Trypanosoma cruzi: ancestral genomes and population structure

Although the genome of Trypanosoma cruzi has been completely sequenced, little is known about its population structure and evolution. Since 1999, two major evolutionary lineages presenting distinct epidemiological characteristics have been recognised: T. cruzi I and T. cruzi II. We describe new and important aspects of the population structure of the parasite, and unequivocally characterise a third ancestral lineage that we propose to name T. cruzi III. Through a careful analysis of haplotypes (blocks of genes that are stably transmitted from generation to generation of the parasite), we inferred at least two hybridisation events between the parental lineages T. cruzi II and T. cruzi III. The strain CL Brener, whose genome was sequenced, is one such hybrid. Based on these results, we propose a simple evolutionary model based on three ancestral genomes, T. cruzi I, T. cruzi II and T. cruzi III. At least two hybridisation events produced evolutionarily viable progeny, and T. cruzi III was the cytoplasmic donor for the resulting offspring (as identified by the mitochondrial clade of the hybrid strains) in both events. This model should be useful to inform evolutionary and pathogenetic hypotheses regarding T. cruzi.

ORIGIN AND PREVALENCE OF HUMAN T-LYMPHOTROPIC VIRUS TYPE 1 (HTLV-1) AND TYPE 2 (HTLV-2) AMONG INDIGENOUS POPULATIONS IN THE AMERICAS

Human T-lymphotropic virus type 1 (HTLV-1) is found in indigenous peoples of the Pacific Islands and the Americas, whereas type 2 (HTLV-2) is widely distributed among the indigenous peoples of the Americas, where it appears to be more prevalent than HTLV-1, and in some tribes of Central Africa. HTLV-2 is considered ancestral in the Americas and is transmitted to the general population and injection drug users from the indigenous population. In the Americas, HTLV-1 has more than one origin, being brought by immigrants in the Paleolithic period through the Bering Strait, through slave trade during the colonial period, and through Japanese immigration from the early 20th century, whereas HTLV-2 was only brought by immigrants through the Bering Strait. The endemicity of HTLV-2 among the indigenous people of Brazil makes the Brazilian Amazon the largest endemic area in the world for its occurrence. A review of HTLV-1 in all Brazilian tribes supports the African origin of HTLV-1 in Brazil. The risk of hyperendemicity in these epidemiologically closed populations and transmission to other populations reinforces the importance of public health interventions for HTLV control, including the recognition of the infection among reportable diseases and events.

Coeficiente de endocruzamento em portadores de esquistossomose mansônica

O coeficiente de endocruzamento (f ou de Wright) foi calculado em 1123 indivíduos de Catolândia, Bahia, área hiperendêmica da esquistossomose mansônica: 148 (13,2%) tinham o coeficiente f > 0. A forma hepatosplênica foi significantemente maior nos indivíduos com f > 0 (26,8%). Nos brancos com f > 0 o risco relativo foi de 14,1; enquanto, nos brancos com f = 0, Q freqüência da hepatosplenomegalia não diferiu dos não-brancos com f = ou f > 0. Com este coeficiente estimou-se a probabilidade de genes alélicos iguais, com origem em ancestral comum; os resultados reforçam a hipótese da regulação genética na susceptibilidade à forma hepatosplênica da esquistossomose mansônica.

Nota prévia sôbre a meiose de Corizus (Liorhyssus) hyalinus (Fabr.) (Hemiptera-Corizidae)

The main facts presented in this paper may be summarized as follows: 1) Corizus (Liorhyssus) hyalinus (Fabr.) has primary spermatocytes provided with 6 autosomal tetrads, one pair of microchromosomes and one sex chromosome. 2) The two microchromosomes present in this species sometimes appear at the primary metaphase as an unequal pair of minute elements. In the secondary spermatocytes the unique microchromosome present may be in the limit of visibility or entirely invisible. This invisibility may be partly due to a loss of colourability. 3) The sex chromosome divides transversely in the first division of the spermatocyte, passing undivided to one pole in the second one. In the latter it becomes fusiform in the beginning of anaphase revealing in this manner its dicentricity. In late anaphase it finishes by passing to one pole leaving in the other pole one of its kinetochores sometimes accompanied by a chromosomal fragment. 4) All the chromosomes divide transversely in both divisions, a diagram being enclosed to elucidate the question. 5) Spermatogonial chromosomes are provided with one kinetochore at each end, being curved toward the poles since the most beginning anaphase. 6) The following hypothesis is presented as an essay to explain the origin of microchromosomes: Since microchromosomes parallel sex chromosomes in most respects, as for instances in heteropycnosis and pairing modus, it seems highly probable that they originate from sex chromosomes. One may suppose that the ancestral form of a given species had a sex chromosome which used to lose a small centric fragment when it divided during meiosis. This fragment might well be at first an unstable one. Later, to compensate the effects of such a deficiency a mechanism arose through evolution which produced two useful results : a) the establishment of the fragment as a permanent structure of the cell nucleus and b) the acquirement by the sex chromosome of the faculty of passing to one pole without losing any of its ends.

O puru-puru da Amazônia (Pinta, Carate, Mal del Pinto etc)

1) "Purú-purú" é uma palavra indígena que quer dizer "pintado" ou "manchado", peculiar à Amazonia Brasileira. Com êsse nome é designada uma dermatose referida entre os selvicolas desde 1774, por Ribeiro Sampaio. Certas tribus, com alta incidência da moléstia passaram a ser cahamadas também "Purú-purús", o mesmo acontecendo com o rio onde habitavam - Rio Purús. 2) A doença existe na bacia do Rio Solimões e seus principais afluentes: Javari, Juruá, Purús, Içá, Japurá, e Negro. Por esses rios, o fóco da dermatose se continua nos países limitrofes com o Brasil: Guianas, Venezuela, Colombia, Perú (Equador) e Bolivia. 3) Desde 1890 essa dermatose foi relacionada à pinta (carate ou mal del pinto) por P. S. de Magalhães, idéa essa depois defendida por Juliano Moreira, Carlos Chagas, Roquete Pinto, Wappeus, O. da Fonseca Filho, Da Matta, Brumpt e outros, baseados na semelhança clínica e na terapêutica. Recentemente (1945), essa provavel identidade das duas dermatoses, recebeu fundamento sorológico de Biocca (que verificou a positividade das reações de Kline e Kahn em doentes de purú-purú), e, pelo presente trabalho, recebe base clínico-epidemio-anatomo-patológica. 4) Sob o ponto de vista clínico, as lesões cutaneas discromicas da moléstia, são de 3 órdens: a) lesões papulo-eritemato-escamosas, isoladas ou não, arredondadas, pruriginosas e de bordos nitidos; b) lesões maculo-escamosas, maiores mais pálidas, ás vezes já mostrando alterações pigmentares na parte central; c) máculas discromod´rmicas, lisas ou ligeiramente escamosas, com maior ou menor alteração pigmentar, as quais assumem diferentes aspéctos, consequentes à hipo - ou hiperpigmentação, variaveis também com a côr do paciente. As colorações predominantes nas manchas, são o branco, o preto e o vermelho, com tonalidades eminentemente variaveis. Embora raramente, nessas extensas dermodiscromias, observa-se superposição de lesões papulo-eritemato-escamosas. O aparecimento dos 3 tipos de leões acima citados, obedece seguramente a um processo evolutivo da dermatose, dando-se na órdem exposta e de acordo com o tempo de doença. Além das lesões discromicas, características da enfermidade, foi observado purido, e infartamento ganglionar. O estado geral dos doentes era bom. A avaliação de anemia e eosinofilia, foi prejudicada pela ocurrência de outros processos mórbidos (malaria e helmintiases). Em 2 pacientes pretos e adultos, havia avançada hiperqueratose palmo-plantar. 5) Sob o ponto de vista epidemiológico, foram feitas as seguintes observações: a) Idade. A dermtose ocorre em tôdas as idades, mais incide principalmente dos 15 aos 29 anos. Tomando um grupo relativamente homogêneo de doéntes de um mesmo local, 53% têm 15 e mais anos de idade. De 36 doentes que deram informações seguras ou aproximadas quanto à idade em que lhes apareceu a doença, verifica-se que 77% já estavam infectados antes dos 15 anos. Em 5 casos, a infecção se deu antes dos 2 anos de idade. b) Sexo. Nos doentes em conjunto, existiam 34 homens e 35 mulheres. Mas, no grupo homogeneo acima citado, havia ligeira predominância do sexo feminino (60.7%). c) Côr ou raça. Foram encontradas as seguintes percentagens: Pretos - 34.8%, brancos - 27.5% índios - 23.2% e mulatos - 14.5%. Essas diferenças não indicam predileção racial. d) Família. A A dermatose é eminentemente familial. Em grupo de 41 doentes, 34 pertenciam a 8 familias. e) Lesão inicial. Contágio. Em 6 casos ainda existia a lesão inicial, chamada "empigem", isolada ou acompanhada de outras lesões semelhantes. De 33 doentes, 26 (78.8%) referiam a lesão inicial nas partes descobertas do corpo (rosto, braços e mãos, pernas e pés), isto é regiões mais sujeitas a pequenos traumas, que servem como "porta de entrada" do treponema. Os AA não acreditam na existência de um vetor. Pensam que o contágio é direto, as condições eficientes e predisponentes do mesmo, coexistindo no domícilio, onde vivem em promiscuidade e falta de higiene, doentes e sadios. Os autores não encontraram treponemas em córtes impregnados de “purú-purú”, tanto de “lesão recente” como de “lesão tardia”. Atribuem o fracasso ao provável uso de antitreponemicos pelos doentes, uma vez que a terapeutica empírica pelo arsênico e mercúrio é muito espalhada na Amazônia. Histopatológicamente, encontraram na “lesão recente”: hiperqueratose, hiperacantose, exocitose, exoserose e espongiose na epiderme; e infiltração de células redondas, edema e diltação dos capilares no derma papilar e subpapilar; pela impregnação, acharam irregularidade na distribuição do pigmento melanico, assim como melanóforos entre as células inflamatórias do derma. Na “lesão tardia” observaram: notável atrofia do epiderme, reduzida às vezes , a 3 a 5 camadas celulares, havendo desaparecimento das papilas dérmicas; no derma, havia discreta infiltração de células redondas, relacionadas aos vasos sanguineos, ao lado de macrófagos melaniferos mais ou menos abundantes; pela impregnação, quanto às alterações pigmentares, foram observadas todas as graduações, desde a completa ausência de pigmento na basal, até um acúmulo notável de melanina, atingindo as próprias células de Malpighi. 7) Com o tratamento pelo “neo-salvarsan” os AA observaram grandes melhoras e mesmo cura aparente, com 6 a 8 injeções. Certas manifestações acromicas vitiligoides, antigas, não mostraram modificações apreciáveis com a terapêutica. 8) No Brasil, fora da Amazônia, tem sido descrito casos isolados de purú-purú, porém, na opinião dos autores, todos ou quase todos, são provavelmente, manifestações discromicas tardias de sífilis ou bouba, semelhantes aos publicados por um deles (F. N. G). Pensam do mesmo modo, quanto aos casos de pinta descritos fora da América: África, Egito, Argeria, Sahara, Trípoli, Turquestão, Filipinas, Iraque, Índia, Ceilão, etc. Ainda nesta mesma ordem de idéas, os autores negam validade ao conceito epidemiológico da existência de “casos isolados”, a não ser procedentes das “zonas pintogenas”. 9) Um dos autores (F. N. G.) emite a seguinte hipótese, que considera sugestiva, embora dificilmente demonstrável: Os treis treponemas (T. pallidum, T. pertenue e T. carateum), oriundos de um ancestral comum. tornaram-se peculiares respectivamente ao branco, ao preto e ao índio, mantendo-se assim isolados. Secundariamente, com as correntes migratórias, misturaram-se as doenças...

The Evolution of Trypanosomes Infecting Humans and Primates

Based on phylogenetic analysis of 18S rRNA sequences and clade taxon composition, this paper adopts a biogeographical approach to understanding the evolutionary relationships of the human and primate infective trypanosomes, Trypanosoma cruzi, T. brucei, T. rangeli and T. cyclops. Results indicate that these parasites have divergent origins and fundamentally different patterns of evolution. T. cruzi is placed in a clade with T. rangeli and trypanosomes specific to bats and a kangaroo. The predominantly South American and Australian origins of parasites within this clade suggest an ancient southern super-continent origin for ancestral T. cruzi, possibly in marsupials. T. brucei clusters exclusively with mammalian, salivarian trypanosomes of African origin, suggesting an evolutionary history confined to Africa, while T. cyclops, from an Asian primate appears to have evolved separately and is placed in a clade with T. (Megatrypanum) species. Relating clade taxon composition to palaeogeographic evidence, the divergence of T. brucei and T. cruzi can be dated to the mid-Cretaceous, around 100 million years before present, following the separation of Africa, South America and Euramerica. Such an estimate of divergence time is considerably more recent than those of most previous studies based on molecular clock methods. Perhaps significantly, Salivarian trypanosomes appear, from these data, to be evolving several times faster than Schizotrypanum species, a factor which may have contributed to previous anomalous estimates of divergence times.

Programmed Cell Death in Procyclic Form Trypanosoma brucei rhodesiense - Identification of Differentially Expressed Genes during Con A Induced Death

Trypanosoma brucei rhodesiense can be induced to undergo apoptosis after stimulation with Con A. As cell death in these parasites is associated with de novo gene expression we have applied a differential display technique, Randomly Amplified Differential Expressed Sequence-Polymerase Chain Reaction (RADES-PCR) to the study of gene expression during Con A induced cell death in these organisms. Twenty-two differentially displayed products have been cloned and sequenced. These represent the first endogenous genes to be identified as implicated in cellular death in trypanosomatids (the most primitive eukaryote in which apoptosis has been described). Evidence for an ancestral death machinery, `proto-apoptosis' in single celled organisms is discussed.

Analysis of genetic diversity of Trypanosoma cruzi: an application of riboprinting and gradient gel electrophoresis methods

Analysis of restriction fragment length polymorphism (RFLP) profiles derived from digestion of polymerase chain reaction (PCR) products of the ribosomal 18S from Trypanosoma cruzi yields a typical `riboprint' profile that can vary intraspecifically. A selection of 21 stocks of T. cruzi and three outgroup taxa: T. rangeli, T. conorhini and Leishmania braziliensis were analysed by riboprinting to assess divergence within and between taxa. T. rangeli, T. conorhini and L. braziliensis could be easily differentiated from each other and from T. cruzi. Phenetic analysis of PCR-RFLP profiles indicated that, with one or two exceptions, stocks of T. cruzi could be broadly partitioned into two groups that formally corresponded to T. cruzi I and T. cruzi II respectively. To test if ribosomal 18S sequences were homogeneous within each taxon, gradient gel electrophoresis methods were employed utilising either chemical or temperature gradients. Upon interpretation of the melting profiles of riboprints and a section of the 18S independently amplified by PCR, there would appear to be at least two divergent 18S types present within T. cruzi. Heterogeneity within copies of the ribosomal 18S within a single genome has therefore been demonstrated and interestingly, this dimorphic arrangement was also present in the outgroup taxa. Presumably the ancestral duplicative event that led to the divergent 18S types preceded that of speciation within this group. These divergent 18S paralogues may have, or had, different functional pressures or rates of molecular evolution. Whether or not these divergent types are equally transcriptionally active throughout the life cycle, remain to be assessed.

The ecotopes and evolution of triatomine bugs (triatominae) and their associated trypanosomes

Triatomine bug species such as Microtriatoma trinidadensis, Eratyrus mucronatus, Belminus herreri, Panstrongylus lignarius, and Triatoma tibiamaculata are exquisitely adapted to specialist niches. This suggests a long evolutionary history, as well as the recent dramatic spread a few eclectic, domiciliated triatomine species. Virtually all species of the genus Rhodnius are primarily associated with palms. The genus Panstrongylus is predominantly associated with burrows and tree cavities and the genus Triatoma with terrestrial rocky habitats or rodent burrows. Two major sub-divisions have been defined within the species Trypanosoma cruzi, as T. cruzi 1 (Z1) and T. cruzi 2 (Z2). The affinities of a third group (Z3) are uncertain. Host and habitat associations lead us to propose that T. cruzi 1 (Z1) has evolved in an arboreal, palm tree habitat with the triatomine tribe Rhodniini, in association with the opossum Didelphis. Similarly we propose that T. cruzi (Z2) and Z3 evolved in a terrestrial habitat in burrows and in rocky locations with the triatomine tribe Triatomini, in association with edentates, and/or possibly ground dwelling marsupials. Both sub-divisions of T. cruzi may have been contemporary in South America up to 65 million years ago. Alternatively, T. cruzi 2 (Z2) may have evolved more recently from T. cruzi 1 (Z1) by host transfers into rodents, edentates, and primates. We have constructed a molecular phylogeny of haematophagous vectors, including triatomine bugs, which suggests that faecal transmission of trypanosomes may be the ancestral route. A molecular clock phylogeny suggests that Rhodnius and Triatoma diverged before the arrival, about 40 million years ago, of bats and rodents into South America.

Evolution of ascariasis in humans and pigs: a multi-disciplinary approach

The nematode parasite Ascaris lumbricoides infects the digestive tracts of over 1.4 billion people worldwide, and its sister species, Ascaris suum, has infected a countless number of domesticated and feral pigs. It is generally thought that the putative ancestor to these worms infected either humans or pigs, but with the advent of domestication, they had ample opportunity to jump to a new host and subsequently specialize and evolve into a new species. While nuclear DNA markers decisively separate the two populations, mitochondrial sequences reveal that three major haplotypes are found in A. suum and in A. lumbricoides, indicating either occasional hybridization, causing introgression of gene trees, or retention of polymorphism dating back to the original ancestral species. This article provides an illustration of the combined contribution of parasitology, archaeoparasitology, genetics and paleogenetics to the history of ascariasis. We specifically investigate the molecular history of ascariasis in humans by sequencing DNA from the eggs of Ascaris found among ancient archeological remains. The findings of this paleogenetic survey will explain whether the three mitochondrial haplotypes result from recent hybridization and introgression, due to intensive human-pig interaction, or whether their co-occurrence predates pig husbandry, perhaps dating back to the common ancestor. We hope to show how human-pig interaction has shaped the recent evolutionary history of this disease, perhaps revealing the identity of the ancestral host.

Polymorphism analysis of the CTLA-4 gene in paracoccidioidomycosis patients

The CTLA-4 protein is expressed in activated T cells and plays an essential role in the immune response through its regulatory effect on T cell activation. Polymorphisms of the CTLA-4 gene have been correlated with autoimmune, neoplastic and infectious illnesses. This work aimed to verify possible associations between single nucleotide polymorphisms (SNPs) in CTLA-4, -318C/T in the promoter and +49A/G in exon 1 and paracoccidioidomycosis (PCM) caused by Paracoccidioides brasiliensis. For this purpose, 66 chronic form PCM patients and 76 healthy controls had their allele, genotype and haplotype frequencies determined. The genetic admixture structure of the patients and controls was evaluated to eliminate ancestral bias. The comparison of frequencies indicated no significant differences between patients and controls that could link the SNPs to PCM. Groups were admixture matched with no difference observed in population ancestry inference, indicating that the absence of association between CTLA-4 polymorphisms and PCM could not be attributed to ancestral bias. This study showed that there was no association between the CTLA-4 SNPs -318 and +49 and the resistance or susceptibility to PCM.

Molecular evidence for a single taxon, Anopheles nuneztovari s.l., from two endemic malaria regions in Colombia

To elucidate the Anopheles nuneztovari s.l. taxonomic status at a microgeographic level in four malaria endemic localities from Antioquia and Córdoba, Colombia, fragments of the cytochrome oxidase subunit I (COI) and the white gene were used. The COI analysis showed low genetic differentiation with fixation index (F ST) levels between -0.02-0.137 and Nm values between 3-∞, indicating the presence of high gene flow among An. nuneztovari s.l. populations from the four localities. The COI network showed a single most common haplotype, type 1 (n = 55), present in all localities, as the likely ancestral haplotype. Analysis of the white gene showed that An. nuneztovari s.l. populations from both departments grouped with haplotypes 19 and 20, which are part of lineage 3 reported previously. The results of the present study suggest that An. nuneztovari s.l. is a single taxon in the area of the present study.

Molecular characterisation of dengue virus type 1 reveals lineage replacement during circulation in Brazilian territory

Dengue fever is the most important arbovirus infection found in tropical regions around the world. Dispersal of the vector and an increase in migratory flow between countries have led to large epidemics and severe clinical outcomes, such as dengue haemorrhagic fever and dengue shock syndrome. This study analysed the genetic variability of the dengue virus serotype 1 (DENV-1) in Brazil with regard to the full-length structural genes C/prM/M/E among 34 strains isolated during epidemics that occurred in the country between 1994-2011. Virus phylogeny and time of divergence were also evaluated with only the E gene of the strains isolated from 1994-2008. An analysis of amino acid differences between these strains and the French Guiana strain (FGA/89) revealed the presence of important nonsynonymous substitutions in the amino acid sequences, including residues E297 (Met→Thr) and E338 (Ser→Leu). A phylogenetic analysis of E proteins comparing the studied isolates and other strains selected from the GenBank database showed that the Brazilian DENV-1 strains since 1982 belonged to genotype V. This analysis also showed that different introductions of strains from the 1990s represented lineage replacement, with the identification of three lineages that cluster all isolates from the Americas. An analysis of the divergence time of DENV-1 indicated that the lineage circulating in Brazil emerged from an ancestral lineage that originated approximately 44.35 years ago.

Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes

In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae). The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome) or both sex chromosomes (X and Y chromosomes). This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes) and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences.

Genotyping Mycobacterium bovis from cattle in the Central Pampas of Argentina: temporal and regional trends

Mycobacterium bovis is the causative agent of bovine tuberculosis (TB), a disease that affects approximately 5% of Argentinean cattle. Among the molecular methods for genotyping, the most convenient are spoligotyping and variable number of tandem repeats (VNTR). A total of 378 samples from bovines with visible lesions consistent with TB were collected at slaughterhouses in three provinces, yielding 265 M. bovis spoligotyped isolates, which were distributed into 35 spoligotypes. In addition, 197 isolates were also typed by the VNTR method and 54 combined VNTR types were detected. There were 24 clusters and 27 orphan types. When both typing methods were combined, 98 spoligotypes and VNTR types were observed with 27 clusters and 71 orphan types. By performing a meta-analysis with previous spoligotyping results, we identified regional and temporal trends in the population structure of M. bovis. For SB0140, the most predominant spoligotype in Argentina, the prevalence percentage remained high during different periods, varying from 25.5-57.8% (1994-2011). By contrast, the second and third most prevalent spoligotypes exhibited important fluctuations. This study shows that there has been an expansion in ancestral lineages as demonstrated by spoligotyping. However, exact tandem repeat typing suggests dynamic changes in the clonal population of this microorganism.