Ancient diversity and geographical sub-structuring in African buffalo Theileria parva populations revealed through metagenetic analysis of antigen-encoding loci

An infection and treatment protocol involving infection with a mixture of three parasite isolates and simultaneous treatment with oxytetracycline is currently used to vaccinate cattle against Theileria parva. While vaccination results in high levels of protection in some regions, little or no protection is observed in areas where animals are challenged predominantly by parasites of buffalo origin. A previous study involving sequencing of two antigen-encoding genes from a series of parasite isolates indicated that this is associated with greater antigenic diversity in buffalo-derived T. parva. The current study set out to extend these analyses by applying high-throughput sequencing to ex vivo samples from naturally infected buffalo to determine the extent of diversity in a set of antigen-encoding genes. Samples from two populations of buffalo, one in Kenya and the other in South Africa, were examined to investigate the effect of geographical distance on the nature of sequence diversity. The results revealed a number of significant findings. First, there was a variable degree of nucleotide sequence diversity in all gene segments examined, with the percentage of polymorphic nucleotides ranging from 10% to 69%. Second, large numbers of allelic variants of each gene were found in individual animals, indicating multiple infection events. Third, despite the observed diversity in nucleotide sequences, several of the gene products had highly conserved amino acid sequences, and thus represent potential candidates for vaccine development. Fourth, although compelling evidence for population differentiation between the Kenyan and South African T. parva parasites was identified, analysis of molecular variance for each gene revealed that the majority of the underlying nucleotide sequence polymorphism was common to both areas, indicating that much of this aspect of genetic variation in the parasite population arose prior to geographic separation.     

Does the host matter? Variable influence of host traits on parasitism rates

Parasitism of mammals is ubiquitous, but the processes driving parasite aggregation on hosts are poorly understood, as each system seems to show unique correlations between parasitism and host traits such as sex, age, size and body mass. Genetic diversity is also posited to influence susceptibility to parasitism, and provides a quantifiable measure of an intrinsic unchanging host property, but this link has not been well established. A lack of consistency in host traits predicting parasite heterogeneity may derive from the contribution of environmental factors to parasite aggregation. To evaluate this question, a large dataset was leveraged to explore the relationship between unchanging, intrinsic host traits (heterozygosity and sex), variable host traits (age, length and body mass), and extrinsic factors (sampling date/year and population) and flea presence/absence, abundance and intensity on two species of social burrowing mammal, the black-tailed prairie dog (Cynomys ludovicianus) and the Gunnison’s prairie dog (Cynomys gunnisoni). Prairie dogs experience frequent parasitism by fleas, but the distribution of fleas among individuals is highly skewed. In these systems, intrinsic host traits were nuanced in how they predicted flea aggregation on individual prairie dogs, with sex unimportant to parasitism rates and heterozygosity increasing the probability of infection and influencing the number of fleas in divergent ways. Variable host traits interacted with each other and with environmental or geographic stochasticity to influence flea aggregation. Length and age tended to increase parasitism, whereas the effects of body mass and condition were mediated by date and other host traits to produce both positive and negative effects on parasitism. This finding suggests that the factors affecting ectoparasite infection on individuals are complex, even within species. Importantly, there was no correlation between the number of fleas on an individual in one year and the number of fleas on the same individual the next year, supporting the idea that flea aggregation is not driven by unchanging, intrinsic characteristics of the host. Rather, these findings indicate that host traits influence parasitism in nuanced ways, including interactions with environmental characteristics and stochastic factors.     

Diversity at two genetic loci associated with the major histocompatibility complex in the golden snub-nosed monkey (Rhinopithecus roxellana)

Habitat loss via human activity has fragmented populations of the golden snub-nosed monkey (Rhinopithecus roxellana), and thus affected patterns of gene flow. We investigated in-depth a single troop in the Qinling Mountains, central China, two major histocompatibility complex (MHC) class II loci, DQA1 and DQB1, and compared the resulting data with data from troops from the wider Qinling Mountains region. We found that a novel DQB1 allele was only present in the study troop and relatively few divergent alleles at the DQA1 and DQB1 loci were present compared with the wider population. The inbreeding coefficient (F_is) at the MHC region was lower than previous measurements, which may have reflected different sampling strategies. However, R. roxellana has relatively high diversity in MHC genes, even though it has probably experienced serious past population bottlenecks and reduced gene flow between populations. We also found that some alleles present in the wider population had been lost in the study troop, and suggest that conservation management strategies be implemented to increase gene flow between troops in order to increase genetic variation.     

GST M1/T1 and MTHFR polymorphisms as risk factors for hypertension

The aim of this study is to investigate GSTM1, GSTT1 and MTHFR genetic polymorphisms and its relation with total plasma glutathione (tGSH) levels in hypertension. Genotype distributions of GSTM1 and GSTT1 deletion polymorphisms and C677T variant of MTHFR were examined in a sample of 94 hypertensive patients with congestive heart failure and 207 healthy unrelated Portuguese individuals using PCR techniques. Plasma GST activity was determined spectrophotometrically. The antioxidant status was evaluated by fluorometric assays of tGSH. Genotype distributions of GSTT1 (chi2 test; p < 0.01) and MTHFR (chi2 test; p < 0.01) differ significantly between control and hypertensive patients with a greater prevalence of "non-null GSTT1/M1" and CT (heterozygous) genotypes. Moreover, GST activity and tGSH were markedly decreased in hypertension but there is no correlation with the studied polymorphisms. GSH depletion confirmed the possible involvement of oxidative stress in this pathology. Deletion of GSTT1 gene might be considered as protective factor for hypertension.     

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes.

The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intra-ecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification. Received: 25 September 1998 / Accepted: 3 March 1999     

Comparison of DNA marker and pedigree-based methods of genetic analysis in plantain and banana (Musa spp.) clones. II. Predicting hybrid performance

 Pedigree and DNA marker-based methods were used to predict the performance of triploid progeny from tetraploid-diploid crosses, based on parental heterozygosity, genetic relatedness, and expected contribution to their progeny. There was no significant correlation between parental and progeny performance. Prediction of progeny bunch weight was best when based on genealogical distance and equal parental contribution. Predicted fruit size was most accurate when DNA marker data were used and the assumption of an unequal parental contribution was made. Consideration of parental heterozygosity produced larger residuals for all traits. No statistically significant differences were found between the mean residuals obtained under the assumption of an equal vs an unequal contribution of the 4x and 2x genotypes to their 3x progeny, regardless of the method used to estimate genetic relationships. Received: 29 October 1997 / Accepted: 14 July 1998     

Growth and protection against oxidative stress in young clones and mature spruce trees (Picea abies L.) at high altitudes

Clones of Norway spruce (Picea abies L.) were grown for several years on an altitudinal gradient (1750 m, 1150 m and 800 m above sea level) to study the effects of environmental × genetic interactions on growth and foliar metabolites (protein, pigments, antioxidants). Clones at the tree line showed 4.3-fold lower growth rates and contained 60% less chlorophyll (per gram of dry matter) than those at valley level. The extent of growth reduction was clone-dependent. The mortality of the clones was low and not altitude-dependent. At valley level, but not at high altitude, needles of mature spruce trees showed lower pigment and protein concentrations than clones. In general, antioxidative systems in needles of the mature trees and young clones did not increase with increasing altitude. Needles of all trees at high altitude showed higher concentrations of dehydroascorbate than at lower altitudes, indicating higher oxidative stress. In one clone, previously identified as sensitive to acute ozone doses, this increase was significantly higher and the growth reduction was stronger than in the other genotypes. This clone also displayed a significant reduction in glutathione reductase activity at high altitude. These results suggest that induction of antioxidative systems is apparently not a general prerequisite to cope with altitude in clones whose mother plants originated from higher altitudes (about 650–1100 m above sea level, Hercycnic-Carpathian distribution area), but that the genetic constitution for maintenance of high antioxidative protection is important for stress compensation at the tree line. Received: 13 October 1998 / Accepted: 22 June 1999     

In vitro versus in vivo genetic divergence in potato

 The objective of this study was to compare the genetic divergence pattern in potato (Solanum tuberosum L.) under in vitro and in vivo conditions. Twenty two potato genotypes were evaluated for ten morphological characters under four in vitro conditions, and for 20 characters under four in vivo seasons. Mahalanobis’ generalized intra- and inter-group genetic distances, and the distribution of genotypes into different clusters, led to the same conclusions under both in vitro and in vivo conditions: (1) genetic diversity was not related to geographic diversity, (2) genetic distances were higher between Tuberosum and Andigena than within Tuberosum and Andigena, and (3) present-day Indian varieties have more resemblance to Tuberosum than to the Andigena group. The in vitro approach was more effective than the in vivo approach for differentiating the genotypes per se, although its effectiveness for cross prediction is known to be low. Received: 15 September 1997 / Accepted: 15 July 1998     

A 25-kDa dehydrin associated with genotype- and age-dependent leaf freezing-tolerance in Rhododendron: a genetic marker for cold hardiness?

Dehydrins are plant proteins that may play a critical role in stabilizing cell functions during freezing and other dehydrative stresses. This study examines whether dehydrin expression in leaves is associated with varying levels of freezing-tolerance among F₂ segregants, species, and cultivars of evergreen Rhododendron. Experiments were also conducted to determine whether physiological and chronological aging affects freezing-tolerance and dehydrin accumulation in Rhododendron leaf tissues. Our results indicate that in cold-acclimated F₂ populations, levels of a 25-kDa dehydrin were closely associated with differences in leaf freezing-tolerance (LFT) among segregants. Studies of wild and cultivated plants indicated that LFT increased with both chronological age and developmental phase-change (juvenile to mature plants) and that this trend was accompanied by increased accumulation of the 25-kDa dehydrin. It is suggested that presence or absence of the 25-kDa dehydrin could serve as a genetic marker to distinguish between super cold-hardy and less cold-hardy rhododendron genotypes. Similarly, the relative level of this protein within a genotype can serve as a physiological indicator of freezing-tolerance status under a range of phenological (acclimation) or developmental (age) conditions. Received: 5 March 1999 / Accepted: 12 May 1999