pathology or, inversely, contributing
to sustained protection. Powerful population biology tools are now
available, allowing to investigate genetic exchanges within natural
population and to identify factors structuring parasitic and vector
populations. Nevertheless, important impediments persist, including
the complexity of experimental systems and the unclear relevance
of animals models. Numerous challenges are to be faced; they call
upon a more efficient organisation of research efforts in the systematic
explorations using the powerful novel post-genomic technologies,
as well as the development of new tools and experimental models required
by functional genomics and integrative biology.},
keywords = {plasmodium},
pmid = {15662935},
timestamp = {2006.04.13}
}
@article{Shock2007Whole-genome,
author = {Shock, J. L. and Fischer, K. F. and DeRisi, J. L.},
title = {Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals
a global lengthening of mRNA half-life during the intra-erythrocytic
development cycle.},
journal = {Genome Biol.},
year = {2007},
volume = {8},
pages = {R134},
number = {7},
abstract = {BACKGROUND: The rate of mRNA decay is an essential element of post-transcriptional
regulation in all organisms. Previously, studies in several organisms
found that the specific half-life of each mRNA is precisely related
to its physiologic role, and plays an important role in determining
levels of gene expression. RESULTS: We used a genome-wide approach
to characterize mRNA decay in Plasmodium falciparum. We found that,
globally, rates of mRNA decay increase dramatically during the asexual
intra-erythrocytic developmental cycle. During the ring stage of
the cycle, the average mRNA half-life was 9.5 min, but this was extended
to an average of 65 min during the late schizont stage of development.
Thus, a major determinant of mRNA decay rate appears to be linked
to the stage of intra-erythrocytic development. Furthermore, we found
specific variations in decay patterns superimposed upon the dominant
trend of progressive half-life lengthening. These variations in decay
pattern were frequently enriched for genes with specific cellular
functions or processes. CONCLUSION: Elucidation of Plasmodium mRNA
decay rates provides a key element for deciphering mechanisms of
genetic control in this parasite, by complementing and extending
previous mRNA abundance studies. Our results indicate that progressive
stage-dependent decreases in mRNA decay rate function are a major
determinant of mRNA accumulation during the schizont stage of intra-erythrocytic
development. This type of genome-wide change in mRNA decay rate has
not been observed in any other organism to date, and indicates that
post-transcriptional regulation may be the dominant mechanism of
gene regulation in P. falciparum.},
doi = {10.1186/gb-2007-8-7-r134},
institution = {Department of Biochemistry and Biophysics, University of California
San Francisco, 1700 4th Street, San Francisco, California 94158-2330,
USA.},
keywords = {plasmodium},
owner = {jp},
pii = {gb-2007-8-7-r134},
pmid = {17612404},
timestamp = {2009.01.21},
url = {http://dx.doi.org/10.1186/gb-2007-8-7-r134}
}
@article{Sinden2004proteomic,
author = {R. E. Sinden},
title = {A proteomic analysis of malaria biology: integration of old literature
and new technologies.},
journal = {Int. J. Parasitol.},
year = {2004},
volume = {34},
pages = {1441--1450},
number = {13-14},
month = {Dec},
abstract = {The genomic revolution has brought a new vitality into research on
Plasmodium, its insect and vertebrate hosts. At the cellular level
nowhere is the impact greater than in the analysis of protein expression
and the 'assembly' of the supramolecular machines that together comprise
the functional cell. The repetitive phases of invasion and replication
that typify the malaria life cycle, together with the unique phase
of sexual differentiation provide a powerful platform on which to
investigate the 'molecular machines' that underpin parasite strategy
and stage-specific functions. This approach is illustrated here in
an analysis of the ookinete of Plasmodium berghei. Such analyses
are useful only if conducted with a secure understanding of parasite
biology. The importance of carefully searching the older literature
to reach this understanding cannot be over-emphasised. When viewed
together, the old and new data can give rapid and penetrating insights
into what some might now term the 'Systems-Biology' of Plasmodium.},
doi = {10.1016/j.ijpara.2004.10.005},
pdf = {../local/Sinden2004proteomic.pdf},
file = {Sinden2004proteomic.pdf:local/Sinden2004proteomic.pdf:PDF},
keywords = {plasmodium},
pii = {S0020-7519(04)00210-3},
pmid = {15582521},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1016/j.ijpara.2004.10.005}
}
@article{Winzeler2006Applied,
author = {E. A Winzeler},
title = {{A}pplied systems biology and malaria.},
journal = {Nat. Rev. Microbiol.},
year = {2006},
volume = {4},
pages = {145--151},
number = {2},
month = {Feb},
abstract = {One of the goals of systems-biology research is to discover networks
and interactions by integrating diverse data sets. So far, systems-biology
research has focused on model organisms, which are well characterized
and therefore suited to testing new methods. Systems biology has
great potential for use in the search for therapies for disease.
Here, the potential of systems-biology approaches in the search for
new drugs and vaccines to treat malaria is examined.},
doi = {10.1038/nrmicro1327},
pdf = {../local/Winzeler2006Applied.pdf},
file = {Winzeler2006Applied.pdf:local/Winzeler2006Applied.pdf:PDF},
keywords = {plasmodium},
pii = {nrmicro1327},
pmid = {16362033},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1038/nrmicro1327}
}
@article{Young2005Plasmodium,
author = {Jason A Young and Quinton L Fivelman and Peter L Blair and Patricia
de la Vega and Karine G Le Roch and Yingyao Zhou and Daniel J Carucci
and David A Baker and Elizabeth A Winzeler},
title = {{T}he {P}lasmodium falciparum sexual development transcriptome: a
microarray analysis using ontology-based pattern identification.},
journal = {Mol. Biochem. Parasitol.},
year = {2005},
volume = {143},
pages = {67--79},
number = {1},
month = {Sep},
abstract = {The sexual stages of malarial parasites are essential for the mosquito
transmission of the disease and therefore are the focus of transmission-blocking
drug and vaccine development. In order to better understand genes
important to the sexual development process, the transcriptomes of
high-purity stage I-V Plasmodium falciparum gametocytes were comprehensively
profiled using a full-genome high-density oligonucleotide microarray.
The interpretation of this transcriptional data was aided by applying
a novel knowledge-based data-mining algorithm termed ontology-based
pattern identification (OPI) using current information regarding
known sexual stage genes as a guide. This analysis resulted in the
identification of a sexual development cluster containing 246 genes,
of which approximately 75\% were hypothetical, exhibiting highly-correlated,
gametocyte-specific expression patterns. Inspection of the upstream
promoter regions of these 246 genes revealed putative cis-regulatory
elements for sexual development transcriptional control mechanisms.
Furthermore, OPI analysis was extended using current annotations
provided by the Gene Ontology Consortium to identify 380 statistically
significant clusters containing genes with expression patterns characteristic
of various biological processes, cellular components, and molecular
functions. Collectively, these results, available as part of a web-accessible
OPI database (http://carrier.gnf.org/publications/Gametocyte), shed
light on the components of molecular mechanisms underlying parasite
sexual development and other areas of malarial parasite biology.},
doi = {10.1016/j.molbiopara.2005.05.007},
pdf = {../local/Young2005Plasmodium.pdf},
file = {Young2005Plasmodium.pdf:local/Young2005Plasmodium.pdf:PDF},
keywords = {plasmodium},
pii = {S0166-6851(05)00162-3},
pmid = {16005087},
timestamp = {2006.04.13},
url = {http://dx.doi.org/10.1016/j.molbiopara.2005.05.007}
}
@article{Young2005Using,
author = {J. A. Young and E. A. Winzeler},
title = {{U}sing expression information to discover new drug and vaccine targets
in the malaria parasite {P}lasmodium falciparum.},
journal = {Pharmacogenomics},
year = {2005},
volume = {6},
pages = {17--26},
number = {1},
month = {Jan},
abstract = {The recent completion of the malaria parasite Plasmodium falciparum
genome has opened the door for applying a variety of genomic-based
systems biology approaches that complement existing gene-by-gene
methods of investigation. Transcriptomic analyses of P.falciparum
using DNA microarrays has allowed for the rapid elucidation of gene
function, parasite drug response, and invivo expression profiles,
as well as general mechanisms guiding the parasite life cycle that
are vital to disease pathogenesis. The results of these studies have
identified promising novel gene targets for the development of new
drug and vaccine therapies.},
keywords = {plasmodium},
pii = {PGS060105},
pmid = {15723602},
timestamp = {2006.04.13}
}
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