Sequence-specific "gene signatures" can be obtained by PCR with single specific primers at low stringency

Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region

BACKGROUND

Trypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have significant biological differences from one another. However, there is currently no methodological strategy for the direct typing of biological materials that has sufficient sensitivity, specificity, and reproducibility. The high diversity and copy number of the minicircle hypervariable regions (mHVRs) makes it a viable target for typing.

METHODOLOGY/PRINCIPAL FINDINGS

Approximately 24 million reads obtained by amplicon sequencing of the mHVR were analyzed for 62 strains belonging to the six main T. cruzi DTUs. To build reference databases of mHVR diversity for each DTU and to evaluate this target as a typing tool. Strains of the same DTU shared more mHVR clusters than strains of different DTUs, and clustered together. Different identity thresholds were used to build the reference sets of the mHVR sequences (85% and 95%, respectively). The 95% set had a higher specificity and was more suited for detecting co-infections, whereas the 85% set was excellent for identifying the primary DTU of a sample. The workflow's capacity for typing samples obtained from cultures, a set of whole-genome data, under various simulated PCR settings, in the presence of co-infecting lineages and for blood samples was also assessed.

CONCLUSIONS/SIGNIFICANCE

We present reference databases of mHVR sequences and an optimized typing workflow for T. cruzi including a simple online tool for deep amplicon sequencing analysis (https://ntomasini.github.io/cruzityping/). The results show that the workflow displays an equivalent resolution to that of the other typing methods. Owing to its specificity, sensitivity, relatively low cost, and simplicity, the proposed workflow could be an alternative for screening different types of samples.

Genotypic profiles of Leishmania (Viannia) braziliensis strains from cutaneous leishmaniasis patients and their relationship with the response to meglumine antimoniate treatment: a pilot study

Background: Forty-four strains isolated from a cohort of cutaneous leishmaniasis (CL) patients who did or did not respond to one course of treatment with meglumine antimoniate were investigated to explore genetic polymorphisms in parasite kinetoplast DNA minicircles. Leishmania (Viannia) braziliensis strains isolated from responder (R) and non-responder (NR) patients who acquired infection in Rio de Janeiro or in other Brazilian states were studied using low-stringency single-specific primer polymerase chain reaction (LSSP-PCR) to identify genetic polymorphisms. Results: Polymorphisms were observed in parasites recovered from patient lesions. No association was found between a specific genotype and R or NR patients. Phenetic analysis grouped the genotypes into three main clusters, with similarity indices varying from 0.72 to 1.00. Although no specific genotype association was detected, at least one group of L. (V.) braziliensis genotypes that circulates in Rio de Janeiro was discriminated in clusters I and III, showing phenotypes of good and poor responses to treatment, respectively. Cluster I comprised parasite profiles recovered from R patients from Rio de Janeiro and in cluster III, NR samples were prevalent. Cluster II comprised 24 isolates, with 21 from Rio de Janeiro and three from other states, equally distributed between R and NR patients. Additionally, we found that parasites sharing all common genetic characteristics acted differently in response to treatment. Conclusions: These results are of clinical-epidemiological importance since they demonstrate that populations of L. (V.) braziliensis that exhibit high levels of genetic similarity also display different phenotypes associated with meglumine antimoniate responses in cutaneous leishmaniasis patients.

Host-Parasite Interactions in Chagas Disease: Genetically Unidentical Isolates of a Single Trypanosoma cruzi Strain Identified In Vitro via LSSP-PCR

The present study aims at establishing whether the diversity in pathogenesis within a genetically diverse host population infected with a single polyclonal strain of Trypanosoma cruzi is due to selection of specific subpopulations within the strain. For this purpose we infected Swiss mice, a genetically diverse population, with the polyclonal strain of Trypanosoma cruzi Berenice-78 and characterized via LSSP-PCR the kinetoplast DNA of subpopulations isolated from blood samples collected from the animals at various times after inoculation (3, 6 and 12 months after inoculation). We examined the biological behavior of the isolates in acellular medium and in vitro profiles of infectivity in Vero cell medium. We compared the characteristics of the isolates with the inoculating strain and with another strain, Berenice 62, isolated from the same patient 16 years earlier. We found that one of the isolates had intermediate behavior in comparison with Berenice-78 and Berenice-62 and a significantly different genetic profile by LSSP-PCR in comparison with the inoculating strain. We hereby demonstrate that genetically distinct Trypanosoma cruzi isolates may be obtained upon experimental murine infection with a single polyclonal Trypanosoma cruzi strain.

Between a bug and a hard place: Trypanosoma cruzi genetic diversity and the clinical outcomes of Chagas disease

Over the last 30 years, concomitant with successful transnational disease control programs across Latin America, Chagas disease has expanded from a neglected, endemic parasitic infection of the rural poor to an urbanized chronic disease, and now a potentially emergent global health problem. Trypanosoma cruzi infection has a highly variable clinical course, ranging from complete absence of symptoms to severe and often fatal cardiovascular and/or gastrointestinal manifestations. To date, few correlates of clinical disease progression have been identified. Elucidating a putative role for T. cruzi strain diversity in Chagas disease pathogenesis is complicated by the scarcity of parasites in clinical specimens and the limitations of our contemporary genotyping techniques. This article systematically reviews the historical literature, given our current understanding of parasite genetic diversity, to evaluate the evidence for any association between T. cruzi genotype and chronic clinical outcome, risk of congenital transmission or reactivation and orally transmitted outbreaks.

LSSP-PCR of Trypanosoma cruzi: how the single primer sequence affects the kDNA signature

Background

Low-stringency single specific primer PCR (LSSP-PCR) is a highly sensitive and discriminating technique that has been extensively used to genetically characterize Trypanosoma cruzi populations in the presence of large amounts of host DNA. To ensure high sensitivity, in most T. cruzi studies, the variable regions of the naturally amplified kinetoplast DNA (kDNA) minicircles were targeted, and this method translated the intraspecific polymorphisms of these molecules into specific and reproducible kDNA signatures. Although the LSSP-PCR technique is reproducible under strict assay conditions, the complex banding pattern generated can be significantly altered by even a single-base change in the target DNA. Our survey of the literature identified eight different primers with similar, if not identical, names that have been used for kDNA amplification and LSSP-PCR of T. cruzi. Although different primer sequences were used in these studies, many of the authors cited the same reference report to justify their primer choice. We wondered whether these changes in the primer sequence could affect also the parasite LSSP-PCR profiles.

Findings

To answer this question we compared the kDNA signatures obtained from three different and extensively studied T. cruzi populations with the eight primers found in the literature. Our results clearly demonstrate that even minimal modifications in the oligonucleotide sequences, especially in the 3′ or 5′ end, can significantly change the kDNA signature of a T. cruzi strain.

Conclusions

These results highlight the necessity of careful preservation of primer nomenclature and sequence when reproducing an LSSP-PCR work to avoid confusion and allow comparison of results among different laboratories.

KDNA genetic signatures obtained by LSSP-PCR analysis of Leishmania (Leishmania) infantum isolated from the new and the old world

BACKGROUND

Visceral Leishmaniasis (VL) caused by species from the Leishmania donovani complex is the most severe form of the disease, lethal if untreated. VL caused by Leishmania infantum is a zoonosis with an increasing number of human cases and millions of dogs infected in the Old and the New World. In this study, L. infantum (syn. L.chagasi) strains were isolated from human and canine VL cases. The strains were obtained from endemic areas from Brazil and Portugal and their genetic polymorphism was ascertained using the LSSP-PCR (Low-Stringency Single Specific Primer PCR) technique for analyzing the kinetoplastid DNA (kDNA) minicircles hypervariable region.

PRINCIPAL FINDINGS

KDNA genetic signatures obtained by minicircle LSSP-PCR analysis of forty L. infantum strains allowed the grouping of strains in several clades. Furthermore, LSSP-PCR profiles of L. infantum subpopulations were closely related to the host origin (human or canine). To our knowledge this is the first study which used this technique to compare genetic polymorphisms among strains of L. infantum originated from both the Old and the New World.

CONCLUSIONS

LSSP-PCR profiles obtained by analysis of L. infantum kDNA hypervariable region of parasites isolated from human cases and infected dogs from Brazil and Portugal exhibited a genetic correlation among isolates originated from the same reservoir, human or canine. However, no association has been detected among the kDNA signatures and the geographical origin of L. infantum strains.

Genetic Variability of Trypanosoma cruzi:Implications for the Pathogenesis of Chagas Disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or even overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but genetic variation of both the host and parasite is likely to be important. Here, Andréa M. Macedo and Sérgio D.J. Pena review the evidence showing a role for the genetic constitution of T. cruzi in determining the clinical characteristics of Chagas disease, and propose a ;clonal-histotropic model' for the pathogenesis of this disease.

Differential tissue tropism of Trypanosoma cruzi strains: an in vitro study

We have previously demonstrated selection favoring the JG strain of Trypanosoma cruzi in hearts of BALB/c mice that were chronically infected with an equal mixture of the monoclonal JG strain and a clone of the Colombian strain, Col1.7G2. To evaluate whether cell invasion efficiency drives this selection, we infected primary cultures of BALB/c cardiomyocytes using these same T. cruzi populations. Contrary to expectation, Col1.7G2 parasites invaded heart cell cultures in higher numbers than JG parasites; however, intracellular multiplication of JG parasites was more efficient than that of Col1.7G2 parasites. This phenomenon was only observed for cardiomyocytes and not for cultured Vero cells. Double infections (Col1.7G2 + JG) showed similar results. Even though invasion might influence tissue selection, our data strongly suggest that intracellular development is important to determine parasite tissue tropism.

Trypanosoma cruzi persistence at oral inflammatory foci in chronic chagasic patients

The persistence of Trypanosoma cruzi in seropositive individuals, previously diagnosed as chronic chagasic patients (CCP), was detected for the first time in biopsies taken from gingival inflammatory foci processed by polymerase chain reaction (PCR). Seven out of 31 (22.5%) gum samples from selected unquestionably CCP showing different degrees of gingival inflammation revealed T. cruzi-DNA using 3 specific PCR assays. All the included CCP had been diagnosed in previous studies carried out over the last 19 years. Samples of inflamed gums were recently taken from the indicated patients at: an outpatient hospital cardiac unit; a village where Chagas disease is endemic; and a specialized diagnostic research center, showing molecular evidence of parasite persistence in 17.6%, 42.8% and 14.3% of them, respectively. The relatively frequent parasite persistence, demonstrated here in oral inflammatory processes of treated and/or untreated patients bearing long term T. cruzi-infection, suggests the establishment of secondary small foci for the maintenance of hidden or inapparent chagasic infection. The easy and low-risk, non-invasive method to get the sample may add the use of gingival biopsy as a potential alternative diagnostic tool to confirm T. cruzi-infection in CCP. The significance of T. cruzi persistence as a primary cause of chronic Chagas disease and the proposal of this mechanism to explain the pathogenesis in CCP are considered.

Geographical clustering of Trypanosoma cruzi I groups from Colombia revealed by low-stringency single specific primer-PCR of the intergenic regions of spliced-leader genes

A low-stringency single-primer polymerase chain reaction (LSSP-PCR) typing procedure targeted to the intergenic regions of spliced-leader genes (SL) was designed to profile Trypanosoma cruzi I stocks from endemic regions of Colombia. Comparison between SL-LSSP-PCR profiles of parasite DNA from vector faeces and cultures isolated from those faeces showed more conservative signatures than profiles using LSSP-PCR targeted to the minicircle variable regions (kDNA). This was also observed by analysing 15 parasite clones from one stock as well as serial samples of a same stock after in vitro culturing or inoculation into mice. Thus, SL-LSSP-PCR appears more appropriate than kDNA-LSSP-PCR for reliable typing of major T. cruzi I groups from in vitro cultured stocks and triatomine faeces. SL-LSSP-PCR grouped 46 of 47 T. cruzi I Colombian stocks according to their geographical procedences in four clusters: Cluster Cas from Casanare Department, Cluster Mg from Northern Magdalena department, Cluster Mom from Momposina Depression in Southern Magdalena and finally Cluster NW from northwestern Colombia, including Sucre, Chocó, Córdoba and Antioquia departments. Sequence analysis identified punctual mutations among amplicons from each cluster. Within Cluster Mg, sequence polymorphism allowed association with different sylvatic vector species. Novel SL sequences and LSSP-PCR profiles are reported from T. cruzi I infecting Eratyrus cuspidatus, Panstrongylus geniculatus and Rhodnius pallescens vectors.

Biological characterization of Trypanosoma cruzi stocks from domestic and sylvatic vectors in Sierra Nevada of Santa Marta, Colombia

Sierra Nevada of Santa Marta is one of the most endemic regions of Chagas disease in Colombia. In this study, we compared the biological behavior and genetic features of Trypanosoma cruzi stocks that were isolated from domestic and sylvatic insects in this area. Rhodnius prolixus (from domestic environments) and Triatoma dimidiata (from sylvatic, peridomestic and domestic environments) are the most important vectors in this region. Genetic characterization showed that all stocks corresponded to T. cruzi I, but LSSP-PCR analyses indicated that some genotypes were present in both environments. Biological characterization in vitro showed a low growth rate in sylvatic T. cruzi stocks and in some domestic T. cruzi stocks, possibly indicating the presence of stocks with similar behavior in both transmission cycles. In parallel, in vivo behavioral analysis also indicated that T. cruzi stocks are variable and this species did not show a correlation between the environments where they were isolated. In addition, all stocks demonstrated a low mortality rate and histopathological lesions in heart, skeletal muscle and colon tissue. Moreover, our data indicated that experimentally infected chagasic mice displayed a relation between their myocardial inflammation intensity, parasitism tissue and parasite load using the qPCR. In conclusion, our results indicate that the T. cruzi stocks present in SNSM have similar biological behavior and do not show a correlation with the different transmission cycles. This could be explained by the complex transmission dynamics of T. cruzi in Sierra Nevada of Santa Marta, where hosts, vectors (e.g., T. dimidiata) and reservoirs circulate in both environments due to the close contact between the two transmission cycles, favoring environment overlapping. This knowledge is an important key to understanding the epidemiology and pathology of Chagas disease in this Colombian region. Furthermore, our findings could be of significant use in the design of control strategies restricted to a specified endemic region.

Implications of genetic variability of Trypanosoma cruzi for the pathogenesis of Chagas disease

Trypanosoma cruzi, the etiological agent of Chagas disease, presents a high degree of intraspecific genetic variability, with possible implications for the clinical forms of the disease, like the development of cardiopathy, megaesophagus, and megacolon, alone or in combination. This tissue tropism involved in the pathogenesis of Chagas disease has still not been totally elucidated. Thus, the current review approaches key aspects of T. cruzi genetic diversity, the clinical forms of Chagas disease, and the infection of the host cell by the parasite and the immune response. Other aspects discussed here include the release of immunosuppressive factors by the parasite, acting in the host's immune response pathways; host cell apoptosis inhibition; the pathogenesis of chagasic megaesophagus, which can be related to host-parasite interaction; and finally the association between megaesophagus and increased risk for the development of squamous-cell esophageal carcinoma. However, despite great advances in the understanding of this disease, it is still not possible to establish the true relationship between the parasite's genetic variability and the clinical form of Chagas disease.

Selection strategy and the design of hybrid oligonucleotide primers for RACE-PCR: cloning a family of toxin-like sequences from Agelena orientalis

BACKGROUND

The use of specific but partially degenerate primers for nucleic acid hybridisations and PCRs amplification of known or unknown gene families was first reported well over a decade ago and the technique has been used widely since then.

RESULTS

Here we report a novel and successful selection strategy for the design of hybrid partially degenerate primers for use with RT-PCR and RACE-PCR for the identification of unknown gene families. The technique (named PaBaLiS) has proven very effective as it allowed us to identify and clone a large group of mRNAs encoding neurotoxin-like polypeptide pools from the venom of Agelena orientalis species of spider. Our approach differs radically from the generally accepted CODEHOP principle first reported in 1998. Most importantly, our method has proven very efficient by performing better than an independently generated high throughput EST cloning programme. Our method yielded nearly 130 non-identical sequences from Agelena orientalis, whilst the EST cloning technique yielded only 48 non-identical sequences from 2100 clones obtained from the same Agelena material. In addition to the primer design approach reported here, which is almost universally applicable to any PCR cloning application, our results also indicate that venom of Agelena orientalis spider contains a much larger family of related toxin-like sequences than previously thought.

CONCLUSION

With upwards of 100,000 species of spider thought to exist, and a propensity for producing diverse peptide pools, many more peptides of pharmacological importance await discovery. We envisage that some of these peptides and their recombinant derivatives will provide a new range of tools for neuroscience research and could also facilitate the development of a new generation of analgesic drugs and insecticides.

High variability of Colombian Trypanosoma cruzi lineage I stocks as revealed by low-stringency single primer-PCR minicircle signatures

In Colombia, high genetic variability has been found among Trypanosoma cruzi stocks isolated from different vector and host species, using isoenzyme analysis and RFLP of total kinetoplastid DNA (kDNA), suggesting that several genetically related T. cruzi populations might be present within a single geographical area or adjacent ones. The objective of this study was to use the low-stringency single primer (LSSP)-PCR technique on variable regions of kDNA minicircles of T. cruzi to determine possible genetic relationships among stocks from distinct geographical regions of Colombia and different vector species and hosts. Although LSSP-PCR analysis showed a high genetic variability among 30 Colombian T. cruzi stocks, 29 of them belonged to T. cruzi lineage I, confirming that this lineage is predominant in different vector and host species from Colombia. Interestingly, one stock isolated from a Pastrongylus geniculatus bug was identified as T. cruzi lineage IIb, using PCR strategies targeted to the intergenic region of miniexon genes, a sequence encoding the D7 domain of the 24salpha ribosomal genes and the A10 fragment, being this finding, the first description of this lineage in Colombia. The LSSP-PCR signatures allowed correlation of most isolates with their respective geographical origins, and in one case from host and vector specimens at a same region, suggesting a transmission event. Moreover, variations in LSSP-PCR profiles among T. cruzi I stocks from a same region suggest that they may have a multiclonal character. Our results show that LSSP-PCR is a fast, valuable technique for characterization of intra-lineage polymorphism among T. cruzi stocks.

The Trypanosoma rangeli histone H2A gene sequence serves as a differential marker for KP1 strains

Trypanosoma rangeli has recently been divided in two primary lineages denoted as KP1(+) and KP1(-) strains because of epidemiological and evolutionary interest in the molecular differentiation of these two groups. We report the molecular characterization of the genes encoding histone H2A protein from a T. rangeli KP1(+) strain (H14), its comparison to T. rangeli KP1(-) strain (C23) histone H2A coding genes [Puerta, C., Cuervo, P., Thomas, M.C., López, M.C., 2000. Molecular characterization of the histone H2A gene from the parasite Trypanosoma rangeli. Parasitol. Res. 86, 916-922], and its application in a low-stringency single specific primer polymerase chain reaction (LSSP-PCR) assay to differentiate these parasite groups. The results show that the locus encoding the H2A protein in the H14 strain is formed by at least 11 gene units measuring 799 nucleotides in length, organized in tandem, and located in two chromosomes of approximately 1.9 and 1.1Mb in size. Remarkably, in KP1(-) strains these genes are on pairs of chromosomes of about 1.7 and 1.9Mb. In addition, there is a hybridization signal in the compression region above 2.1Mb in all T. rangeli strains. Therefore, the chromosomal location of these genes is a useful marker to distinguish between KP1(+) and KP1(-) T. rangeli strains. The alignment of the H2A nucleotide sequences from H14 and C23 strains showed an identity of 99.5% between the coding regions and an identity of 95% between the non-coding regions. The deduced amino acid sequences proved to be identical. Based on 5% of the difference between the intergenic regions, we developed a LSSP-PCR assay which can differentiate between KP1(+) and KP1(-) strains.

The Trypanosoma cruzi–host-cell interplay: location, invasion, retention

Chagas disease is a debilitating human illness caused by infection with the protozoan Trypanosoma cruzi. A capacity to invade and replicate within many different cell types is a cornerstone of the remarkable fitness of this parasite. Although invasion occurs independently of actin polymerization, the host cell still participates in the process, often in unexpected ways. Recent surprising findings indicate that host-cell lysosomes are indispensable, either by directly mediating invasion or by retaining these highly motile parasites inside cells.

Trypanosoma cruzi: genetic structure of populations and relevance of genetic variability to the pathogenesis of chagas disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or, occasionally, overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but it is likely that the genetic variability of both the host and the parasite are of importance. In this work we review the the genetic structure of T. cruzi populations and analyze the importance of genetic variation of the parasite in the pathogenesis of the disease under the light of the histotropic-clonal model.

Low-stringency single-specific-primer PCR as a tool for detection of mutations in the rpoB gene of rifampin-resistant Mycobacterium tuberculosis

By the low-stringency single-specific-primer PCR technique, a highly sensitive and rapid method for diagnosis of rifampin resistance in Mycobacterium tuberculosis was established. Seven rifampin-resistant and five rifampin-susceptible specimens were analyzed. Rifampin resistance was determined by MIC measurement. A complex electrophoretic pattern consisting of many bands was obtained for both susceptible and rifampin-resistant isolates. The same pattern was obtained for all of the susceptible specimens, but differences between resistant and susceptible isolates were found. DNA sequencing showed that a particular mutation produces a specific electrophoretic pattern.

Concurrent cutaneous, visceral and ocular leishmaniasis caused by Leishmania (Viannia) braziliensis in a kidney transplant patient

Although cases of leishmaniasis co-infection have been described in acquired immunodeficiency syndrome patients as well as those who have undergone organ transplants, to our knowledge, the present report is the first documented case of simultaneous cutaneous, visceral and ocular leishmaniasis due to Leishmania (Viannia) braziliensis in a transplant patient. The patient had been using immunosuppressive drugs since receiving a transplanted kidney. The first clinical signs of leishmaniasis included fever, thoracic pain, hepatosplenomegaly, leucopenia and anemia. The cutaneous disease was revealed by the presence of amastigotes in the skin biopsy. After three months, the patient presented fever with conjunctive hyperemia, intense ocular pain and low visual acuity. Parasites isolated from iliac crest, aqueous humor and vitreous body were examined using a range of molecular techniques. The same strain of L. (V.) braziliensis was responsible for the different clinical manifestations. The immunosuppressive drugs probably contributed to the dissemination of Leishmania.

Advantages of in situ hybridisation over direct or indirect in situ reverse transcriptase-polymerase chain reaction for localisation of galanin mRNA expression in rat small intestine and pituitary

In situ hybridisation (ISH) and direct or indirect in situ reverse transcriptase-polymerase chain reaction (RT-PCR) were used to detect galanin mRNA in paraffin sections of rat intestine and pituitary. With conventional ISH, a subset of intestinal neuronal ganglion cells and anterior pituitary endocrine cells were labelled. Direct in situ RT-PCR also labelled some cells in pituitary but not in intestine. Negative controls were unlabelled, but sections with 3' primer alone for RT-PCR appeared positive. No signal was apparent using the indirect in situ RT-PCR method. Investigation of the specificity of solution phase RT-PCR using RNA extracts from pituitary or intestine revealed that additional PCR products were detected under some conditions. The sequences of these PCR products suggested that one was the result of mispriming and single primer PCR, which could also have occurred in situ. Alternative galanin primers gave only the predicted RT-PCR product in solution phase yet still gave artefacts in tissue sections using direct in situ RT-PCR. ISH with probes transcribed from the correct PCR product gave identical labelling to the original galanin riboprobe. In conclusion, direct in situ RT-PCR is unreliable and requires validation, while indirect in situ RT-PCR may fail even though sufficient target exists for detection with conventional sensitive riboprobe ISH.

A commented dictionary of techniques for genotyping

Several tools, differing in their technical and practical parameters, are available for the detection of point mutations as well as small deletions and insertions. In this article, a dictionary featuring over fifty methods for detection of mutation is presented. The distinguishing principle for each method is briefly explained. Sorting of and discussion on the methods give the reader a brief introduction to the field of genotyping.

A simplified method for sample collection and DNA isolation for polymerase chain reaction detection of Trypanosoma rangeli and Trypanosoma cruzi in triatomine vectors

Due to the overlapping distribution of Trypanosoma rangeli and T. cruzi in Central and South America, sharing several reservoirs and triatomine vectors, we herein describe a simple method to collect triatomine feces and hemolymph in filter paper for further detection and specific characterization of these two trypanosomes. Experimentally infected triatomines feces and hemolymph were collected in filter paper and specific detection of T. rangeli or T. cruzi DNA by polymerase chain reaction was achieved. This simple DNA collection method allows sample collection in the field and further specific trypanosome detection and characterization in the laboratory.

RAPD library fingerprinting of bacterial and human DNA: applications in mutation detection

Random amplified polymorphic DNA (RAPD) fingerprinting is a modification of the polymerase chain reaction (PCR), which utilises a single, arbitrarily-chosen primer to amplify a number of fragments from a given template DNA to generate a discrete "fingerprint" when resolved by gel electrophoresis. Alterations by as little as a single base in the primer sequence lead to marked alterations in the fingerprints generated with a given template under optimised conditions. By inference, single base alterations in the genomic template DNA may also lead to changes in the RAPD fingerprints. We have examined this potential application to detect mutations in bacteria and cultured human cells. We have utilised Escherichia coli and human lymphoblastoid cell lines exposed to UV radiation, selected for by cellular mutation assays, and compared RAPD fingerprints of mutant and non-mutant samples. Polymorphisms became evident as the presence and/or absence of DNA fragments between the two samples. A dose-dependent increase in the number of polymorphic bands was seen with UV irradiation of E. coli. To a lesser degree, polymorphisms were also evident for human lymphoblastoid DNA. The possible underlying mechanisms for these alterations in fingerprints as a result of mutation(s) in the primer binding site(s) are discussed. The ability of RAPD fingerprinting to detect a mutant in a population of non-mutants is evaluated, and whilst the lack of sensitivity inherent in the technique precludes its use as a mutation screening assay, its potential for generation of mutant and non-mutant DNA probes for other mutation detection techniques may prove to be of great merit. Teratogenesis Carcinog. Mutagen. 20:49-63, 2000.

Phylogenetic network of the mtDNA haplogroup U in Northern Finland based on sequence analysis of the complete coding region by conformation-sensitive gel electrophoresis

Mutations in mtDNA have accumulated sequentially, and maternal lineages have diverged to form population-specific genotypes. Classification of the genotypes has been made based on differences found in restriction fragment analysis of the coding region or in the sequence of the hypervariable segment I. Both methods have shortcomings, as the former may not detect all the important polymorphisms and the latter makes use of a segment containing hypervariable nucleotide positions. Here, we have used conformation-sensitive gel electrophoresis (CSGE) to detect polymorphisms within the coding region of mtDNA from 22 Finns belonging to haplogroup U. Sixty-three overlapping PCR fragments covering the entire coding region were analyzed by CSGE, and the fragments that differed in their migration pattern were sequenced. CSGE proved to be a sensitive and specific method for identifying mtDNA substitutions. The phylogenetic network of the 22 coding-region sequences constituted a perfect tree, free of homoplasy, and provided several previously unidentified common polymorphisms characterizing subgroups of U. After contrasting this data with that of hypervariable segment I, we concluded that position 16192 seems to be prone to recurrent mutations and that position 16270 has experienced a back mutation. Interestingly, all 22 samples were found to belong to subcluster U5, suggesting that this subcluster is more frequent in Finns than in other European populations. Complete sequence data of the mtDNA yield a more reliable phylogenetic network and a more accurate classification of the haplogroups than previous ones. In medical genetics, such networks may help to decide between a rare polymorphism and a pathogenic mutation; in population genetics, the networks may enable more detailed analyses of population history and mtDNA evolution.

PCR-based technology in veterinary parasitology

DNA technology is having a major impact in many areas of veterinary parasitology. In particular, the polymerase chain reaction (PCR) has found broad applicability because its sensitivity permits enzymatic amplification of gene fragments from minute quantities of nucleic acids derived from limited amounts of parasite material. This paper discusses some recent applications of PCR-based methods to parasites and highlights their usefulness or potential for those of veterinary importance. The focus is on PCR tools for the accurate identification of parasites and their genetic characterisation, the diagnosis of infections, the isolation and characterisation of expressed genes, the detection of anthelmintic resistance, and mutation scanning approaches for the high resolution analysis of PCR products.

Differential tissue distribution of diverse clones of Trypanosoma cruzi in infected mice

Chagas disease, caused by the protozoan Trypanosoma cruzi, presents variable clinical course but the phenomena underlying this variability remain largely unknown. T. cruzi has a clonal population structure and infecting strains are often multiclonal. T. cruzi genetic variability could be a determinant of differential tissue tropism or distribution and consequently of the clinical forms of the disease. We tested this hypothesis by using low-stringency single specific primer polymerase chain reaction (LSSP-PCR) to type genetically the parasites in tissues of experimental infected mice. BALB/c mice were simultaneously inoculated with two different T. cruzi populations (JG strain and Coll.7G2 clone). Doubly infected animals showed clear differential tissue distribution for the two populations (chronic phase). Our results indicate a significant influence of the genetic polymorphism of infecting T. cruzi populations in the pathogenesis of chronic Chagas disease.

Characterization of Trypanosoma rangeli strains isolated in Central and South America: an overview

Trypanosoma rangeli is a hemoflagelate parasite that infects domestic and sylvatic animals, as well as man, in Central and South America. T. rangeli has an overlapping distribution with T. cruzi, the etiological agent of Chagas disease, sharing several animal reservoirs and triatomine vectors. We have isolated T. rangeli strains in the State of Santa Catarina, in southern Brazil, which dramatically increased the distribution area of this parasite. This brief review summarizes several studies comparing T. rangeli strains isolated in Santa Catarina with others isolated in Colombia, Honduras and Venezuela. The different methods used include indirect immunofluorescence and western blot assays, lectin agglutination, isoenzyme electrophoresis and random amplified polymorphic DNA analysis, triatomine susceptibility, in vitro cell infection assays, and mini-exon gene analysis.

Genotype-related fingerprints from HLA-DPB1 exon 2 low-stringency PCR

Techniques based on the formation of heteroduplexes between relevant heterologous amplified HLA loci have proved to be simple and cost-effective screening methods for the detection of DNA sequence diversity. However, the banding patterns produced may not be as complex as required. We used the original procedure of Pena et al. (Proceedings of the National Academy of Sciences USA 91, 1946-1949, 1994) to generate fingerprints from a specific, polymorphic PCR product. HLA-DPB1 exon 2 was amplified, recovered from agarose gel, and used as a template for subsequent low-stringency (30 degrees C) amplification cycles (LS-PCR) in the presence of a single primer. The LS-PCR products were run on 8% PAGE and silver-stained. In total, 22 subjects were characterized by this method. The issues of the reproducibility and specificity of the patterns obtained were addressed by comparing fingerprints from individuals with the same genotype. The results showed that LS-PCR was robust. A further step was the evaluation of the diversity that can be generated, i.e. the sensitivity of the method. Genotype-related fingerprints were produced, and differences as small as a single nucleotide in heterozygous samples could be detected. We then demonstrated the usefulness of LS-PCR in the evaluation of donor/recipient pairs. We believe that LS-PCR may be a valuable adjunct to the battery of tests aimed at the verification of HLA matching before unrelated bone marrow transplantation. We suggest that it could be used to speed up the search process when several candidate donors are retrieved from registries before embarking on SSOP typing or sequencing.

Characterization of mitochondrial DNA using low-stringency single specific primer amplification analyzed by laser induced fluorescence--capillary electrophoresis

Polymerase chain reaction (PCR)-based DNA typing is routinely used in forensics for identity testing. Those assays that distinguish single nucleotide polymorphisms (SNPs) require other biochemical reactions in addition to PCR to identify the sequence polymorphisms. Low-stringency sequence-specific PCR (LSSP-PCR) is an example of a recent method that does not require additional biochemical treatments. The analysis of LSSP-PCR by capillary electrophoresis (CE) to discriminate the highly polymorphic mitochondrial DNA (mtDNA) D-loop region is described. The DNA from five individuals were amplified (first step) using sequence-specific primers to produce 1021 bp fragments containing the D-loop region. Each fragment was isolated by electroelution using CE and UV detection, and subjected to a second amplification (second step) using a single primer annealed under low stringency conditions. This generated a range or profile of PCR products for each sample, which were resolved and analyzed by CE with the intercalator TOTO-1 and laser-induced fluorescence (LIF) detection. The LSSP-PCR profiles were unique for each individual, indicating that this technique may be applicable for forensic identity testing.

Practical methods of mutation detection

The past few years have seen a marked increase in the demand for practical methods of mutation detection. Over this period of time, both the development of new methods and improvements in existing methods have made mutation detection in the research setting a less cumbersome task. Nevertheless, all of the commonly used approaches to this problem are labor intensive, and truly practical mutation detection methods in the clinical setting will depend on the development of more fully automated technology.

Mitochondrial D-loop "signatures" produced by low-stringency single specific primer PCR constitute a simple comparative human identity test

We have developed a technique called "LSSP-PCR" (low-stringency single specific primer PCR) that detects single or multiple mutations in DNA. A purified DNA fragment is submitted to PCR by using a single primer specific for one of the extremities of the fragment, under conditions of very low stringency. The primer hybridizes specifically to its complementary extremity and nonspecifically to multiple sites within the fragment, in a sequence-dependent manner. A complex set of reaction products is thus created that, when separated by electrophoresis, constitutes a unique "gene signature." We here report the application of LSSP-PCR to the detection of sequence variation in the control (D-loop) region of human mtDNA, which is known to differ significantly between unrelated individuals. We prepared human DNA samples from blood and amplified a 1024-bp portion of the mtDNA control region, using primers L15996 and H408. The amplified mtDNA fragments were then reamplified under LSSP-PCR conditions by using L15996 or H408 as drivers to produce complex signatures that always differed between unrelated individuals and yet were highly reproducible. In contrast, all mother-child pairs tested were identical, as expected from the matrilineal inheritance of mtDNA. Thus, the use of LSSP-PCR to produce D-loop signatures constitutes a powerful new technique for mtDNA-based comparative identity testing.

A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans

Mammalian mitochondrial DNA sequences evolve more rapidly than nuclear sequences. Although the rapid rate of evolution is an advantage for the study of closely related species and populations, it presents a problem in situations where related species, used as outgroups in phylogenetic analyses, have accumulated so much change that multiple substitutions obliterate the phylogenetic information. However, mitochondrial DNA sequences are frequently inserted into the nuclear genome, where they presumably evolve as nuclear pseudogene sequences and therefore more slowly than their mitochondrial counterparts. Such sequences thus represent molecular 'fossils' that could shed light on the evolution of the mitochondrial genome and could be used as outgroups in situations where no appropriate outgroup species exist. Here we show that human chromosome 11 carries a recent integration of the mitochondrial control region that can be used to gain further insight into the origin of the human mitochondrial gene pool.

DNA diagnosis of human genetic individuality

DNA studies of the human genome have shown polymorphic variation at thousands of sites, defining an absolute genetic uniqueness for each individual. There are many circumstances in which it may be desirable to diagnose this molecular individuality, as for instance, in criminal investigations or paternity testing. Several techniques can be used for this DNA diagnosis and we can choose among them the one that best suits the specific problem at hand. In this review we describe the main methodologies in current use to investigate human DNA polymorphisms, discussing the best application of each option, as well as their advantages and disadvantages.

Segregation patterns of a novel mutation in the mitochondrial tRNA glutamic acid gene associated with myopathy and diabetes mellitus

We have identified a novel mtDNA mutation in a 29-year-old man with myopathy and diabetes mellitus. This T-->C transition at mtDNA position 14709 alters an evolutionarily conserved nucleotide in the region specifying for the anticodon loop of the mitochondrial tRNA(Glu). The nt-14709 mutation was heteroplasmic but present at very high levels in the patient's muscle, white blood cells (WBCs), and hair follicles; lower proportions of mutated mtDNA were observed in WBCs and hair follicles of all examined maternal relatives. In the patient's muscle, abnormal fibers showed mitochondrial proliferation, severe focal defects in cytochrome c oxidase activity, and absence of cross-reacting material for mitochondrially synthesized polypeptides. These fibers had higher levels of mutated mtDNA than did surrounding "normal" fibers. Although the percentage of mutated mtDNA in WBCs from family members were distributed around the percentage observed in the mothers, the pattern was different in hair follicles, where the mutated population tended to increase in subsequent generations. PCR/RFLP analysis of single hairs showed that the intercellular variations in the percentage of mutated mtDNA differed among family members, with younger generations having a more homogeneous distribution of mutated mtDNA in different hair follicles. These results suggest that the intercellular distribution of the mutated and wild-type mtDNA populations may drift toward homogeneity in subsequent generations.

Theoretical basis of one-dimensional genome scanning: a direct method to identify the site of a mutation

Genome scanning is a technique designed to uncover a net genetic difference between otherwise identical DNA samples. As such, it can be used to directly identify the site of a gene mutation, facilitating the cloning of DNA fragments from that site. Unlike other conventional positional cloning methods, one-dimensional genome scanning does not require prior knowledge of the location of the gene or mutation nor does it require closely linked markers. Rather, this method can directly identify the site of a net genomic change, such as a deletion or duplication caused by a mutation. Thus, the genome scanning method can be used in place of classic positional cloning strategies because prior positioning or mapping of the objective gene is unnecessary. By using this approach, we have identified and cloned a DNA fragment duplicated in the p(un) mutation of the mouse pink-eyed dilution locus (Brilliant et al., Science 1991, 252, 566-569). However, no other similar attempt using one-dimensional genome scanning has been reported so far, in spite of the simplicity of the procedure and its success in identifying and ultimately characterizing the pink-eyed dilution gene of the mouse. The lack of other reports of its success are perhaps not because of the practical difficulties of this method, but may be due to the false presumption that the probability for directly identifying the mutation site using genome scanning is extremely low. The theoretical probability was calculated and is presented here.(ABSTRACT TRUNCATED AT 250 WORDS)

A sensitive method for detection of mutations--a PCR-based RNase protection assay

Several techniques are currently available for detecting point mutations in DNA. The most widely used methods either use hazardous chemicals (chemical mismatch cleavage) or can detect mutations only in short (200- to 500-bp) fragments (single-stranded conformational polymorphism and denaturing gradient gel electrophoresis). In an effort to develop a sensitive and reliable method for the detection of mutations in large segments of DNA, a novel RNase protection assay using RNase I was developed. In this method, the desired portion of the gene is amplified by the polymerase chain reaction (PCR) using specific oligonucleotides and hybridized to a 32P-labeled RNA probe containing the wild-type sequence. The RNA/DNA hybrid is subsequently digested with RNase I, which cleaves the RNA at the mismatch sites. The protected RNA fragments are separated on a denaturing polyacrylamide-urea gel and detected by autoradiography. Four different RNA probes from two protein tyrosine phosphatases (PTP1C and PTP2C) were assayed using this procedure. Several mutants of the two enzymes were tested using wild-type RNA probes. Single-base changes involving all four bases at the mismatch site could be detected efficiently. The ability of this method to detect insertions and single-base deletions was also demonstrated. Using a PCR-based RNase protection assay, a single-base deletion in PTP1C in the motheaten mutation in mice could be detected. Using fragments amplified from genomic DNA, mice that were heterozygous for the motheaten mutation could be distinguished from wild type and homozygotes for this mutation.(ABSTRACT TRUNCATED AT 250 WORDS)