Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively and non-overlapping blocks of m bases in this system. The function P(S) about the number of the consecutive C-G or A-T content cluster conforms to the relation P(S) proportional, variante(-alphas); values of the scaling exponent alpha(CG) are much larger than alpha(AT); and alpha(AT) of 14 chromosomes are hardly changed, whereas alpha(CG) of 14 chromosomes have a number of fluctuations. We found maximum value of A-T cluster size is much larger than C-G, which implies the existence of large A-T cluster. Our study of the width function xi(m) of cluster C-G content showed that follows good power law xi(m) proportional, variantm(-gamma). The average gamma for 14 chromosomes is 0.931. These investigations provide some insight into the nucleotide clusters of DNA sequences, and help us understand other properties of DNA sequences.
Animals ; Base Composition ; Base Sequence ; Chromosomes ; genetics ; DNA, Protozoan ; genetics ; Genome, Protozoan ; Genomics ; Nucleotides ; genetics ; Plasmodium falciparum ; genetics

Piroplasms are tick-transmitted, intracellular, hemoprotozoan parasites that cause anorexia, fever, anemia, and icterus. Theileriosis is caused by Theileria sergenti and causes major economic losses in grazing cattle in Japan and Korea. In May 2003, we examined the antigenic diversity of the major piroplasm surface protein (MPSP) gene in 35 healthy Jeju black cattle that were born and raised at the National Institute of Subtropical Agriculture. On microscopic examination of Giemsa-stained blood smears, 9 of 35 cattle had intra-erythrocytic piroplasms. Hematological data were within normal range for all 35 cattle. Amplification of DNA from all blood samples using universal MPSP gene primers showed mixed infections with C, I, and B type Theileria spp. Type C was identified in 20 of 35 blood samples, and type B was identified in 17 samples. Allelic variation was seen in type B.
Animals ; Antigens, Protozoan/*genetics ; Base Sequence ; Cattle ; DNA Primers/genetics ; *Genetic Variation ; Korea ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; Theileria/*genetics ; Theileriasis/*parasitology

This study was directed to determine the nucleotide sequence of the ITS (internal transcribed spacer) gene of Leishmania donovani isolates from desert foci (L. d XJ771), hill foci (L. d SC10) and plain foci (L. d SD2), and to find out the differences of the sequences of ITS gene among these three isolates. The specific ITS fragments from nuclear DNA of three Leishmania isolates were amplified by PCR, cloned into PMD18-T vector, and then sequenced by the dideoxy chain termination method. Sequence analysis showed that the amplified DNA fragments of the three isolates were 1 086 bp (L. d XJ771), 1 027 bp (L. d SC10) and 1 028 bp (L. d SD2). There were obvious sequence differences among L. d XJ771, L. d SC10 and L. d SD2. The differences between L. d XJ771 (desert foci isolate) and L. d SC10 (hill foci isolate) were less than the differences between L. d XJ771 (desert foci isolate ) and L. d SD2. (plain foci isolate).
China ; Cloning, Molecular ; DNA, Protozoan ; genetics ; DNA, Ribosomal Spacer ; genetics ; Environment ; Leishmania donovani ; genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA

PCR detection of intestinal protozoa is often restrained by a poor DNA recovery or by inhibitors present in feces. The need for an extraction protocol that can overcome these obstacles is therefore clear. QIAamp(R) DNA Stool Mini Kit (Qiagen) was evaluated for its ability to recover DNA from oocysts/cysts directly from feces. Twenty-five Giardia-positive, 15 Cryptosporidium-positive, 15 Entamoeba histolytica-positive, and 45 protozoa-free samples were processed as control by microscopy and immunoassay tests. DNA extracts were amplified using 3 sets of published primers. Following the manufacturer's protocol, the kit showed sensitivity and specificity of 100% towards Giardia and Entamoeba. However, for Cryptosporidium, the sensitivity and specificity were 60% (9/15) and 100%, respectively. A series of optimization experiments involving various steps of the kit's protocol were conducted using Cryptosporidium-positive samples. The best DNA recoveries were gained by raising the lysis temperature to the boiling point for 10 min and the incubation time of the InhibitEX tablet to 5 min. Also, using a pre-cooled ethanol for nucleic acid precipitation and small elution volume (50-100 microl) were valuable. The sensitivity of the amended protocol to Cryptosporidium was raised to 100%. Cryptosporidium DNA was successfully amplified by either the first or the second primer set. When applied on parasite-free feces spiked with variable oocysts/cysts counts, approximately 2 oocysts/cysts were theoretically enough for detection by PCR. To conclude, the Qiagen kit with the amended protocol was proved to be suitable for protozoan DNA extraction directly from feces and support PCR diagnosis.
DNA, Protozoan/*isolation & purification ; Feces/*parasitology ; Humans ; Molecular Diagnostic Techniques/*methods ; Polymerase Chain Reaction/*methods ; Protozoan Infections/*diagnosis ; Sensitivity and Specificity ; Specimen Handling/*methods ; Spores, Protozoan/*genetics

Randomly selected 435 clones from Acanthamoeba healyi cDNA library were sequenced and a total of 387 expressed sequence tags (ESTs) had been generated. Based on the results of BLAST search, 130 clones (34.4%) were identified as the genes encoding surface proteins, enzymes for DNA, energy production or other metabolism, kinases and phosphatases, protease, proteins for signal transduction, structural and cytoskeletal proteins, cell cycle related proteins, transcription factors, transcription and translational machineries, and transporter proteins. Most of the genes (88.5%) are newly identified in the genus Acanthamoeba. Although 15 clones matched the genes of Acanthamoeba located in the public databases, twelve clones were actin gene which was the most frequently expressed gene in this study. These ESTs of Acanthamoeba would give valuable information to study the organism as a model system for biological investigations such as cytoskeleton or cell movement, signal transduction, transcriptional and translational regulations. These results would also provide clues to elucidate factors for pathogenesis in human granulomatous amoebic encephalitis or keratitis by Acanthamoeba.
Acanthamoeba/cytology/*genetics/pathogenicity ; Amebiasis/parasitology ; Animals ; DNA, Protozoan/*genetics ; *Expressed Sequence Tags ; Gene Library ; Human ; Protozoan Proteins/genetics ; *Sequence Analysis, DNA ; Signal Transduction ; Support, Non-U.S. Gov't

Trichomonad species inhabit a variety of vertebrate hosts; however, their potential zoonotic transmission has not been clearly addressed, especially with regard to human infection. Twenty-one strains of trichomonads isolated from humans (5 isolates), pigs (6 isolates), rodents (6 isolates), a water buffalo (1 isolate), a cow (1 isolate), a goat (1 isolate), and a dog (1 isolate) were collected in Indonesia and molecularly characterized. The DNA sequences of the partial 18S small subunit ribosomal RNA (rRNA) gene or 5.8S rRNA gene locus with its flanking regions (internal transcribed spacer region, ITS1 and ITS2) were identified in various trichomonads; Simplicimonas sp., Hexamastix mitis, and Hypotrichomonas sp. from rodents, and Tetratrichomonas sp. and Trichomonas sp. from pigs. All of these species were not detected in humans, whereas Pentatrichomonas hominis was identified in humans, pigs, the dog, the water buffalo, the cow, and the goat. Even when using the high-resolution gene locus of the ITS regions, all P. hominis strains were genetically identical; thus zoonotic transmission between humans and these closely related mammals may be occurring in the area investigated. The detection of Simplicimonas sp. in rodents (Rattus exulans) and P. hominis in water buffalo in this study revealed newly recognized host adaptations and suggested the existence of remaining unrevealed ranges of hosts in the trichomonad species.
Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal Spacer/genetics ; Humans ; Indonesia/epidemiology ; *Mammals ; Protozoan Infections/epidemiology/*parasitology ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Trichomonadida/*classification/*genetics/isolation & purification

OBJECTIVETo characterize the immune response induced by SAG1 encoding plasmid combined with IL-2 gene adjuvant in mice and to assess the protective effect of this vaccination against toxoplasmosis.

METHODSMice were co-injected intramuscularly with plasmid encoding Toxoplasma gondii SAG1 plus murine IL-2 expression vector at a dose of 100 microg. Booster immunizations were employed 2 more times at 3-week interval. As controls, mice were inoculated with PBS or empty plasmid pcDNA3. Humoral and cellular responses were assayed using ELISA for the determination of Ab, Ab isotype and IFN-gamma, as well as IL-4. To detect the integration and dissemination of DNA in the injected mice, PCR and in situ hybridization were performed. All mice were then infected with highly virulent RH tachyzoites of Toxoplasma gondii intraperitoneally.

RESULTSSignificant increases in specific IgG levels were observed in mice after immunization three times with SAG1 expression plasmid. With respect to the IgG isotype, co-inoculation of IL-2 expression plasmid enhanced the level of IgG2a and the production of IFN-gamma. Challenging mice by vaccinating with combined plasmids with RH tachyzoites resulted in prolonged survival.

CONCLUSIONHumoral and cytokine responses elicited by SAG1 DNA immunization can be modulated by co-inoculation with IL-2 expression plasmid. The use of DNA vaccine in combination with an appropriate cytokine gene to prevent T. gondii infection warrants further investigation.

Animals ; Antibodies, Protozoan ; blood ; Antigens, Protozoan ; Cytokines ; biosynthesis ; Female ; Immunization ; Immunoglobulin G ; blood ; classification ; Interleukin-2 ; genetics ; Mice ; Protozoan Proteins ; genetics ; Protozoan Vaccines ; immunology ; Toxoplasma ; immunology ; Toxoplasmosis, Animal ; prevention & control ; Vaccines, DNA ; immunology

The completion of many malaria parasite genomes provides great opportunities for genomewide characterization of gene expression and high-throughput genotyping. Substantial progress in malaria genomics and genotyping has been made recently, particularly the development of various microarray platforms for large-scale characterization of the Plasmodium falciparum genome. Microarray has been used for gene expression analysis, detection of single nucleotide polymorphism (SNP) and copy number variation (CNV), characterization of chromatin modifications, and other applications. Here we discuss some recent advances in genetic mapping and genomic studies of malaria parasites, focusing on the use of high-throughput arrays for the detection of SNP and CNV in the P. falciparum genome. Strategies for genetic mapping of malaria traits are also discussed.
Animals ; *Chromosome Mapping ; DNA, Protozoan/*genetics ; Gene Dosage ; *Microarray Analysis ; Plasmodium falciparum/*genetics ; Polymorphism, Genetic

Plasmodium falciparum malaria is a major public health problem in Thailand due to the emergence of multidrug resistance. The understanding of genetic diversity of malaria parasites is essential for developing effective drugs and vaccines. The genetic diversity of the merozoite surface protein-1 (PfMSP-1) and merozoite surface protein-2 (PfMSP-2) genes was investigated in a total of 145 P. falciparum isolates collected from Mae Sot District, Tak Province, Thailand during 3 different periods (1997-1999, 2005-2007, and 2009-2010). Analysis of genetic polymorphisms was performed to track the evolution of genetic change of P. falciparum using PCR. Both individual genes and their combination patterns showed marked genetic diversity during the 3 study periods. The results strongly support that P. falciparum isolates in Thailand are markedly diverse and patterns changed with time. These 2 polymorphic genes could be used as molecular markers to detect multiple clone infections and differentiate recrudescence from reinfection in P. falciparum isolates in Thailand.
Antigens, Protozoan/*genetics ; DNA, Protozoan/genetics ; Evolution, Molecular ; Humans ; Malaria, Falciparum/parasitology ; Merozoite Surface Protein 1/*genetics ; Plasmodium falciparum/*classification/*genetics/isolation & purification ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Protozoan Proteins/*genetics ; Thailand

Amebiasis is a protozoan disease caused by Entamoeba histolytica and a potential health threat in areas where sanitation and hygiene are inappropriate. Highly sensitive PCR methods for detection of E. histolytica in clinical and environmental samples are extremely useful to control amebiasis and to promote public health. The present study compared several primer sets for small subunit (SSU) rDNA and histone genes of E. histolytica cysts. A 246 bp of the SSU rDNA gene of pure cysts contained in phosphate-buffered saline (PBS) and in stool samples was successfully amplified by nested PCR, using the 1,147-246 bp primer set, of the primary PCR products which were pre-amplified using the 1,147 bp primer as the template. The detection limit of the nested PCR using the 1,147-246 primer set was 10 cysts in both groups (PBS and stool samples). The PCR to detect histone gene showed negative results. We propose that the nested PCR technique to detect SSU rDNA can be used as a highly sensitive genetic method to detect E. histolytica cysts in stool samples.
DNA Primers/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Entamoeba histolytica/genetics/*isolation & purification ; Entamoebiasis/*diagnosis ; Histones/genetics ; Humans ; Molecular Diagnostic Techniques/*methods ; Parasitology/*methods ; Polymerase Chain Reaction/*methods ; Protozoan Proteins/genetics ; Sensitivity and Specificity