Asian genotypes of JC virus in Native Americans and in a Pacific Island population: Markers of viral evolution and human migration

The human polyomavirus JC (JCV) causes the central nervous system demyelinating disease progressive multifocal leukoencephalopathy. Previously, we showed that 40% of Caucasians in the United States excrete JCV in the urine as detected by PCR. We have now studied 68 Navaho from New Mexico, 25 Flathead from Montana, and 29 Chamorro from Guam. By using PCR amplification of a fragment of the VP1 gene, JCV DNA was detected in the urine of 45 (66%) Navaho, 14 (56%) Flathead, and 20 (69%) Chamorro. Genotyping of viral DNAs in these cohorts by cycle sequencing showed predominantly type 2 (Asian), rather than type 1 (European). Type 1 is the major type in the United States and Hungary. Type 2 can be further subdivided into 2A, 2B, and 2C. Type 2A is found in China and Japan. Type 2B is a subtype related to the East Asian type, and is now found in Europe and the United States. The large majority (56–89%) of strains excreted by Native Americans and Pacific Islanders were the type 2A subtype, consistent with the origin of these strains in Asia. These findings indicate that JCV infection of Native Americans predates contact with Europeans, and likely predates migration of Amerind ancestors across the Bering land bridge around 12,000–30,000 years ago. If JCV had already differentiated into stable modern genotypes and subtypes prior to first settlement, the origin of JCV in humans may date from 50,000 to 100,000 years ago or more. We conclude that JCV may have coevolved with the human species, and that it provides a convenient marker for human migrations in both prehistoric and modern times.

A molecular analysis of dietary diversity for three archaic Native Americans

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2–4 different animal species and 4–8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Susceptibility of cloned K+ channels to reactive oxygen species.

Free radical-induced oxidant stress has been implicated in a number of physiological and pathophysiological states including ischemia and reperfusion-induced dysrhythmia in the heart, apoptosis of T lymphocytes, phagocytosis, and neurodegeneration. We have studied the effects of oxidant stress on the native K+ channel from T lymphocytes and on K+ channels cloned from cardiac, brain, and T-lymphocyte cells and expressed in Xenopus oocytes. The activity of three Shaker K+ channels (Kv1.3, Kv1.4, and Kv1.5), one Shaw channel (Kv3.4), and one inward rectifier K+ channel (IRK3) was drastically inhibited by photoactivation of rose bengal, a classical generator of reactive oxygen species. Other channel types (such as Shaker K+ channel Kv1.2, Shab channels Kv2.1 and Kv2.2, Shal channel Kv4.1, inward rectifiers IRK1 and ROMK1, and hIsK) were completely resistant to this treatment. On the other hand tert-butyl hydroperoxide, another generator of reactive oxygen species, removed the fast inactivation processes of Kv1.4 and Kv3.4 but did not alter other channels. Xanthine/xanthine oxidase system had no effect on all channels studied. Thus, we show that different types of K+ channels are differently modified by reactive oxygen species, an observation that might be of importance in disease states.

Serological diagnosis of echinococcosis: the diagnostic potential of native antigens

PURPOSE: Human alveolar (AE) and cystic echinococcosis (CE) caused by the metacestode stages of Echinococcus multilocularis and E. granulosus, respectively, lack pathognomonic clinical signs. Diagnosis therefore relies on the results of imaging and serological studies. The primary goal of this study was to evaluate the efficacy of several easy-to-produce crude or partially purified E. granulosus and E. multilocularis metacestode-derived antigens as tools for the serological diagnosis and differential diagnosis of patients suspicious for AE or CE. METHODS: The sera of 51 treatment-naïve AE and 32 CE patients, 98 Swiss blood donors and 38 patients who were initially suspicious for echinococcosis but suffering from various other liver diseases (e.g., liver neoplasia, etc.) were analysed. RESULTS: According to the results of enzyme-linked immunosorbent assays (ELISA), metacestode-derived antigens of E. granulosus had sensitivities varying from 81 to 97% and >99.9% for the diagnosis of CE and AE, respectively. Antigens derived from E. multilocularis metacestodes had sensitivities ranging from 84 to 91% and >99.9% for the diagnosis of CE and AE, respectively. Specificities ranged from 92 to >99.9%. Post-test probabilities for the differential diagnosis of AE from liver neoplasias, CE from cystic liver lesions, and screening for AE in Switzerland were around 95, 86 and 2.2%, respectively. Cross-reactions with antibodies in sera of patients with other parasitic affections (fasciolosis, schistosomosis, amebosis, cysticercosis, and filarioses) did occur at variable frequencies, but could be eliminated through the use of confirmatory testing. CONCLUSIONS: Different metacestode-derived antigens of E. granulosus and E. multilocularis are valuable, widely accessible, and cost-efficient tools for the serological diagnosis of echinococcosis. However, confirmatory testing is necessary, due to the lack of species specificity and the occurrence of cross-reactions to other helminthic diseases.

Targeting genetic resource conservation in widespread species: a case study of Cedrela odorata L.

Conservation of genetic resources is a recognised necessity for the long term maintenance of evolutionary potential. Effective assessment and implementation Strategies are required to permit rapid evaluation and protection of resources. Here we use information from the chloroplast, total genome and quantitative characters assayed across wide-ranging populations to assess genetic resources in a Neotropical tree, Cedrela odorata. A major differentiation identified for organelle, total genomic and quantitative variation was found to coincide with an environmental gradient across Costa Rica. However, a major evolutionary divergence between the Yucatan region and Honduras/Nicaragua identified within the chloroplast genome was not differentiated using quantitative characters. Based on these and other results, a three-tiered conservation genetic prioritisation process is recommended. In order of importance, and where information is available, conservation units should be defined using quantitative (expressed genes), nuclear (genetic connectivity) and organellar (evolutionary) measures. Where possible, information from range wide and local scale studies should be combined and emphasis should be placed on coincidental disjunctions for two or more measures. However, if only rapid assessments of diversity are possible, then assessment of organelle variation provides the most cautious assessment of genetic resources, at least for C. odorata, and can be used to propose initial conservation units. When considering effective implementation of genetic resource management strategies a final tier should be considered, that of landuse/geopolitical divisions. (C) 2004 Elsevier B.V. All rights reserved.

Variations in cyclotide expression in Viola species

Cyclotides, a family of approximately 50 mini-proteins isolated from various Violaceae and Rubiaceae plants, are characterized by their circular peptide backbone and six conserved cysteine residues arranged in a cystine knot motif. Cyclotides show a wide range of biological activities, making them interesting targets for both pharmaceutical and agrochemical research, but little is known about their natural function and the events that trigger their expression. An investigation of the geographical and seasonal variations of cyclotide profiles has been performed, using the native Australian violet, Viola hederacea, and the Swedish sweet violet, Viola odorata, as model plants. The results showed that in the Australian violet the relative peptide levels of some cyclotides remained almost constant throughout the year, while other cyclotides were present only at certain times of the year. Therefore, it appears that V. hederacea expresses a basic armory of cyclotides as well as special add-ons whose levels are influenced by external factors. In the Swedish violet, cyclotide levels were increased up to 14 times during the warmest period of the year. The larger variation in expression levels of the Swedish plants may be a reflection of a greater climatic variation.

Biology and phenology of the eriophyid mite, Floracarus perrepae, on its native host in Australia, Old World climbing fern, Lygodium microphyllum

The biology and phenology of the eriophyid mite, Floracarus perrepae Knihinicki and Boczek,a potential biological control agent of Lygodium microphyllum (Cav.) R. Br., was studied in its native range - Queensland, Australia. F. perrepae forms leaf roll galls oil tile subpinnae of L. microphyllum. It has a simple biology, with females and males produced throughout the year. Tile Population was female biased at 10.5 to 1. The immature development time was 8.9 ± 0.1 and 7.0 ± 0.1 days; adult longevity was 30.6 ± 1.6 and 19.4 ± 1.2 days and mean fecundity per female was 54.5 ± 3.2 and 38.5 ± 1.6 eggs at 21 and 26 ° C, all respectively. Field studies showed that tile mite was active year round, with populations peaking when temperatures were cool and soil moisture levels were highest. Two species of predatory mites, Tarsonemus sp. and a species of Tydeidae, along with the pathogen Hirsutella thompsonii, had significant effects oil all life stages of F. perrepae. Despite high levels of predators and the pathogen, F. perrepae caused consistent damage to L. microphyllum at all the field sites over the entire 2 years of the study.

Boron nutrition and chilling tolerance of warm climate crop species

Background Field observations and glasshouse studies have suggested links between boron (B)-deficiency and leaf damage induced by low temperature in crop plants, but causal relationships between these two stresses at physiological, biochemical and molecular levels have yet to be explored. Limited evidence at the whole-plant level suggests that chilling temperature in the root zone restricts B uptake capacity and/or B distribution/utilization efficiency in the shoot, but the nature of this interaction depends on chilling tolerance of species concerned, the mode of low temperature treatment (abrupt versus gradual temperature decline) and growth conditions (e.g. photon flux density and relative humidity) that may exacerbate chilling stress. Scope This review explores roles of B nutrition in chilling tolerance of continual root or transient shoot chills in crop species adapted to warm season conditions. It reviews current research on combined effects of chilling temperature (ranging from > 0 to 20 degrees C) and B deficiency on growth and B nutrition responses in crop species differing in chilling tolerance. Conclusion For subtropical/tropical species (e.g. cucumber, cassava, sunflower), root chilling at 10-17 degrees C decreases B uptake efficiency and B utilization in the shoot and increases the shoot : root ratio, but chilling-tolerant temperate species (e.g. oilseed rape, wheat) require much lower root chill temperatures (2-5 degrees C) to achieve the same responses. Boron deficiency exacerbates chilling injuries in leaf tissues, particularly under high photon flux density. Suggested mechanisms for B x chilling interactions in plants are: (a) chilling-induced reduction in plasmalemma hydraulic conductivity, membrane fluidity, water channel activity and root pressure, which contribute to the decrease in root hydraulic conductance, water uptake and associated B uptake; (b) chilling-induced stomatal dysfunction affecting B transport from root to shoot and B partitioning in the shoot; and (c) B deficiency induced sensitivity to photo-oxidative damage in leaf cells. However, specific evidence for each of the mechanisms is still lacking. Impacts of B status on chilling tolerance in crop species have important implications for the management of B supply during sensitive stages of growth, such as early growth after planting and early reproductive development, both of which can coincide with the occurrence of chilling temperatures in the field.

Patch dynamics in grazed subtropical native pastures in south-east Queensland

Patch formation is common in grazed grasslands but the mechanisms involved in the formation and maintenance of patches are not clear. To increase our knowledge on this subject we examined possible reasons for patch formation and the influence of management on changes between patch states in three experiments in native pasture communities in the Crows Nest district, south-east Queensland. In these communities, small-scale patches (tall grassland (dominated by large and medium tussock grasses), short swards (dominated by short tussock grasses and sedges), and lawns (dominated by stoloniferous and/or rhizomatous grasses)) are readily apparent. We hypothesized that the formation of short sward and lawn patches in areas of tall grassland was due to combinations of grazing and soil fertility effects. This was tested in Experiment 1 by applying a factorial combination of defoliation, nutrient application and transplants of short tussock and stoloniferous species to a uniform area of tall grassland. Total species density declined during the experiment, was lower with high nutrient applications, but was not affected by defoliation. There were significant changes in abundance of species that provided support for our hypotheses. With light defoliation and low nutrients, the tall grassland remained dominated by large tussock grasses and contained considerable amounts of forbs. With heavy defoliation, the pastures were dominated by medium tussock grasses and there were significant decreases in forbs and increases in sedges (mainly with low nutrients) and stoloniferous grasses (mainly with high nutrients). Total germinable seed densities and those of most species groups were significantly lower in the heavy defoliation than the light defoliation plots. Total soil seed numbers were not affected by nutrient application but there were fewer seeds of the erect forbs and more sedge seeds in plots with high nutrients. The use of resting from grazing and fire to manage transitions between patches was tested. In Experiment 2, changes in species density and abundance were measured for 5 years in the three patch types with and without grazing. Experiment 3 examined the effects of fire, grazing and resting on short sward patches over 4 years. In Experiment 2, total species density was lower in lawn than short sward or tall grassland patches, and there were more species of erect forbs than other plant groups in all patch types. The lawn patches were originally dominated by Cynodon spp. This dominance continued with grazing but in ungrazed patches the abundance of Cynodon spp. declined and that of forbs increased. In the short sward patches, dominance of short tussock grasses continued with grazing but in ungrazed plots their abundance declined while that of large tussock grasses increased. The tall grassland patches remained dominated by large and medium tussock species. In Experiment 3, fire had no effect on species abundance. On the grazed plots the short tussock grasses remained dominant but where the plots were rested from grazing the small tussock grasses declined and the large tussock grasses increased in abundance. The slow and relatively small changes in these experiments over 4 or 5 years showed how stable the composition of these pastures is, and that rapid changes between patch types are unlikely.

Effects of nitrogen source and ectomycorrhizal association on growth and delta N-15 of two subtropical Eucalyptus species from contrasting ecosystems

Ectomycorrhizal (EM) associations facilitate plant nitrogen (N) acquisition, but the contribution of EM associations to tree N nutrition is difficult to ascertain in ecosystems. We studied the abilities of subtropical EM fungi and nutritionally contrasting Eucalyptus species, Eucalyptus grandis W. Hill ex Maiden and Eucalyptus racemosa Cav, to use N sources in axenic and soil cultures, and determined the effect of EM fungi on plant N use and plant N-15 natural abundance (delta N-15). As measured by seedling growth, both species showed little dependence on EM when growing in the N-rich minerotrophic soil from E. grandis rainforest habitat or in axenic culture with inorganic N sources. Both species were heavily dependent on EM associations when growing in the N-poor, organotrophic soil from the E. racemosa wallum habitat or in axenic culture with organic N sources. In axenic culture, EM associations enabled both species to use organic N when supplied with amide-, peptide- or protein-N. Grown axenically with glutamine- or protein-N, delta N-15 of almost all seedlings was lower than source N. The delta N-15 of all studied organisms was higher than the N source when grown on glutathione. This unexpected N-15 enrichment was perhaps due to preferential uptake of an N moiety more N-15-enriched than the bulk molecular average. Grown with ammonium-N, the delta N-15 of non-EM seedlings was mostly higher than that of source N. In contrast, the delta N-15 of EM seedlings was mostly lower than that of source N, except at the lowest ammonium concentration. Discrimination against N-15 was strongest when external ammonium concentration was high. We suggest that ammonium assimilation via EM fungi may be the cause of the often observed distinct foliar delta N-15 of EM and non-EM species, rather than use of different N sources by species with different root specialisations. In support of this notion, delta N-15 of soil and leaves in the rainforest were similar for E. grandis and co-occurring non-mycorrhizal Proteaceae. In contrast, in wallum forest, E. racemosa leaves and roots were strongly N-15-depleted relative to wallum soil and Proteaceae leaves. We conclude that foliar delta N-15 may be used in conjunction with other ecosystem information as a rapid indicator of plant dependency on EM associations for N acquisition.

Variation in hydraulic conductivity of mangroves: influence of species, salinity, and nitrogen and phosphorus availability

We investigated how species identity and variation in salinity and nutrient availability influence the hydraulic conductivity of mangroves. Using a fertilization study of two species in Florida, we found that stem hydraulic conductivity expressed on a leaf area basis (K-leaf) was significantly different among species of differing salinity tolerance, but was not significantly altered by enrichment with limiting nutrients. Reviewing data from two additional sites (Panama and Belize), we found an overall pattern of declining leaf-specific hydraulic conductivity (K-leaf) with increasing salinity. Over three sites, a general pattern emerges, indicating that native stem hydraulic conductivity (K-h) and K-leaf are less sensitive to nitrogen (N) fertilization when N limits growth, but more sensitive to phosphorus (P) fertilization when P limits growth. Processes leading to growth enhancement with N fertilization are probably associated with changes in allocation to leaf area and photosynthetic processes, whereas water uptake and transport processes could be more limiting when P limits growth. These findings suggest that whereas salinity and species identity place broad bounds on hydraulic conductivity, the effects of nutrient availability modulate hydraulic conductivity and growth in complex ways.

Sustainable Native Floriculture?

The Centre for Native Floriculture (CNF) commenced in May 2003 at The University of Queensland, Gatton. The CNF is a joint initiative with the Queensland State Government, with funding for an initial 3-year period. The phase-out of bush-picking under the South East Queensland Forests Agreement was a catalyst for the Centres establishment. The CNF vision is: ‘to help create an internationally competitive and environmentally sustainable native floriculture industry that provides significant employment opportunities in Queensland’. The Centre is comprised of three research, development and extension programs. The Value Chain Program assists native floriculture industry groups in developing efficient consumer-orientated production, handling and marketing systems for select high potential species. These value chain systems will serve as models for realizing the market potential of and regional fiscal returns on other native ornamental species identified as crop ideotypes that are sought after by end-users (e.g. florists). The Floriculture Program supports the value chain by working to enhance germplasm for the native floriculture industry through selection and breeding, optimize cultivation protocols and overcome any technical barriers that arise. Such barriers include propagation constraints, disease problems and post-harvest limitations. The Capacity Building Program operates to transfer technology and other skills (e.g. value chain management principles) to industry members, train operatives for the industry and promote native floriculture. Conservation of native flora is encouraged through cultivation and community engagement. Protection of biodiversity is advocated via regional production systems that spare natural areas and educate the public as to the biological, floricultural and aesthetic values of native flora. Eco-agricultural tourism focused on wildflowers both in nature and in cultivation is also advocated by the CNF.

Public choice of species for the 'Ark': Phylogenetic similarity and preferred wildlife species for survival

Humans play a role in deciding the fate of species in the current extinction wave. Because of the previous Similarity Principle, physical attractiveness and likeability, it has been argued that public choice favours the survival of species that satisfy these criteria at the expense of other species. This paper empirically tests this argument by considering a hypothetical ‘Ark’ situation. Surveys of 204 members of the Australian public inquired whether they are in favour of the survival of each of 24 native mammal, bird and reptile species (prior to and after information provision about each species). The species were ranked by percentage of ‘yes’ votes received. Species composition by taxon in various fractions of the ranking was determined. If the previous Similarity Principle holds, mammals should rank highly and dominate the top fractions of animals saved in the hierarchical list. We find that although mammals would be over-represented in the ‘Ark’, birds and reptiles are unlikely to be excluded when social choice is based on numbers ‘voting’ for the survival of each species. Support for the previous Similarity Principle is apparent particularly after information provision. Public policy implications of this are noted and recommendations are given.

The C1q binding activity of IgG is modified in vitro by reactive oxygen species: implications for rheumatoid arthritis

IgG can be denatured in vitro by reactive oxygen species (ROS). Native IgG activates the complement cascade through C1q. Using a modified ELISA, C1q binding activity of rheumatoid IgG has been compared to IgG denatured by neutrophil-derived ROS. The C1q binding activity of rheumatoid synovial fluid IgG is greater than the corresponding serum IgG (P < 0.01). Denaturation of IgG by activated polymorphs or the Fenton reaction decreased its C1q binding activity (P < 0.01). In vitro exposure of IgG to OH. and ROO. increased its interaction with C1q (P < 0.01). Hypochlorous acid had no effect. ROS-induced alteration to IgG-C1q binding activity may promote the inflammatory response in rheumatoid arthritis.

Probing molecular changes induced in DNA by reactive oxygen species with monoclonal antibodies

Antibodies reactive with native double stranded DNA are characteristic of the chronic inflammatory disease systemic lupus erythematosus. Native DNA is however, a poor immunogen and the mechanism of anti-DNA antibody production is incompletely understood. Modification of DNA can increase its immunogenicity and in inflammatory disease states reactive oxygen species produced from phagocytic cells have been shown to thus modify DNA. In this study, monoclonal antibodies produced spontaneously by two mice strains with lupus-like disease were used in a competition ELISA to monitor changes to DNA induced by reactive oxygen species. Different procedures for reactive oxygen species generation were found to cause distinct and characteristic changes to DNA involving modifications of base residues, the sugar-phosphate backbone and the gross conformational structure of double-stranded DNA. In view of this, it may be possible to use these antibodies further to probe DNA and infer the source and nature of the reactive oxygen species it has been exposed to, particularly in vivo.