Trypanosoma evansi: molecular homogeneity as inferred by phenetical analysis of ribosomal internal transcribed spacers DNA of an eclectic parasite

The protozoan Trypanosoma evansi is described as presenting high morphological and genetic similarities among the isolates despite its biological heterogeneity and wide geographical distribution. PCR amplification of the internal transcribed spacers of the ribosomal gene in combination with the coding region of the 5.8S ribosomal subunit further submitted to restriction enzymes digestion were carried out in DNAs extracted from 41 T. evansi strains isolated from horses, dogs, coatis and capybaras from two distinct regions of the Brazilian Pantanal. We also used one T. evansi isolate from Africa, one from Asia and one isolate of T. b. brucei from Africa. Analysis of the RFLP profiles yielded a unique "riboprinting" that does not vary intraspecifically. These results provide insights on the ribosomal gene organization of T. evansi and showed that ITS analysis by RFLP show high genetic similarity of this locus among isolates of this protozoan parasite.     

Genetic relatedness among Trypanosoma evansi stocks by random amplification of polymorphic DNA and evaluation of a synapomorphic DNA fragment for species-specific diagnosis.

In this study we employed randomly amplified polymorphic DNA patterns to assess the genetic relatedness among 14 Brazilian Trypanosoma evansi stocks from domestic and wild hosts, which are known to differ in biological characteristics. These akinetoplastic stocks were compared with one another, to three Old World (Ethiopia, China and Philippines) dyskinetoplastic stocks of T. evansi, and also with Trypanosoma equiperdum, Trypanosoma brucei brucei, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. Randomly amplified polymorphic DNA analysis showed limited heterogeneity in T. evansi stocks from different hosts and geographical regions of the world, or in other species of the subgenus Trypanozoon. However, minor variations generated random amplification of polymorphic DNA analysis disclosed a pattern consisting of a unique synapomorphic DNA fragment (termed Te664) for the T. evansi cluster that was not detected in any other trypanosome species investigated. Pulsed field gel electrophoresis analysis demonstrated that the Te664 fragment is a repetitive sequence, dispersed in intermediate and minichromosomes of T. evansi. Based on this sequence, we developed a conventional PCR assay for the detection of T. evansi using crude preparations of blood collected either on glass slides or on filter paper as template DNA. Our results showed that this assay may be useful as a diagnostic tool for field-epidemiological studies of T. evansi.     

VSG 117 gene is conservatively present and early expressed in Trypanosma evansi YNB stock

African trypanosomes, including Trypanosoma brucei and the closely related species Trypanosoma evansi, are flagellated unicellular parasites that proliferate extracellularly in the mammalian bloodstream and tissue spaces. They evade host immune system by periodically switching their variant surface glycoprotein (VSG) coat. Each trypanosome possesses a vast archive of VSGs with distinct sequence identity and different strains contain different archive of VSGs. VSG 117 was reported as a widespread VSG detected in the genomes of all the T. brucei strains. In this study, the presence and expression of VSG 117 gene was observed in T. evansi YNB stock by RT-PCR with VSG-specific primers. We further confirmed that this VSG tends to be expressed in the early stage of T. evansi infections (on day 12-15) by immuno-screening the previously isolated infected blood samples. It is possible that the VSG 117 gene evolved and spread through the African trypanosome population via genetic exchange, before T. evansi lost its ability to infect tsetse fly. Our finding provided an evidence of the close evolutionary relationship between T. evansi and T. brucei, in the terms of VSG genes.     

Characterization of di-, tri-, and tetranucleotide microsatellite markers with perfect repeats for Trypanosoma brucei and related species

Trypanosoma brucei, unicellular parasites causing human sleeping sickness and animal nagana, have a great impact on the socio-economic environment of sub-Saharan Africa. The dynamics of the parasite are still poorly understood. We have characterized 14 polymorphic di-, tri-, and tetranucleotide microsatellite loci with perfect repeats (only one motif) exhibiting between 5 and 16 alleles in T. brucei isolates from all over Africa and from all described subspecies. The microsatellites will be useful in addressing population genetic questions in T. brucei to better understand the population structure and spread of this important parasite.     

What happens when Trypanosoma brucei leaves Africa

Julius Lukes and co-workers evaluated the evolutionary origin of Trypanosoma equiperdum and Trypanosoma evansi, parasites that cause horse and camel diseases. Although similar to T. brucei, the sleeping-sickness parasite, these trypanosomes do not cycle through the tsetse fly and have been able to spread beyond Africa. Transmission occurs sexually, or via blood-sucking flies or vampire bats. They concluded that these parasites, which resemble yeast petite mutants, are T. brucei sub-species, which have evolved recently through changes in mitochondrial DNA.     

Trypanosoma equiperdum: master of disguise or historical mistake?

After 100 years of research, only a small number of laboratory strains of Trypanosoma equiperdum exists, and the history of most of the strains is unknown. No definitive diagnosis of dourine can be made at the serological or molecular level. Only clinical signs are pathognomonic and international screening relies on an outdated cross-reactive serological test (the complement-fixation test) from 1915, resulting in serious consequences at the practical level. Despite many characterization attempts, no clear picture has emerged of the position of T. equiperdum within the Trypanozoon group. In this article, we highlight the controversies that exist regarding T. equiperdum, and the overlap that occurs with Trypanosoma evansi and Trypanosoma brucei brucei. By revisiting the published data, from the early decades of discovery to the recent serological- and molecular-characterization studies, a new hypothesis arises in which T. equiperdum no longer exists as a separate species and in which current strains can be divided into T. evansi (the historical mistake) and Trypanosoma brucei equiperdum (the master of disguise). Hence, dourine is a disease caused by specific host immune responses to a T. b. equiperdum or T. evansi infection.     

Cultivation in a semi-defined medium of animal infective forms of Trypanosoma brucei, T. equiperdum, T. evansi, T. rhodesiense and T. gambiense.

A semi-defined medium for the cultivation of bloodstream forms of the African trypanosome brucei subgroup was developed. Out of 14 different strains tested, 10 could be cultured including Trypanosoma brucei, T. equiperdum, T. evansi, T. rhodesiense and T. gambiense. The presence of a reducing agent (2-mercaptoethanol or thioglycerol) was found to be essential for growth. The standard medium consisted of Hepes buffered minimum essential medium with Earle's salts supplemented with 0.2 mM 2-mercaptoethanol, 2 mM pyruvate and 10% inactivated serum either from rabbit (T. brucei, T. equiperdum, T. evansi and T. rhodesiense) or human (T. gambiense). Although a general medium could be defined for the long-term maintenance of trypanosome cultures, the initiation to culture nevertheless required particular conditions for the different strains. The cultured trypanosomes had all the characteristics of the in vivo bloodstream forms including: morphology, infectivity, antigenic variation and glucose metabolism.     

Trypanosoma evansi: demonstration of a transferrin receptor derived from expression site-associated genes 6 and 7.

In Trypanosoma brucei, uptake of host transferrin is mediated by a heterodimeric, glycosylphosphatidylinositol-anchored receptor derived from the 2 expression site-associated genes 6 and 7 (ESAG6 and ESAG7). By using specific antibodies, it is shown here that T. evansi, a trypanosome species transmitted mechanically by biting flies, also expresses a transferrin receptor composed of ESAG6 and ESAG7. The cellular uptake of transferrin in T. evansi is completely inhibited with anti-T. brucei (ESAG6/7 heterodimer) antibodies. The demonstration of a functional ESAG6/7 transferrin receptor in T. evansi supports further its close relationship to T. brucei.     

Population structure and conservation genetic assessment of the endangered Pugnose Shiner,Notropis anogenus

The Pugnose Shiner is a small minnow with a fragmented distribution across the Great Lakes and Upper Mississippi River in North America. The species is listed federally as endangered in Canada, and in the United States its status varies by state, from Special Concern to Endangered (as well as Extirpated). We conducted a thorough genetic assessment of the Pugnose Shiner using both microsatellite loci and mitochondrial DNA collected for samples across the species range. Our results indicate high levels of population differentiation suggesting restricted dispersal, in some cases at very small geographical scales. We also found strong evidence of small effective population sizes and one case of a genetic bottleneck. Although significant range-wide genetic variation was observed in both microsatellite loci and mitochondrial DNA, the species is best characterized as a single evolutionarily significant unit for conservation purposes.     

Genetic differentiation of pink salmon oncorhynchus gorbuscha Walbaum in the Asian part of the range

Genetic variation at 19 allozyme (including 11 polymorphic) and 10 microsatellite loci was examined in the population samples of odd- and even-broodline pink salmon from the southern part of Sakhalin Island, Southern Kuril Islands, and the northern coast of the Sea of Okhotsk. The estimates of relative interpopulation component of genetic variation over the allozyme loci, per broodline, were on average 0.43% (GST), while over the microsatellite loci it was 0.26% (the theta(ST) coefficient, F-statistics based on the allele frequency variance), and 0.90% (the rho(ST) coefficient, R-statistics based on the allele size variance). The values of interlinear component constituted 2.34, 0.31, and 1.05% of the total variation, respectively. Using the allozyme loci, statistically significant intralinear heterogeneity was demonstrated among the regions, as well as among the populations of Southern Sakhalin Island. Multivariate scaling based on the allozyme data demonstrated regional clustering of the sample groups, representing certain populations during the spawning run or in different years. Most of the microsatellite loci examined were found to be highly polymorphic (mean heterozygosity > 0.880). The estimates of interlinear, interregional, and interpopulation variation over these loci in terms of theta(ST) values were substantially lower than in terms of rho(ST) values. Regional genetic differentiation, mostly expressed at the allozyme loci among the populations from the northern and southern parts of the Sea of Okhotsk (i.e., between the Sakhalin and Kuril populations), was less expressed at the microsatellite loci. The differentiation between these regions observed can be considered as the evidence in favor of a large-scale isolation by distance characterizing Asian pink salmon. It is suggested that in pink salmon, low genetic differentiation at neutral microsatellite loci can be explained by extremely high heterozygosity,of the loci themselves, as well as by the migration gene exchange among the populations (the estimate of the genetic migration coefficient inferred from the "private" allele data constituted 2.6 to 3.4%), specifically, by the ancient migration exchange, which occurred during postglacial colonization and colonization of the range.     

Population genetic consequences of feeding habits in some forest lepidoptera

By surveying variation at allozyme loci in several phytophagous lepidopteran species (Geometridae), we have tested two hypotheses about the relationship of genetic variation to environmental heterogeneity: (1) that allozyme polymorphisms may exist because of associations between genotypes and "niches" (different host plants, in this instance), and (2) that the overall genetic variation of a species is correlated with environmental heterogeneity (or breadth of the species' overall ecological niche).—Genetic differentiation among samples of oligophagous or polyphagous species taken from different host species was observed in one of three species, at only one of seven polymorphic loci. The data thus provide no evidence for pronounced genetic substructuring, or "host race" formation in these sexually reproducing species, although host plant-genotype associations in a parthenogenetic moth give evidence of the potential for diversifying selection.—In a comparison of allozyme variation in polyphagous ("generalized") and oligophagous ("specialized") species, heterozygosity appeared to be higher in specialized species, at all polymorphic loci but one. It is possible that this unexpected result arises from a functional relation between breadth of diet and genetic variation.     

RNA-interference silencing of the adenosine transporter-1 gene in Trypanosoma evansi confers resistance to diminazene aceturate

Drug resistance of trypanosomes is now a problem, but its underlying mechanisms are not fully understood. Cellular uptake of the major trypanocidal drugs is thought to occur through an adenosine transporter. The adenosine transporter-1 gene, TbAT1, encoding a P2-like nucleoside transporter has previously been cloned from Trypanosoma brucei brucei, and when expressed in yeast, it showed very similar substrate specificity to the P2-nucleoside transporter, but could not transport diamidines (pentamidine and diminazene). We have cloned and sequenced a similar gene (TevAT1) from Trypanosoma evansi and found it to have 99.7% identity to the TbAT1 gene. To elucidate the role of the TevAT1 gene on diamidine trypanocidal effect, we genetically engineered T. evansi for conditional knock-out of the TevAT1 gene by RNA interference (RNAi). Induction of the RNAi resulted in 10-fold depletion of TevAT1 mRNA, with concomitantly significant resistance to diminazene aceturate (berenil). The induced parasites propagated normally and attained peak cell density at an in vitro concentration of berenil, 5.5-fold higher than the IC(100) of the wild-type. TevAT1 knock-out had no effect on the trypanocidal activity of suramin and antrycide, but conferred some resistance to samorin. Our findings validate the significance of the TevAT1 adenosine transporter-1 gene in mediating the trypanocidal effect of diamidines in T. evansi. Further, we show for the first time that RNAi gene silencing in T. evansi can be induced using plasmids designed for T. brucei. We also demonstrate the usefulness of real-time PCR in rapidly quantifying mRNA levels in trypanosomes.     

Statistical properties of the variation at linked microsatellite loci: implications for the history of human Y chromosomes [published erratum appears in Mol Biol Evol 1997 Mar;14(3):354]

It has recently been suggested that observed levels of variation at microsatellite loci can be used to infer patterns of selection in genomes and to assess demographic history. In order to evaluate the feasibility of these suggestions it is necessary to know something about how levels of variation at microsatellite loci are expected to fluctuate due simply to stochasticity in the processes of mutation and inheritance (genetic sampling). Here we use recently derived properties of the stepwise mutation model to place confidence intervals around the variance in repeat score that is expected at mutation-drift equilibrium and outline a statistical test for whether an observed value differs significantly from expectation. We also develop confidence intervals for the time course of the buildup of variation following a complete elimination of variation, such as might be caused by a selective sweep or an extreme population bottleneck. We apply these methods to the variation observed at human Y-specific microsatellites. Although a number of authors have suggested the possibility of a very recent sweep, our analyses suggest that a sweep or extreme bottleneck is unlikely to have occurred anytime during the last approximately 74,000 years. To generate this result we use a recently estimated mutation rate for microsatellite loci of 5.6 x 10(-4) along with the variation observed at autosomal microsatellite loci to estimate the human effective population size. This estimate is 18,000, implying an effective number of 4,500 Y chromosomes. One important general conclusion to emerge from this study is that in order to reject mutation-drift equilibrium at a set of linked microsatellite loci it is necessary to have an unreasonably large number of loci unless the observed variance is far below that expected at mutation-drift equilibrium.      

Low genetic variation in muskoxen (Ovibos moschatus) from western Greenland using microsatellites

Muskoxen are large herbivores living in Arctic environments. Lack of genetic variation in allozymes has made it difficult to study the social and genetic structure of this species. In this study, we have tried to find polymorphic microsatellite loci using both cattle-derived microsatellite primers and primers developed from a genomic plasmid library of muskoxen. Only limited variation was found for both sets of microsatellite loci. We conclude that this consistent low genetic variation is probably due to demographic features of the muskoxen populations rather than to methodological constraints caused by the transfer of microsatellites between species.     

黑头酸臭蚁微卫星标记的分离与开发(英文)

【目的】本研究旨在分离黑头酸臭蚁Tapinoma melanocephalum基因组微卫星标记,确定这些微卫星位点的多态性。【方法】使用454 GS-FLX焦磷酸测序技术开发来自中国华南陆地和岛屿的11个黑头酸臭蚁地理种群基因组微卫星位点。从随机设计的100对微卫星引物中筛选出10对引物,用于确定黑头酸臭蚁4个地理种群［东澳岛(DAD)、荷包岛(HBD)、梅州(MZ)和山咀(SJ)］10个微卫星位点的多态性,分析种群遗传多样性和种群分化。【结果】从11个黑头酸臭蚁地理种群基因组中成功开发和分离10对微卫星引物。在DAD, HBD, MZ和SJ 4个地理种群中,10个微卫星位点中7个有高多态性,这10个位点均显著偏离Hardy-Weinberg平衡;每个位点的等位基因数量(A)是3.50~9.00个,每个地理种群每个位点等位基因丰富度(A_R)在1.992~12.938之间。岛屿地理种群(DAD和HBD)的AR和预期杂合度(H_E)与大陆地理种群(MZ和SJ)的相比差异不显著。4个地理种群均显示高水平遗传分化(F_ST=0.15969);HBD和MZ种群与其他配对地理种群相比,遗传分化较高(F_ST=0.185),基因流较低,说明这两个种群基因流被限制。此外,遗传变异来自种群内个体之间。【结论】筛选新的微卫星位点能够为研究黑头酸臭蚁种群结构和繁殖结构提供有效工具,以深入了解其传播机制。     

Genetic and behavioural evidence for a city-wide supercolony of the invasive Argentine ant Linepithema humile (Mayr) (Hymenoptera: Formicidae) in southeastern Australia

The success of invasive ants is frequently attributed to genetic and behavioural shifts in colony structure during or after introduction. The Argentine ant ( Linepithema humile ), a global invader, differs in colony genetic structure and behaviour between native populations in South America and introduced populations in Europe, Japan, New Zealand and North America. However, little is known about its colony structure in Australia. We investigated the genetic structure and behaviour of L. humile across Melbourne, Victoria by quantifying variation at four microsatellite loci and assaying intraspecific aggression at neighbourhood (30–200 m), fine (1–3.3 km) and regional (5–82 km) spatial scales. Hierarchical analyses across these scales revealed that most genetic variation occurred among workers within nests (∼98%). However, although low genetic differentiation occurred among workers between nests at the fine and regional scales (∼2%), negligible differentiation was detected among workers from neighbouring nests. Spatial genetic autocorrelation analysis confirmed that neighbouring nests were genetically more similar to each other. Lack of aggression within and across these scales supported the view that L. humile is unicolonial and forms a large supercolony across Melbourne. Comparisons of genetic structure of L. humile among single nests sampled from Adelaide, Brisbane, Hobart and Perth with Melbourne showed no greater levels of genetic differentiation or dissimilar spatial structure, suggesting an Australia-wide supercolony.     

Microsatellite and major histocompatibility complex variation in an endangered rattlesnake,the Eastern Massasauga (Sistrurus catenatus)

Genetic diversity is fundamental to maintaining the long‐term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.     

Microgeographic structure of Anopheles gambiae in western Kenya based on mtDNA and microsatellite loci

The population genetic structure of the Anopheles gambiae in western Kenya was studied using length variation at five microsatellite loci and sequence variation in a 648-nt mtDNA fragment. Mosquitoes were collected from houses in villages spanning up to 50 km distance, The following questions were answered, (i) Are mosquitoes in a house more related genetically to each other than mosquitoes between houses? (ii) What degree of genetic differentiation occurs on these geographical scales? (iii) How consistent are the results obtained with both types of genetic markers? At the house level, no differentiation was detected by F_ST and R_ST, and the band sharing index test revealed no significant associations of alleles across loci. Likewise, indices of kinship based on mtDNA haplotypes in houses were even lower than in the pooled sample. Therefore, the hypothesis that mosquitoes in a house are more related genetically was rejected. At increasing geographical scales, microsatellite allele distributions were similar among all population samples and no subdivision of the gene pool was detected by F_ST or R_ST. Likewise, estimates of haplotype divergence of mtDNA between populations were not higher than the within population estimates, and mtDNA-based F_ST values were not significantly different from zero. That sequence variation in mtDNA provided matching results with microsatellite loci (while high genetic variation was observed in all loci), suggested that this pattern represents the whole genome. The minimum area associated with a deme of A. gambiae in western Kenya is therefore larger than 50 km in diameter.