The ribosomal gene spacer as a tool for the taxonomy of Leishmania

Leishmania mexicana differentiation involves a selective plasma membrane autophagic-like process

Parasites of the Leishmania genus, which are the causative agents of leishmaniasis, display a complex life cycle, from a flagellated form (promastigotes) residing in the midgut of the phlebotomine vector to a non-flagellated form (amastigote) invading the mammalian host. The cellular process for the conversion between these forms is an interesting biological phenomenon involving modulation of the plasma membrane. In this study, we describe a selective autophagic-like process during the in vitro differentiation of Leishmania mexicana promastigote to amastigote-like cells. This process is responsible for size reduction and shape change of the promastigote (15-20 μm long) to the rounded amastigote-like form (4-5 μm long), identical to the one that infects host macrophages. This autophagic-like process is characterized by a profound folding of the plasma membrane and the presence of abundant cytoplasmic lipid droplets that may be the product of changes in the lipid metabolism. The key feature for the differentiation process at either pH 7.0 or pH 5.5 is the shift in temperature from 25 to 35 °C. Flagella shortening during the differentiation process appears as the product of continuous flagellar microtubular disassembly that is also accompanied by changes in mitochondrion localization. Drugs directed at blocking the parasite autophagic-like process could be important as new strategies to fight the disease.

Regulatory volume decrease in Leishmania mexicana: effect of anti-microtubule drugs

The trypanosomatid cytoskeleton is responsible for the parasite's shape and it is modulated throughout the different stages of the parasite's life cycle. When parasites are exposed to media with reduced osmolarity, they initially swell, but subsequently undergo compensatory shrinking referred to as regulatory volume decrease (RVD). We studied the effects of anti-microtubule (Mt) drugs on the proliferation of Leishmania mexicana promastigotes and their capacity to undergo RVD. All of the drugs tested exerted antiproliferative effects of varying magnitudes [ansamitocin P3 (AP3)> trifluoperazine > taxol > rhizoxin > chlorpromazine]. No direct relationship was found between antiproliferative drug treatment and RVD. Similarly, Mt stability was not affected by drug treatment. Ansamitocin P3, which is effective at nanomolar concentrations, blocked amastigote-promastigote differentiation and was the only drug that impeded RVD, as measured by light dispersion. AP3 induced 2 kinetoplasts (Kt) 1 nucleus cells that had numerous flagella-associated Kts throughout the cell. These results suggest that the dramatic morphological changes induced by AP3 alter the spatial organisation and directionality of the Mts that are necessary for the parasite's hypotonic stress-induced shape change, as well as its recovery.

Cloning of a 1.8 kb repeated sequence for the identification and comparison of Giardia intestinalis isolates

Restriction enzyme digestion of bulk DNA from Giardia intestinalis reveals the presence of repeated sequences. A prominent 1.8 kb band in the Alu I profile was cloned into the pUC8 plasmid (pGI7) and used for comparing strains. When blots of DNA of 34 isolates from different geographic areas are probed with pGI7, hybridization with identical intensities can be detected. However, some strains give different hybridization patterns with several restriction enzymes. No hybridization of pGI7 can be detected with DNA from Trypanosoma brucei, Naegleria fowleri, Entamoeba histolytica and Trichomonas vaginalis. Therefore probe pGI7 may be useful in comparing different isolates as well as in screening for G. intestinalis infection.

Leishmania mexicana: Identification and characterization of an aspartyl proteinase activity

An aspartyl proteinase activity was detected in the soluble fraction (SF) of Leishmania mexicana promastigotes by the use of the synthetic substrate benzoyl-Arg-Gly-Phe-Phe-Leu-4-methoxy-beta-naphthylamide selective for Cathepsin D like aspartyl-proteinases. This peptide was hydrolyzed with an apparent K(m) of 2.3+/-0.3 microM. The classic inhibitor of aspartyl-proteinases, diazo-acetyl-norleucinemethylester (DAN) inhibited the proteolytic activity with an IC(50) of 400 microM. The soluble fraction degraded (in absence of thiol groups) human fibrinogen with a specific activity of 533 U/mg protein. When tested for the ability to inhibit the "in vitro" proliferation of L. mexicana promastigotes, DAN showed concentration dependent anti-proliferative effects with a LD(50) of 466 microM at 48 h, with a significant fall in this value to 22 microM after 72 h. This is the first characterization of an aspartyl-proteinase activity in Leishmania, calling for further studies directed towards the physiologic role of these enzymes in the parasite. The anti-proliferative effect of its inhibition makes this enzyme a putative new target for the development of leishmanicidal drugs.

PCR identification of Leishmania in diagnosis and control of canine leishmaniasis

Leishmaniases are endemic in many countries, mainly in rural areas. In Brazil, Leishmania infection is responsible for many cases of Leishmaniases, including recent reports in urban regions. Despite their sensitivity, traditional serological and parasitological methods for detecting Leishmaniases have proven inadequate for species discrimination. This study aimed to identify Leishmania species in biological samples by a fast methodology, avoiding "in vitro" cultivation. Knowledge of the Leishmania species is an important tool in regions where both New World visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL) are prevalent. As these new foci appear in areas not traditionally endemic for VL, the main problem is to distinguish between true autochthonous infections and infections acquired in other well-known endemic areas. Since, domestic dogs are known to be the main VL and CL reservoir, they are regularly investigated in endemic areas to prevent, principally, severe and often fatal VL in humans. However, several infected dogs present no clinical signs or clinical signs similar to other canine diseases. Here, we evaluated the ability of PCR to diagnose VL and distinguish L. (L.) chagasi from other Leishmania species in domestic dogs. Samples from 114 dogs from 30 cities (Sao Paulo, Brazil) were divided into two groups: 44 symptomatic and 70 asymptomatic. They were assayed by parasitological methods (culture and microscopic examination) and PCR to determine L. (L.) chagasi, L. (V.) braziliensis; and in some cases, Leishmania spp. Parasitological tests and PCR-L. chagasi were concordant in 105 samples (92%). VL was confirmed in 49 dogs, while 56 had negative results. Of the 114 samples, 9 had discordant results, but were further tested by PCR-Leishmania spp. with positive results. VL was also confirmed in 4 dogs having negative parasitological tests and positive PCR-L. chagasi. Consequently, this PCR was positive for 100% (53/49) of dogs with parasites detected in parasitological tests. Also, PCR demonstrated high specificity detecting 61 dogs negative for VL. Leishmania infection was negative in 56 dogs, and 5 with positive culture and PCR-Leishmania spp. had CL since they were positive in PCR-L. braziliensis. This study shows the importance of including PCR in diagnosis of Leishmaniases by differential diagnosis contributing to the surveillance and control of VL programs.

Characterization of Leishmania isolates from Nepalese patients with visceral leishmaniasis

In Nepal, visceral leishmaniasis (VL) is endemic in 13 districts of the central and eastern regions. A total of 166 bone-marrow aspirates were obtained from patients with suspected VL. Ninety-seven were identified as positive by microscopy, and 29 of those were successfully isolated and cultured. We characterized these isolates by molecular analysis and by their ability to infect mice. PCR-restriction fragment length polymorphism analysis of the mini-exon and the cysteine proteinase b gene showed that all isolates were Leishmania donovani, and the restriction pattern of the Nepalese isolates corresponded to the standard Indian strain of L. donovani but differed from that of the Kenyan strain. The single-strand conformation polymorphism analysis of ribosomal internal transcribed spacer showed no genetic heterogeneity within Nepalese isolates. Intraperitoneal inoculation with the promastigotes of all isolates resulted in amastigote proliferation in the spleen of 20 nude mice, of which ten isolates were highly infective, and ten were moderately infective, including one BALB/c mouse. Of the 20 amastigotes isolated from the spleen of nude mice, only the ten highly infective isolates infected BALB/c mice, of which, two isolates were considered to have low infectivity, three isolates were considered to be moderately infective, and five isolates were considered to be highly infective.

Leishmania major: genetic heterogeneity of Iranian isolates by single-strand conformation polymorphism and sequence analysis of ribosomal DNA internal transcribed spacer

Protozoan parasites of Leishmania major are the causative agents of cutaneous leishmaniasis in different parts of Iran. We applied PCR-based methods to analyze L. major parasites isolated from patients with active lesions from different geographic areas in Iran in order to understand DNA polymorphisms within L. major species. Twenty-four isolates were identified as L. major by RFLP analysis of the ribosomal internal transcribed spacer 1 (ITS1) amplicons. These isolates were further studied by single-strand conformation polymorphism (SSCP) analysis and sequencing of ITS1 and ITS2. Data obtained from SSCP analysis of the ITS1 and ITS2 loci revealed three and four different patterns among all studied samples, respectively. Sequencing of ITS1 and ITS2 confirmed the results of SSCP analysis and showed the potential of the PCR-SSCP method for assessing genetic heterogeneity within L. major. Different patterns in ITS1 were due to substitution of one nucleotide, whereas in ITS2 the changes were defined by variation in the number of repeats in two polymorphic microsatellites. In total five genotypic groups LmA, LmB, LmC, LmD and LmE were identified among L. major isolates. The most frequent genotype, LmA, was detected in isolates collected from different endemic areas of cutaneous leishmaniasis in Iran. Genotypes LmC, LmD and LmE were found only in the new focus of CL in Damghan (Semnan province) and LmB was identified exclusively among isolates of Kashan focus (Isfahan province). The distribution of genetic polymorphisms suggests the existence of distinct endemic regions of L. major in Iran.

Characterization of the Leishmania donovani ribosomal RNA promoter

The rRNA genes of Leishmania donovani are organized on chromosome 27 as tandem repeats of approximately 12.5-kb units that each contain a promoter, the subunit rRNAs, and approximately 39 copies of a 64-bp species-specific sequence. The transcription initiation site was mapped to 1020 bp upstream of the 18S rRNA gene by RNase protection and primer extension. A 349-bp sequence between the 64-bp repeats and the 18S rRNA gene appears to contain a promoter, since it directs a 60-fold increase in luciferase expression over the no-insert control in transient transfection assays. Stepwise deletion and 10-bp replacement studies identified three domains that affect promoter activity. In strain LSB-51.1, a naturally occurring gene conversion with a portion of the LD1 sequence from chromosome 35 replaced the rRNA genes within one repeat unit, from downstream of the promoter to within the 64-bp repeats. Northern blot analysis of RNA from LSB-51.1 showed large transcripts from the external spacer regions that are not normally transcribed. These results imply that the gene conversion eliminated sequences at or near the 5' terminus of the 64-bp repeats which normally function in transcription termination.

The genomic fingerprinting of the coding region of the beta-tubulin gene in Leishmania identification

We have demonstrated the polymorphism of the beta-tubulin gene region in Leishmania and its value in the identification of the parasite. In this work we have shown that the coding region of the gene has sufficient variation to accurately discriminate these parasites at the subgenus level. Nevertheless, intrasubgenus diversity, for particular restriction enzymes, was found in New World Leishmania belonging to the Leishmania subgenus. For instance, differences were found between mexicana and amazonensis strains. A unique pattern at the species level was found in particular species of both subgenera, e.g. L. (L.) major strain P and L. (L.) tropica belonging to the Leishmania subgenus, and L. (V.) panamensis strain LS94 from the Viannia subgenus. Particular endonucleases are diagnostic in Leishmania species discrimination as in the case of PvuII for the mexicana and amazonensis. This variation evidenced in the beta-tubulin gene region of Leishmania also occurred in other Kinetoplastida e.g. Trypanosoma cruzi, Leptomonas spp. and Crithidia spp. Moreover, these organisms showed a different genomic fingerprinting for the beta-tubulin gene among them and also Leishmania. Thus, the polymorphism of the coding region of the beta-tubulin gene can be used as a molecular marker for the identification of Leishmania.

Evolution of the genus Leishmania revealed by comparison of DNA and RNA polymerase gene sequences

Previous hypotheses of Leishmania evolution are undermined by limitations in the phylogenetic reconstruction method employed or due to the omission of key parasites. In this experiment, sequences of the gene encoding the DNA polymerase alpha catalytic polypeptide (POLA) were analysed phylogenetically in combination with those encoding the RNA polymerase II largest subunit gene (RPOIILS) to infer a comprehensive phylogeny of Leishmania. Nineteen species of parasites were studied, comprising representatives of each Leishmania species-complex (Leishmania Leishmania tropica, Leishmania Leishmania donovani, Leishmania Leishmania mexicana, Leishmania Leishmania hertigi and Leishmania Viannia braziliensis), as well as parasites of questionable taxonomy (Leishmania herreri, Sauroleishmania adleri, Sauroleishmania deanei, Sauroleishmania gymnodactyli and Sauroleishmania tarentolae). The analyses presented here provide strong support for the hypothesis that the Leishmania that infect reptiles (also known as Sauroleishmania) evolved from mammalian Leishmania. One implication of this finding is that the taxonomic definition of Leishmania should be broadened to encompass characteristics of the reptilian parasites. However, this taxonomic revision is complicated in that Leishmania (L.) hertigi, Leishmania (L.) deanei and Leishmania herreri, which exhibit some biological properties of Leishmania, are more closely related to Endotrypanum on the basis of these sequence comparisons. Consequently, the taxonomic discrimination between Leishmania that infect mammals, Leishmania that infect reptiles and Endotrypanum may be more problematic than has been previously thought. Since our resulting phylogenetic hypothesis is supported by the analyses of two different genes, we speculate on the origin and evolutionary expansion of this lineage of kinetoplastid protozoa.

Naturally azole-resistant Leishmania braziliensis promastigotes are rendered susceptible in the presence of terbinafine: comparative study with azole-susceptible Leishmania mexicana promastigotes

Leishmania braziliensis (isolate 2903) was naturally resistant to ketoconazole or the bis-triazole D0870, inhibitors of sterol C-14 demethylase, which produced only moderate effects on the proliferation of promastigotes at 10 microM. In contrast, Leishmania mexicana (isolate NR) was extremely susceptible to the azoles, as complete growth arrest and cell lysis were induced by incubation of the parasites with 0.05 microM concentrations of the drugs for 72 h. The opposite response was observed with terbinafine, an inhibitor of squalene epoxidase: L. braziliensis 2903 was three times more susceptible to the drug than L. mexicana NR (MICs of 5 and 15 microM, respectively). However, when the L. braziliensis stock was grown in the presence of 1 microM terbinafine, which by itself produced only marginal (< 10%) effects on growth, it became highly susceptible to the azoles, with an MIC of 0.03 microM. Analysis of cellular free sterols by high-resolution capillary gas chromatography coupled to mass spectrometry showed that 14-methyl sterols can support normal growth of L. braziliensis 2903 but not of L. mexicana NR. On the other hand, the higher susceptibility of the L. braziliensis isolate to terbinafine was correlated with a massive accumulation of squalene in the presence of the allylamine while no significant effects on L. mexicana sterol composition were observed at drug concentrations up to 1 microM. Thus, the > 300-fold increase in the susceptibility of L. braziliensis promastigotes to azoles in the presence of terbinafine was attributed to the combined effect of squalene and the methylated sterol precursors on the physical properties of the cell's membranes, leading to the loss of cell viability. Combination therapy with azoles and terbinafine in the treatment of human L. braziliensis infections deserves further study.

An oligonucleotide probe derived from kDNA minirepeats is specific for Leishmania (Viannia)

Sequence analysis of Leishmania (Viannia) kDNA minicircles and analysis of multiple sequence alignments of the conserved region (minirepeats) of five distinct minicircles from L. (V.) braziliensis species with corresponding sequences derived from other dermotropic leishmanias indicated the presence of a sub-genus specific sequence. An oligonucleotide bearing this sequence was designed and used as a molecular probe, being able to recognize solely the sub-genus Viannia species in hybridization experiments. A dendrogram reflecting the homologies among the minirepeat sequences was constructed. Sequence clustering was obtained corresponding to the traditional classification based on similarity of biochemical, biological and parasitological characteristics of these Leishmania species, distinguishing the Old World dermotropic leishmanias, the New World dermotropic leishmanias of the sub-genus Leishmania and of the sub-genus Viannia.

Intergenic region typing (IRT): a rapid molecular approach to the characterization and evolution of Leishmania

In the New World, Leishmania of the Viannia subgenus cause both cutaneous and mucocutaneous disease. These parasites show considerable intra-species genetic diversity and variation, which complicates taxonomic classification and epidemiology. We have used the variability of the transcribed noncoding regions between the small and large subunit rRNA genes to examine relationships in this group. In a method termed intergenic region typing (IRT), PCR amplification products were obtained for the rapidly evolving 1-1.2-kb internal transcribed spacers (ITS) between the SSU and LSU rRNAs, from 50 parasites isolated from different hosts and geographic areas. Amplified DNAs were digested with 10 different enzymes, and fragment patterns compared after acrylamide gel electrophoresis. High levels of intra- and inter-specific variation were observed, and quantitative similarity comparisons were used to associate different lineages. A complex evolutionary tree was obtained. Some species formed tight clusters (L. equatorensis, L. panamensis, L. guyanensis, L. shawi), while L. braziliensis was highly polymorphic and L. naiffi showed intraspecific distances comparable to the largest obtained within all Viannia. L. colombiensis, L. equatorensis and L. lainsoni clearly represent distinct lineages. Good agreement was obtained with molecular trees based upon isoenzyme or mini-exon repeat sequence comparisons. Overall, IRT appears to be a superb method for epidemiological and taxonomic studies of Leishmania, being sensitive, rapid and quantitative while simultaneously revealing considerable molecular diversity. IRT could also be applied to other nonconserved intergenic regions, including those separating protein-coding genes.

Differences in the lymphoproliferative pattern to Leishmania mexicana antigens recognized by immunized and infected mice

Immunity to leishmanial infection depends primarily on the activities initiated by T lymphocytes which have been sensitized to a diverse pool of parasitic antigens. In this study, the pattern of the lymphoproliferative responses of lymph node and spleen cells isolated from BALB/c and C57BL/6 mice previously infected with Leishmania mexicana was heterogeneous. However, we observed more pronounced responses to antigen fractions with molecular masses of 63 and 10-15 kDa, based on T cell immunoblotting. Responses were stronger and more persistent in the intermediate resistant C57BL/6 strain, as compared to the more evanescent response in the highly susceptible BALB/c mice. Similar responses in terms of immunodominant fractions were also consistently seen in total and T lymphocytes isolated from BALB/c mice which had been immunized with a soluble extract of Leishmania mexicana. These results are discussed in terms of general requirements for an effective vaccine against human leishmaniasis.

Identification and diagnosis of Leishmania mexicana complex isolates by polymerase chain reaction

Following cloning of Leishmania (L.) amazonensis kinetoplast DNA two recombinant clones were identified: one specific for L. (L.) amazonensis and the other specific for L. (L.) amazonensis and closely related isolates. DNA sequences from these clones were compared with those of other kinetoplastids and oligonucleotide primers were designed to be used in the polymerase chain reaction. A pair of these primers has been shown not only to be highly specific for L. mexicana complex isolates but can also be used to distinguish between L. (L.) mexicana and L. (L.) amazonensis isolates. These primers have been tested with water-lysed cultures, crude DNA extracts from human patients, potential host reservoirs, sandfly vectors and with cell pellets after isoenzyme characterization. The results of these tests indicate that the primers can be used specifically in the presence of excess host DNA originating from the majority of South American countries.

Discrimination amongst Leishmania by polymerase chain reaction and hybridization with small subunit ribosomal DNA derived oligonucleotides

A method for discriminating among Leishmania is described, based upon small subunit ribosomal DNA sequence differences. The method was to amplify the entire 2.2 kb small subunit rDNA by polymerase chain reaction using conserved primers specific for the 5' and 3' termini of the small subunit ribosomal RNA, and then hybridize the product dotted onto nylon membranes with labeled oligonucleotides. The design of the hybridization probes was based upon complete small subunit rDNA sequences from L. amazonensis, L. major and L. guyanensis and partial sequences of L. mexicana, L. braziliensis, L. tropica and L. chagasi. A high degree of sequence similarity (> 99%) among species was found. However, sufficient sequence divergence occurred to permit the design of internal oligonucleotide probes specific for species complexes. This procedure successfully discriminated amongst a wide range of Leishmania isolates. The method detected as few as 10 cultured organisms and detected parasites in tissue samples from experimentally infected animals. Non-radioactive labeling showed the same specificity and sensitivity as radioactive probes.

Presence of Leishmania braziliensis in blood samples from cured patients or at different stages of immunotherapy

By using a PCR assay specific for Leishmania braziliensis in blood samples, we detected this parasite in patients cured by immunotherapy or at different stages of treatment. We also found the parasite in subjects who had never suffered leishmaniasis but who had lived in endemic areas and migrated to nonendemic ones many years ago. These results suggest that L. braziliensis infections are difficult to eradicate and that a clinical cure but rarely a complete elimination of the parasite is generally accomplished.

DNA-based methods for the identification of insect vectors

Many insect vectors are members of complexes composed of morphologically identical sibling species. The identification of individual species, a requirement of epidemiological studies and control programmes, has traditionally relied upon techniques such as chromosomal analysis or isoenzyme typing. Owing to the limitations of these techniques, the last few years have seen many developments in DNA-based technologies for identification. DNA-based protocols have advantages over the other techniques utilized, in that they may identify all insect stages of both sexes using alcohol-preserved, dried, fresh or frozen specimens. The methods ultimately rely upon either DNA probe hybridization or the polymerase chain reaction (PCR). This review describes a number of approaches taken towards the development of these techniques. The aim of these approaches, whether directed or random, is to produce a methodology that is cheap, accurate and easy to use. In this review, the DNA-based techniques developed for the identification of Anopheles gambiae complex mosquitoes are used to illustrate the power of these methods, although, as the review demonstrates, the technology is directly applicable to many other mosquito or insect vectors. In addition, the methods discussed may be utilized for generating additional epidemiological data, such as identification of parasites within the vector or origin of the bloodmeal. A comprehensive survey of the probe systems available for the identification of insect vectors and the disease-causing organisms they transmit to the human population is therefore included. Given further advances in this technology, it may be anticipated that DNA-based approaches to identification may eventually supersede more traditional methodologies in the fields of tropical medicine and parasitology.

Detection of trypanosomatid Phytomonas parasitic in plants by polymerase chain reaction amplification of small subunit ribosomal DNA

To improve the diagnosis of Phytomonas infections in plants, we developed a polymerase chain reaction (PCR) assay using synthetic oligonucleotides complementary to conserved sequences of the 18S small subunit ribosomal (SSU) gene. From 10 ng upward of DNA of cultures of Phytomonas isolated from plants, fruits, and insects, PCR amplified an 800-bp DNA band that, after restriction analysis and probe hybridization, proved to be of 18S rDNA Phytomonas origin. PCR was also done with sap samples of tomatoes experimentally infected with Phytomonas, yielding amplified 800-bp ribosomal DNA bands before any flagellate could be detected by microscopic examination of the fruit sap.

Identification and detection of Trypanosoma cruzi by using a DNA amplification fingerprint obtained from the ribosomal intergenic spacer

We designed a PCR assay targeted on repeated elements of the ribosomal intergenic spacer which produces highly polymorphic DNA band patterns for different strains of Trypanosoma cruzi. By labeling the PCR products with digoxigenin and by chemiluminescence detection, we improved the assay sensitivity by three orders of magnitude to get T. cruzi strain fingerprints in feces of the trypanosome-infected triatomine bug vector. We also developed a capture assay for the digoxigenin-labeled PCR products that allowed us to detect T. cruzi in triatomine bug vector feces and in human serum samples with a solid support.

Relationships between cell surface protease and acid phosphatase activities of Leishmania promastigote

A correlation between the ratio of the cell surface protease activity to phosphatase activity and the complexity of the pattern of cell surface exposed polypeptides of Leishmania promastigotes was demonstrated for various strains grown under similar conditions. The ratio of the cell surface protease activity to acid phosphatase activity was high for L. major and L.b. panamensis and it correlates with the expression of a single polypeptide of 63 KDa on their cell surface. Intermediate and lower ratios of these enzymatic activities relate with more complex radio-iodinated patterns: two main bands in L.b. guyanensis (70 and 58 KDa) and L.b. braziliensis (72 and 60 KDa) and three main bands 65, 50, 27 KDa in all L.m. mexicana strains tested. Evidence is presented that the acid phosphatase located on the L.m. mexicana cell surface is not an artifact due to a secondary absorption of the secreted acid phosphatase from the culture medium. These results confirm the Leishmania antigen cell surface heterogeneity. The implications on the biology of Leishmania and the clinical manifestation of leishmaniasis are discussed.

Repetitive sequences in the ribosomal intergenic spacer of Trypanosoma cruzi

A fragment of Trypanosoma cruzi ribosomal intergenic spacer (IGS) located at 6.7 kb from the 3' end of the 24S rRNA gene was analyzed. This IGS fragment is characterized by the presence of three types of repetitive elements (designated Spacer Repetitive Elements, SRE), short direct repeats (5-6 bp) and chi-like recombinational sequences. SRE elements are composed of relatively short repeats (43-145 bp) which show variabilities consisting of nucleotide changes, insertions and deletions. SRE-1 element (145 bp) has a short oligo(dA) tail at the end of the repeat and can be found flanked by other SRE elements. SRE elements are species-specific, suggesting that probes based on them may be diagnostic for Trypanosoma cruzi.

Identification of new world Leishmania using ribosomal gene spacer probes

DNA probes from the nontranscribed ribosomal spacer (NTS), of Leishmania garnhami and Leishmania braziliensis were constructed and tested for sensitivity and specificity against different Leishmania isolates. The L. garnhami probes were species-specific under hybridization conditions of high stringency, but displayed specificity for the mexicana complex under conditions of intermediate stringency. The L. braziliensis probes showed 'complex' specificity. RFLP for the nontranscribed spacer within the braziliensis complex revealed very homogeneous patterns even for organisms currently accepted as different species. A PCR assay for the detection of Leishmania from the braziliensis complex is presented.

Ribosomal DNA sequences in the differentiation of pathogenic and non-pathogenic isolates of Entamoeba histolytica

Recombinant ribosomal DNA sequences were amplified by PCR and used as probes to perform a fingerprint analysis of total DNA from different Entamoeba histolytica isolates. RFLPs obtained with one of the probes, R-1, support previous proposals that pathogenic and non-pathogenic E. histolytica are closely related, yet genotypically distinct. Another probe, R-2, while not distinguishing between the two forms of E. hystolytica, was able to differentiate between them and E. moshkovskii, which has morphologically identical cysts and trophozoites. A third probe, BR-1, identified strain-specific RFLPs.

Sequence analysis of small subunit ribosomal RNA genes and its use for detection and identification of Leishmania parasites

The sequence of the most variable part of the small subunit ribosomal RNA (SSU rRNA) gene, comprising 800 bases, was analysed for 9 Leishmania taxa and compared with those of Trypanosoma brucei, Trypanosoma cruzi and Crithidia fasciculata. Considerable differences were observed between the sequence of the Leishmania taxa on the one hand and those of Crithidia and Trypanosoma on the other. Amongst the Leishmania taxa only a few point mutations were found, all located within 2 sequence blocks in the central part of the SSU rRNA gene, which are unique for Kinetoplastida. These unique sequences were used for the development of kinetoplastid-specific probes and a Leishmania-specific PCR assay of high sensitivity (less than 10 parasites could be detected). Based on the observed point-mutations an identification of the Leishmania parasites, according to complex, could be achieved by direct sequencing, restriction fragment analysis or single-stranded conformation polymorphism of the PCR-generated fragments.

Leishmania: genus identification based on a specific sequence of the 18S ribosomal RNA sequence

The analysis of PvuII restriction patterns of Leishmania spp. and Trypanosoma spp. genomic DNA showed genus distinctive profiles. A specific PvuII site was detected in the 5' domain of 18S ribosomal DNA of Leishmania. A 20-mer oligonucleotide encompassing this PvuII region was synthesized. This sequence, when utilized as probe, on short exposures of dot tests, detected 10(3) whole promastigotes of all Leishmania species analyzed but did not hybridize with T. cruzi or human nucleic acids. Two other oligonucleotides were synthesized to be used as primers for amplification through polymerase chain reaction of the 18S ribosomal DNA region containing the PvuII site. The probes described may be useful for the detection of Leishmania spp. under clinical and epidemiological trials.

Eimeria species: studies using rRNA and rDNA probes

rRNA and a heterologous cloned rDNA probe have been used to detect the rRNA genes of Eimeria species which infect the chicken, and has allowed the isolation and preliminary characterization of cloned rDNA sequences from a genomic DNA library of Eimeria tenella. It is demonstrated that rRNA and rDNA probes can be used to identify individual Eimeria species by the restriction fragment patterns detected after Southern hybridization. In addition, studies have shown that the large and small subunit rRNAs are expressed throughout sporulation.

Restriction fragment length polymorphisms in the ribosomal gene spacers of Trypanosoma cruzi and Trypanosoma conorhini

The ribosomal RNA genes of two species of Trypanosoma, Trypanosoma cruzi, the etiological agent of Chagas' disease, and Trypanosoma conorhini, a non-pathogenic rodent trypanosome, were cloned and partially characterized. The physical maps derived for their rRNA genes were similar throughout the region that encompasses the SSU-and LSU-rRNA coding sequences. However, the non-transcribed spacer DNA of both T. cruzi and T. conorhini was found to be polymorphic for several restriction enzyme sites. We show that strains of T. cruzi can be typed according to the characteristic restriction fragment length polymorphism of their NTS DNAs.

Sequence of the 24S alpha ribosomal RNA gene and characterization of a corresponding pseudogene from Trypanosoma cruzi

Two genomic clones which cover a 30-kb region containing the ribosomal RNA cistron from Trypanosoma cruzi have been isolated. The location of the 18S, 24S alpha and 24S beta RNA species within the cistron was determined. The complete sequences of the genes corresponding to the 24S alpha RNA and to a small RNA (S1), as well as two internal transcribed spacers were obtained by sequencing a cDNA and a genomic fragment. A locus containing sequences related to the 24S alpha RNA has been determined. Sequence data and structural characterization of this locus strongly suggest that this region contains a 24S alpha RNA pseudogene.

Biochemical evidence of the antigenic cell surface heterogeneity of Leishmania mexicana

In the present study, an enzymatical and structural analysis of Leishmania mexicana cell-surface components was carried out, demonstrating that protease and acid phosphatase activities were present at the L. mexicana cell surface. These findings correlate with the expression of the main components detected on the surface of L. mexicana promastigotes: the 50-kDa component is responsible for the acid phosphatase activity, whereas glycoprotein 65 (gp65) was characterized as the structural polypeptide of the surface protease. Furthermore, the 50- and 65-kDa antigens were found to be structurally different, inasmuch as no homology was observed in their peptide digestion profiles. The results presented in this communication confirm heterogeneity in the expression of the surface components of L. mexicana promastigotes at both the structural and the biochemical level.

A kinetoplast DNA probe diagnostic for Leishmania major: sequence homologies between regions of Leishmania minicircles

A restriction fragment from a cloned kinetoplast minicircle DNA has been shown to be diagnostic for Leishmania major. This 402-bp TaqI fragment has been used routinely (as a radiolabelled probe) to detect 10(4) parasites in simple dot blots, both experimentally and in epidemiological surveys. It positively identified all stocks of L. major tested (including all six known zymodemes) and showed very low homology to kinetoplast DNA (kDNA) and chromosomal DNA of Leishmania infantum and Leishmania tropica, two species commonly isolated from patients and wild hosts within foci of L. major in the Old World. DNA sequence analysis of a minicircle of L. major is reported for the first time, and it is demonstrated that this species shares with Leishmania aethiopica, Sauroleishmania tarentolae and several species of Trypanosoma a region of conserved sequence that is involved in DNA replication, a process that could present targets for selective chemotherapeutic attack. Sequence and restriction fragment analyses have indicated the difficulties of selecting species-specific sequences from kDNA which, even in the same parasite clone, contains several predominant minicircle classes, not all of which contain diagnostic sequences.

Circular DNA of Entamoeba histolytica encodes ribosomal RNA

The presence of repeated DNA sequences encoding RNA in Entamoeba histolytica has been reported. In the present study we demonstrate by agarose gel electrophoresis. DNase digestion and electron microscopic analysis that these genes are located on extrachromosomal circular DNA molecules with an approximate size of 26 kb. Detection of replication intermediates suggests the episomal nature of these molecules. Amplified, extrachromosomal rRNA genes appear to be a common feature among the lower eukaryotes, occurring more commonly as linear molecules and less commonly as circles. Entamoeba histolytica is 1 of the few organisms studied in which rRNA genes are located predominantly on extrachromosomal circles.

Identification of 'Old World' Leishmania by DNA recombinant probes

Leishmania are usually identified by iso-enzyme analysis. This method works well, but there is a need for an additional, more simple, method of identification. Here we present data that show that in a Southern blot analysis, recombinant DNA probes in combination with certain restriction enzymes can differentiate between taxa of Leishmania. Probes based on clones selected from a L. infantum cDNA library gave characteristic patterns on Southern blots for reference strains of the different types of Leishmania found in Europe, Africa and Asia. Within the different taxa little or no variation was observed. Although the L. infantum derived probes showed a somewhat stronger hybridization for strains of the L. donovani complex, the signal obtained with most probes was satisfactory for L. major, L. aethiopica and L. tropica. Within the L. donovani complex none of the selected probes differentiated between isolates belonging to L. infantum, L. chagasi or L. donovani. Probes containing kinetoplast DNA showed considerable variation in hybridization within a taxon.

Molecular approaches to DNA diagnosis

The DNA of a parasite is the ultimate blueprint of that parasite, the one characteristic which normally remains unchanged during every stage of the life-cycle. All the DNA sequence in the egg of a species of parasite are also in the larvae and adults of the same species. The same DNA is present in the parasite whether it is in a free-living stage, in an invertebrate vector or in a vertebrate host such as man. The molecular basis for DNA diagnosis is to allow labelled single-stranded species or strain-specific DNA sequences, selected from well-characterized reference species, to find and hybridize with homologous DNA from, or in, the unknown isolates of parasites. DNA probes are now available for most vector borne parasitic diseases. Parasitological identification problems are mostly concerned with distinguishing closely related strains or subspecies, for example detecting Taenia solium eggs as opposed to T. saginata eggs, or finding which of the 15 man-infecting subspecies of Leishmania is present in a single cutaneous lesion, the commonest clinical sign of the disease, or in a sandfly. For efficient hybridization by the present methods there has to be enough of a particular sequence present in a parasite's genome to make a feasible target. Therefore, DNA probes for parasites have been selected from repetitive, reiterated or multicopy DNA with intrinsic extensive sequence variation. DNA, which is free of coding restraint, can evolve rapidly to give differences between species, so that introns, ribosome gene spacers, variant genes, pseudo-genes and non-conserved DNA have all been used for DNA diagnosis. The major problems of sequence selection have been greatly aided by the use of recombinant DNA methods, which have the added advantage of economical production of DNA probes. The unique characteristics of kinetoplast mini-circle DNA in Leishmania has allowed the selection of a complex species, subspecies, strain and even isolate-specific DNA probes. These have been used successfully for Southern filter endonuclease fragment DNA identification, for dot-blot recognition of less than 200 parasites and non-radioactive detection of DNA sequence homology by 'in situ' hybridization and light microscopy in a single Leishmania cell.(ABSTRACT TRUNCATED AT 400 WORDS)

The heterogeneity of Leishmania cell-surface antigens

A comparative study of the radioiodinated promastigote cell-surface antigens of Leishmania mexicana and L. major was carried out under reduced and nonreduced conditions by means of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by autoradiography. Under reduced conditions, the cell surface of L. mexicana promastigotes showed three iodinated polypeptides with molecular weights of 65,000, 50,000 and 27,000 daltons, whereas L. major promastigotes displayed a single polypeptide of 63,000 daltons. Under nonreduced conditions, the radioiodinated cell-surface component of L. major shifted to a mol.wt. of 51,000 daltons, whereas only one of the three components of L. mexicana (mol.wt., 65,000 daltons) underwent a large shift (to 59,000 daltons). The different immunochemical nature of the L. mexicana cell-surface antigens was demonstrated by using different anti-Leishmania sera. The rabbit anti-promastigote serum immunoprecipitated mainly the 50,000- and 27,000-dalton L. mexicana cell-surface polypeptides, whereas the rabbit anti-amastigote serum as well as a serum from a patient with cutaneous leishmaniasis immunoprecipitated almost exclusively the 65,000-dalton polypeptide. Immunoblot studies using a rabbit antibody against the L. major deglycosylated major surface antigen gp63 confirmed the differences in nature of the 65,000- and 50,000-dalton cell-surface antigens of L. mexicana. The results obtained are discussed in the light of the differences in antigenic cell-surface expression among Leishmania isolates and their consequences in the development of a differential diagnosis of leishmaniasis.

Molecular karyotype of five species of Leishmania and analysis of gene locations and chromosomal rearrangements

The molecular karyotypes of five species of Leishmania were studied by pulsed field gradient gel electrophoresis (PFGGE) of chromosome-sized DNA bands. Each species exhibits a unique pattern of 22-28 bands in the size range approximately 200-2200 kb whereas strains of one species exhibit similar karyotypes. Analysis of the behaviour of kinetoplast DNA during PFGGE showed that minicircle DNA remains confined to the gel slot but a proportion of the maxicircle DNA fractionates as a low molecular weight band below band 1. The band location of genes for alpha and beta tubulin, the 5' spliced leader sequence (5'SL), heat shock proteins 70 (hsp 70) and 83 (hsp 83) and thymidylate synthase-dihydrofolate reductase (TS-DHFR) were analysed. Housekeeping genes are not clustered in Leishmania but are found on at least 7 bands in L. major. The hsp 83 gene is linked to the tandemly repeated beta tubulin allele on band 21 in L. major. Among different species, the location of the unlinked hsp 83 and hsp 70 genes is conserved whereas the TS-DHFR and 5'SL sequences are found on bands of varying size. The 5'SL gene may be rearranged in L. enriettii and two 5'SL loci were identified in L. donovani and L. tropica. The conservation of loci in strains of L. major suggests that the chromosomal genetic linkage map should be a reliable marker for identifying unknown isolates of Leishmania. Sequences on one band in L. mexicana sp. were shared among several bands and distributed on homologous and non-homologous bands in other species showing that DNA sequences are rearranged during speciation in Leishmania.