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White PJ, Bruggeman JE, Garrott RA. Irruptive population dynamics in Yellowstone pronghorn. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2007; 17:1598-606. [PMID: 17913126 DOI: 10.1890/06-2032.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Irruptive population dynamics appear to be widespread in large herbivore populations, but there are few empirical examples from long time series with small measurement error and minimal harvests. We analyzed an 89-year time series of counts and known removals for pronghorn (Antilocapra americana) in Yellowstone National Park of the western United States during 1918-2006 using a suite of density-dependent, density-independent, and irruptive models to determine if the population exhibited irruptive dynamics. Information-theoretic model comparison techniques strongly supported irruptive population dynamics (Leopold model) and density dependence during 1918-1946, with the growth rate slowing after counts exceeded 600 animals. Concerns about sagebrush (Artemisia spp.) degradation led to removals of >1100 pronghorn during 1947-1966, and counts decreased from approximately 700 to 150. The best models for this period (Gompertz, Ricker) suggested that culls replaced intrinsic density-dependent mechanisms. Contrary to expectations, the population did not exhibit enhanced demographic vigor soon after the termination of the harvest program, with counts remaining between 100 and 190 animals during 1967 1981. However, the population irrupted (Caughley model with a one-year lag) to a peak abundance of approximately 600 pronghorn during 1982-1991, with a slowing in growth rate as counts exceeded 500. Numbers crashed to 235 pronghorn during 1992-1995, perhaps because important food resources (e.g., sagebrush) on the winter range were severely diminished by high densities of browsing elk, mule deer, and pronghorn. Pronghorn numbers remained relatively constant during 1996-2006, at a level (196-235) lower than peak abundance, but higher than numbers following the release from culling. The dynamics of this population supported the paradigm that irruption is a fundamental pattern of growth in many populations of large herbivores with high fecundity and delayed density-dependent effects on recruitment when forage and weather conditions become favorable after range expansion or release from harvesting. Incorporating known removals into population models that can describe a wide range of dynamics can greatly improve our interpretation of observed dynamics in intensively managed populations.
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Garrott RA, Bruggeman JE, Becker MS, Kalinowski ST, White PJ. Evaluating prey switching in wolf-ungulate systems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2007; 17:1588-97. [PMID: 17913125 DOI: 10.1890/06-1439.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Wolf restoration has become a widely accepted conservation and management practice throughout North America and Europe, though the ecosystem effects of returning top carnivores remain both scientific and societal controversies. Mathematical models predicting and describing wolf-ungulate interactions are typically limited to the wolves' primary prey, with the potential for prey switching in wolf-multiple-ungulate systems only suggested or assumed by a number of investigators. We used insights gained from experiments on small taxa and field data from ongoing wolf-ungulate studies to construct a model of predator diet composition for a wolf-elk-bison system in Yellowstone National Park, Wyoming, USA. The model explicitly incorporates differential vulnerability of the ungulate prey types to predation, predator preference, differences in prey biomass, and the possibility of prey switching. Our model demonstrates wolf diet shifts with changes in relative abundance of the two prey, with the dynamics of this shift dependent on the combined influences of preference, differential vulnerability, relative abundances of prey, and whether or not switching occurs. Differences in vulnerability between elk and bison, and strong wolf preference for elk, result in an abrupt dietary shift occurring only when elk are very rare relative to bison, whereas incorporating switching initiates the dietary shift more gradually and at higher bison-elk ratios. We demonstrate how researchers can apply these equations in newly restored wolf-two-prey systems to empirically evaluate whether prey switching is occurring. Each coefficient in the model has a biological interpretation, and most can be directly estimated from empirical data collected from field studies. Given the potential for switching to dramatically influence predator-prey dynamics and the wide range of expected prey types and abundances in some systems where wolves are present and/or being restored, we suggest that this is an important and productive line of research that should be pursued by ecologists working in wolf-ungulate systems.
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White PJ, Bowen HC, Marshall B, Broadley MR. Extraordinarily high leaf selenium to sulfur ratios define 'Se-accumulator' plants. ANNALS OF BOTANY 2007; 100:111-8. [PMID: 17525099 PMCID: PMC2735298 DOI: 10.1093/aob/mcm084] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 03/12/2007] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Selenium (Se) and sulfur (S) exhibit similar chemical properties. In flowering plants (angiosperms) selenate and sulfate are acquired and assimilated by common transport and metabolic pathways. It is hypothesized that most angiosperm species show little or no discrimination in the accumulation of Se and S in leaves when their roots are supplied a mixture of selenate and sulfate, but some, termed Se-accumulator plants, selectively accumulate Se in preference to S under these conditions. METHODS This paper surveys Se and S accumulation in leaves of 39 angiosperm species, chosen to represent the range of plant Se accumulation phenotypes, grown hydroponically under identical conditions. RESULTS The data show that, when supplied a mixture of selenate and sulfate: (1) plant species differ in both their leaf Se ([Se](leaf)) and leaf S ([S](leaf)) concentrations; (2) most angiosperms show little discrimination for the accumulation of Se and S in their leaves and, in non-accumulator plants, [Se](leaf) and [S](leaf) are highly correlated; (3) [Se](leaf) in Se-accumulator plants is significantly greater than in other angiosperms, but [S](leaf), although high, is within the range expected for angiosperms in general; and (4) the Se/S quotient in leaves of Se-accumulator plants is significantly higher than in leaves of other angiosperms. CONCLUSION The traits of extraordinarily high [Se](leaf) and leaf Se/S quotients define the distinct elemental composition of Se-accumulator plants.
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Bruggeman JE, Garrott RA, White PJ, Watson FGR, Wallen R. Covariates affecting spatial variability in bison travel behavior in Yellowstone National Park. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2007; 17:1411-23. [PMID: 17708218 DOI: 10.1890/06-0196.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Understanding mechanisms influencing the movement paths of animals is essential for comprehending behavior and accurately predicting use of travel corridors. In Yellowstone National Park (USA), the effects of roads and winter road grooming on bison (Bison bison) travel routes and spatial dynamics have been debated for more than a decade. However, no rigorous studies have been conducted on bison spatial movement patterns. We collected 121 380 locations from 14 female bison with GPS collars in central Yellowstone to examine how topography, habitat type, roads, and elevation affected the probability of bison travel year-round. We also conducted daily winter bison road use surveys (2003-2005) to quantify how topography and habitat type influenced spatial variability in the amount of bison road travel. Using model comparison techniques, we found the probability of bison travel and spatial distribution of travel locations were affected by multiple topographic and habitat type attributes including slope, landscape roughness, habitat type, elevation, and distances to streams, foraging areas, forested habitats, and roads. Streams were the most influential natural landscape feature affecting bison travel, and results suggest the bison travel network throughout central Yellowstone is spatially defined largely by the presence of streams that connect foraging areas. Also, the probability of bison travel was higher in regions of variable topography that constrain movements, such as in canyons. Pronounced travel corridors existed both in close association with roads and distant from any roads, and results indicate that roads may facilitate bison travel in certain areas. However, our findings suggest that many road segments used as travel corridors are overlaid upon natural travel pathways because road segments receiving high amounts of bison travel had similar landscape features as natural travel corridors. We suggest that most spatial patterns in bison road travel are a manifestation of general spatial travel trends. Our research offers novel insights into bison spatial dynamics and provides conceptual and analytical frameworks for examining movement patterns of other species.
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White PJ, Broadley MR, Bowen HC, Johnson SE. Selenium and its relationship with sulfur. PLANT ECOPHYSIOLOGY 2007. [DOI: 10.1007/978-1-4020-5887-5_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
Zinc (Zn) is an essential component of thousands of proteins in plants, although it is toxic in excess. In this review, the dominant fluxes of Zn in the soil-root-shoot continuum are described, including Zn inputs to soils, the plant availability of soluble Zn(2+) at the root surface, and plant uptake and accumulation of Zn. Knowledge of these fluxes can inform agronomic and genetic strategies to address the widespread problem of Zn-limited crop growth. Substantial within-species genetic variation in Zn composition is being used to alleviate human dietary Zn deficiencies through biofortification. Intriguingly, a meta-analysis of data from an extensive literature survey indicates that a small proportion of the genetic variation in shoot Zn concentration can be attributed to evolutionary processes whose effects manifest above the family level. Remarkable insights into the evolutionary potential of plants to respond to elevated soil Zn have recently been made through detailed anatomical, physiological, chemical, genetic and molecular characterizations of the brassicaceous Zn hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri.
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Watanabe T, Broadley MR, Jansen S, White PJ, Takada J, Satake K, Takamatsu T, Tuah SJ, Osaki M. Evolutionary control of leaf element composition in plants. THE NEW PHYTOLOGIST 2007; 174:516-523. [PMID: 17447908 DOI: 10.1111/j.1469-8137.2007.02078.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Leaf nitrogen (N) and phosphorus (P) concentrations are correlated in plants. Higher-level phylogenetic effects can influence leaf N and P. By contrast, little is known about the phylogenetic variation in the leaf accumulation of most other elements in plant tissues, including elements with quantitatively lesser roles in metabolism than N, and elements that are nonessential for plant growth. Here the leaf composition of 42 elements is reported from a statistically unstructured data set comprising over 2000 leaf samples, representing 670 species and 138 families of terrestrial plants. Over 25% of the total variation in leaf element composition could be assigned to the family level and above for 21 of these elements. The remaining variation corresponded to differences between species within families, to differences between sites which were likely to be caused by soil and climatic factors, and to variation caused by sampling techniques. While the majority of variation in leaf mineral composition is undoubtedly associated with nonevolutionary factors, identifying higher-level phylogenetic variation in leaf elemental composition increases our understanding of terrestrial nutrient cycles and the transfer of toxic elements from soils to living organisms. Identifying mechanisms by which different plant families control their leaf elemental concentration remains a challenge.
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Hermans C, Hammond JP, White PJ, Verbruggen N. How do plants respond to nutrient shortage by biomass allocation? TRENDS IN PLANT SCIENCE 2006; 11:610-7. [PMID: 17092760 DOI: 10.1016/j.tplants.2006.10.007] [Citation(s) in RCA: 470] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 09/07/2006] [Accepted: 10/24/2006] [Indexed: 05/12/2023]
Abstract
Plants constantly sense the changes in their environment; when mineral elements are scarce, they often allocate a greater proportion of their biomass to the root system. This acclimatory response is a consequence of metabolic changes in the shoot and an adjustment of carbohydrate transport to the root. It has long been known that deficiencies of essential macronutrients (nitrogen, phosphorus, potassium and magnesium) result in an accumulation of carbohydrates in leaves and roots, and modify the shoot-to-root biomass ratio. Here, we present an update on the effects of mineral deficiencies on the expression of genes involved in primary metabolism in the shoot, the evidence for increased carbohydrate concentrations and altered biomass allocation between shoot and root, and the consequences of these changes on the growth and morphology of the plant root system.
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Broadley MR, White PJ, Bryson RJ, Meacham MC, Bowen HC, Johnson SE, Hawkesford MJ, McGrath SP, Zhao FJ, Breward N, Harriman M, Tucker M. Biofortification of UK food crops with selenium. Proc Nutr Soc 2006; 65:169-81. [PMID: 16672078 DOI: 10.1079/pns2006490] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Se is an essential element for animals. In man low dietary Se intakes are associated with health disorders including oxidative stress-related conditions, reduced fertility and immune functions and an increased risk of cancers. Although the reference nutrient intakes for adult females and males in the UK are 60 and 75 microg Se/d respectively, dietary Se intakes in the UK have declined from >60 microg Se/d in the 1970s to 35 microg Se/d in the 1990s, with a concomitant decline in human Se status. This decline in Se intake and status has been attributed primarily to the replacement of milling wheat having high levels of grain Se and grown on high-Se soils in North America with UK-sourced wheat having low levels of grain Se and grown on low-Se soils. An immediate solution to low dietary Se intake and status is to enrich UK-grown food crops using Se fertilisers (agronomic biofortification). Such a strategy has been adopted with success in Finland. It may also be possible to enrich food crops in the longer term by selecting or breeding crop varieties with enhanced Se-accumulation characteristics (genetic biofortification). The present paper will review the potential for biofortification of UK food crops with Se.
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Borkowski JJ, White PJ, Garrott RA, Davis T, Hardy AR, Reinhart DJ. Behavioral responses of bison and elk in Yellowstone to snowmobiles and snow coaches. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2006; 16:1911-25. [PMID: 17069382 DOI: 10.1890/1051-0761(2006)016[1911:brobae]2.0.co;2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Managers of public lands are charged with protecting some of our most important natural resources and ecosystems, while providing for their use and enjoyment by visitors. Almost one million visitors entered Yellowstone National Park by motorized means on snowmobiles (87%) or snow coaches (13%) during 1992-2003. Most vehicles toured the central portion of the park where bison (Bison bison) and elk (Cervus elaphus) concentrate in geothermal areas. We sampled >6500 interactions between groups of these species and groups of snowmobiles and snow coaches (collectively, OSV, over-snow vehicles) during five winters (1999-2000, 2002-2004). Multinomial logits models were used to identify conditions leading to behavioral responses. Elk responded three times as often (52%) as bison (19%) during interactions with groups of snowmobiles and snow coaches due to increased vigilance responses (elk, 44%; bison, 10%). However, the frequency of higher-intensity movement responses by bison and elk were similar (6-7% travel, 1-2% flight, <1% defense) and relatively low compared to other studies of ungulates and snowmobile disturbance. The likelihood of active responses by bison and elk increased significantly if animals were on or near roads, groups were smaller, or humans approached. The likelihood of an active response by bison decreased within winters having the largest visitation, suggesting some habituation to snowmobiles and snow coaches. There was no evidence that snowmobile use during the past 35 years affected the population dynamics or demography of bison or elk. Thus, we suggest that regulations restricting levels and travel routes of over-snow vehicles (OSVs) were effective at reducing disturbances to bison and elk below a level that would cause measurable fitness effects. We recommend park managers consider maintaining OSV traffic levels at or below those observed during our study. Regardless, differing interpretations of the behavioral and physiological response data will continue to exist because of the diverse values and beliefs of the many constituencies of Yellowstone.
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Bruggeman JE, Garrott RA, Bjornlie DD, White PJ, Watson FGR, Borkowski J. Temporal variability in winter travel patterns of Yellowstone bison: the effects of road grooming. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2006; 16:1539-54. [PMID: 16937817 DOI: 10.1890/1051-0761(2006)016[1539:tviwtp]2.0.co;2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The influence of winter recreation on wildlife in Yellowstone National Park (YNP), Wyoming and Montana, USA, is a controversial issue. In particular, the effects of road grooming, done to facilitate snowmobile and snowcoach travel, on bison (Bison bison) ecology are under debate. We collected data during winters, from 1997 to 2005, on bison road use, off-road travel, and activity budgets to quantify temporal trends in the amount of bison road and off-road travel and to identify the ecological factors affecting bison movements and use of the groomed road system in the Madison-Gibbon-Firehole (MGF) area of YNP. Using model comparison techniques, we found bison travel patterns to be influenced by multiple, interacting effects. Road travel was negatively correlated with road grooming, and we found no evidence that bison preferentially used groomed roads during winter. Snow water equivalent, bison density, and the springtime melt period were positively correlated with both bison road and off-road travel. From behavioral scans on 68,791 bison, we found that travel is only a small percentage (11%) of all bison activity, with foraging comprising 67% of observations. Also, only 7% of traveling bison and 30% of foraging bison were displacing snow, and we suggest foraging, rather than traveling, is likely the major energetic cost to bison in winter. Bison utilize their own trail network, connecting foraging areas using stream corridors, geothermal pathways, and self-groomed travel routes. Our results indicate that temporal patterns in bison road travel are a manifestation of general travel behavior and that groomed roads in the MGF do not appear to be a major factor influencing bison ecology and spatial redistribution. We suggest that the changes in bison spatial dynamics during the past three decades have likely been the result of the natural phenomenon of density-dependent range expansion, rather than having been caused by the anthropogenic influence of road grooming.
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White PJ, Clement GT, Hynynen K. Longitudinal and shear mode ultrasound propagation in human skull bone. ULTRASOUND IN MEDICINE & BIOLOGY 2006; 32:1085-96. [PMID: 16829322 PMCID: PMC1560344 DOI: 10.1016/j.ultrasmedbio.2006.03.015] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 03/15/2006] [Accepted: 03/29/2006] [Indexed: 05/04/2023]
Abstract
Recent studies have attempted to dispel the idea of the longitudinal mode being the only significant mode of ultrasound energy transport through the skull bone. The inclusion of shear waves in propagation models has been largely ignored because of an assumption that shear mode conversions from the skull interfaces to the surrounding media rendered the resulting acoustic field insignificant in amplitude and overly distorted. Experimental investigations with isotropic phantom materials and ex vivo human skulls demonstrated that, in certain cases, a shear mode propagation scenario not only can be less distorted, but at times allowed for a substantial (as much as 36% of the longitudinal pressure amplitude) transmission of energy. The phase speed of 1.0-MHz shear mode propagation through ex vivo human skull specimens has been measured to be nearly half of that of the longitudinal mode (shear sound speed = 1500 +/- 140 m/s, longitudinal sound speed = 2820 +/- 40 m/s), demonstrating that a closer match in impedance can be achieved between the skull and surrounding soft tissues with shear mode transmission. By comparing propagation model results with measurements of transcranial ultrasound transmission obtained by a radiation force method, the attenuation coefficient for the longitudinal mode of propagation was determined to between 14 Np/m and 70 Np/m for the frequency range studied, while the same for shear waves was found to be between 94 Np/m and 213 Np/m. This study was performed within the frequency range of 0.2 to 0.9 MHz.
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Gouws E, White PJ, Stover J, Brown T. Short term estimates of adult HIV incidence by mode of transmission: Kenya and Thailand as examples. Sex Transm Infect 2006; 82 Suppl 3:iii51-55. [PMID: 16735294 PMCID: PMC2576735 DOI: 10.1136/sti.2006.020164] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2006] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE Patterns of transmission of HIV are different among different regions of the world and change over time within regions. In order to adapt prevention strategies to changing patterns of risk, we need to understand the behaviours that put people at risk of infection and how new infections are distributed among risk groups. METHODS A model is described to calculate the expected incidence of HIV infections in the adult population by mode of exposure using the current distribution of prevalent infections and the patterns of risk within different populations. For illustration the model is applied to Thailand and Kenya. RESULTS New infections in Kenya were mainly transmitted through heterosexual contact (90%), while a small but significant number were related to injecting drug use (4.8%) and men who have sex with men (4.5%). In Thailand, the epidemic has spread over time to the sexual partners of vulnerable groups and in 2005 the majority of new infections occurred among the low risk heterosexual population (43%). Men having sex with men accounted for 21% and sex work (including sex workers, clients, and partners of clients) for 18% of new infections. Medical interventions did not contribute significantly to new infections in either Kenya or Thailand. CONCLUSIONS The model provides a simple tool to inform the planning of effective, appropriately targeted, country specific intervention programmes. However, better surveillance systems are needed in countries to obtain more reliable biological and behavioural data in order to improve the estimates of incidence by risk group.
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Abstract
The development of large-aperture multiple-source transducer arrays for ultrasound transmission through the human skull has demonstrated the possibility of controlled and substantial acoustic energy delivery into the brain parenchyma without the necessitation of a craniotomy. The individual control of acoustic parameters from each ultrasound source allows for the correction of distortions arising from transmission through the skull bone and also opens up the possibility for electronic steering of the acoustic focus within the brain. In addition, the capability to adjust the frequency of insonation at different locations on the skull can have an effect on ultrasound transmission. To determine the efficacy and applicability of a multiple-frequency approach with such a device, this study examined the frequency dependence of ultrasound transmission in the range of 0.6-1.4 MHz through a series of 17 points on four ex vivo human skulls. Effects beyond those that are characteristic of frequency-dependent attenuation were examined. Using broadband pulses, it was shown that the reflected spectra from the skull revealed information regarding ultrasound transmission at specific frequencies. A multiple-frequency insonation with optimized frequencies over the entirety of five skull specimens was found to yield on average a temporally brief 230% increase in the transmitted intensity with an 88% decrease in time-averaged intensity transmission within the focal volume. This finding demonstrates a potential applicability of a multiple-frequency approach in transcranial ultrasound transmission.
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Hammond JP, Bowen HC, White PJ, Mills V, Pyke KA, Baker AJM, Whiting SN, May ST, Broadley MR. A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. THE NEW PHYTOLOGIST 2006; 170:239-60. [PMID: 16608451 DOI: 10.1111/j.1469-8137.2006.01662.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Whole-genome transcriptome profiling is revealing how biological systems are regulated at the transcriptional level. This study reports the development of a robust method to profile and compare the transcriptomes of two nonmodel plant species, Thlaspi caerulescens, a zinc (Zn) hyperaccumulator, and Thlaspi arvense, a nonhyperaccumulator, using Affymetrix Arabidopsis thaliana ATH1-121501 GeneChip arrays (Affymetrix, Santa Clara, CA, USA). Transcript abundance was quantified in the shoots of agar- and compost-grown plants of both species. Analyses were optimized using a genomic DNA (gDNA)-based probe-selection strategy based on the hybridization efficiency of Thlaspi gDNA with corresponding A. thaliana probes. In silico alignments of GeneChip probes with Thlaspi gene sequences, and quantitative real-time PCR, confirmed the validity of this approach. Approximately 5000 genes were differentially expressed in the shoots of T. caerulescens compared with T. arvense, including genes involved in Zn transport and compartmentalization. Future functional analyses of genes identified as differentially expressed in the shoots of these closely related species will improve our understanding of the molecular mechanisms of Zn hyperaccumulation.
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White PJ, Broadley MR. Biofortifying crops with essential mineral elements. TRENDS IN PLANT SCIENCE 2005; 10:586-93. [PMID: 16271501 DOI: 10.1016/j.tplants.2005.10.001] [Citation(s) in RCA: 321] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 09/05/2005] [Accepted: 10/18/2005] [Indexed: 05/03/2023]
Abstract
Humans require more than 22 mineral elements, which can all be supplied by an appropriate diet. However, the diets of populations subsisting on cereals, or inhabiting regions where soil mineral imbalances occur, often lack Fe, Zn, Ca, Mg, Cu, I or Se. Traditional strategies to deliver these minerals to susceptible populations have relied on supplementation or food fortification programs. Unfortunately, these interventions have not always been successful. An alternative solution is to increase mineral concentrations in edible crops. This is termed 'biofortification'. It can be achieved by mineral fertilization or plant breeding. There is considerable genetic variation in crop species that can be harnessed for sustainable biofortification strategies. Varieties with increased mineral concentrations in their edible portions are already available, and new genotypes with higher mineral densities are being developed.
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White PJ, Broadley MR. Biofortifying crops with essential mineral elements. TRENDS IN PLANT SCIENCE 2005. [PMID: 16271501 DOI: 10.1016/j.plants.2005.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Humans require more than 22 mineral elements, which can all be supplied by an appropriate diet. However, the diets of populations subsisting on cereals, or inhabiting regions where soil mineral imbalances occur, often lack Fe, Zn, Ca, Mg, Cu, I or Se. Traditional strategies to deliver these minerals to susceptible populations have relied on supplementation or food fortification programs. Unfortunately, these interventions have not always been successful. An alternative solution is to increase mineral concentrations in edible crops. This is termed 'biofortification'. It can be achieved by mineral fertilization or plant breeding. There is considerable genetic variation in crop species that can be harnessed for sustainable biofortification strategies. Varieties with increased mineral concentrations in their edible portions are already available, and new genotypes with higher mineral densities are being developed.
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Gray AC, Coupar IM, White PJ. Comparison of opioid receptor distributions in the rat ileum. Life Sci 2005; 78:1610-6. [PMID: 16289621 DOI: 10.1016/j.lfs.2005.07.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Accepted: 07/26/2005] [Indexed: 11/20/2022]
Abstract
The cellular expression patterns of mu-, delta- and kappa-opioid receptors in the rat ileum were examined using fluorescence immunohistochemistry. Double-labelling was used to examine cellular receptor co-localisation as a pre-requisite for intracellular molecular interactions, such as heterodimerisation. Tissues were stained as whole-mount preparations. Strong, broadly distributed immunoreactivity (ir) was observed for each receptor in the myenteric and submucous plexuses. Although intracellular mu- and delta-ir patterns differed in ganglion neurons, mu/delta co-expression was extensive in these cells. mu/delta co-expression was also observed in interstitial cells, which were diffusely distributed in submucous plexus preparations but generally located adjacent to myenteric plexus structures. Punctate kappa-ir was seen broadly in nerve fibres in both plexuses, suggesting localisation in varicosities. Neuronal mu/kappa co-localisation was not apparent, although kappa-ir fibres were often apposed against mu-ir cells. mu/kappa co-localisation was detected in interstitial cells in submucous plexus preparations. Similarities in mu and delta expression patterns might reflect similar functional properties previously detected for these receptors. This study indicates that the rat gastrointestinal tract might provide a useful tool for the future study of molecular interactions between opioid receptor types.
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Hammond JP, Broadley MR, Craigon DJ, Higgins J, Emmerson ZF, Townsend HJ, White PJ, May ST. Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. PLANT METHODS 2005; 1:10. [PMID: 16280083 PMCID: PMC1308859 DOI: 10.1186/1746-4811-1-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 11/09/2005] [Indexed: 05/05/2023]
Abstract
High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip technology are amongst the most widely used, although GeneChip arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip array is available, using a GeneChip array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.
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Morgan JAW, Bending GD, White PJ. Biological costs and benefits to plant-microbe interactions in the rhizosphere. JOURNAL OF EXPERIMENTAL BOTANY 2005; 56:1729-39. [PMID: 15911554 DOI: 10.1093/jxb/eri205] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
This review looks briefly at plants and their rhizosphere microbes, the chemical communications that exist, and the biological processes they sustain. Primarily it is the loss of carbon compounds from roots that drives the development of enhanced microbial populations in the rhizosphere when compared with the bulk soil, or that sustains specific mycorrhizal or legume associations. The benefits to the plant from this carbon loss are discussed. Overall the general rhizosphere effect could help the plant by maintaining the recycling of nutrients, through the production of hormones, helping to provide resistance to microbial diseases and to aid tolerance to toxic compounds. When plants lack essential mineral elements such as P or N, symbiotic relationships can be beneficial and promote plant growth. However, this benefit may be lost in well-fertilized (agricultural) soils where nutrients are readily available to plants and symbionts reduce growth. Since these rhizosphere associations are commonplace and offer key benefits to plants, these interactions would appear to be essential to their overall success.
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White PJ. Methodological concerns when designing trials for the efficacy of acupuncture for the treatment of pain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2005; 546:217-27. [PMID: 15584377 DOI: 10.1007/978-1-4757-4820-8_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The aim of all clinical research must surely be to assess an intervention or process or relationship between variables, ultimately in order to be able to improve clinical practice and healthcare for patients/consumers. As such, evidence gathered must have external validity (generalisability) and it must be relevant to clinical practice. It can be seen therefore that research into acupuncture for pain relief is an inherently difficult task, which requires much sensitivity and careful planning in order to minimise error when drawing conclusions. The researcher needs to adequately address problems such as sample size, blinding, randomisation and appropriate use of control and treatment. It is also most important to be able to clarify that the placebo (if used) is credible to the patient. The field of acupuncture has been overwhelmed with hundreds of sub-standard trials and much doubt still surrounds the issue of efficacy. Few good quality rigorous trials exist to support the use of acupuncture for pain relief in general. It has also been noted that the question of long-term efficacy has not been assessed by the many trials and this needs to be addressed prior to its acceptance. Further well conducted rigorous trials are therefore needed, utilising the lessons learnt through the substantial number of previous trials, in order to adequately assess the efficacy of acupuncture for painful conditions. Such trials must therefore: Utilise a placebo control. Be randomised and stratified. Ensure patient blinding. Use self completed outcome measures and blinded assessors. Have sufficient and well validated outcome measures. Check credibility of treatment. Have a well defined entry criteria which includes a single condition only. Have a long term follow up. Enrol sufficient subjects, the number to be determined by a power calculation. Provide adequate acupuncture treatment as would be found in clinical practice. Be group comparative so as to negate any carry-over effects. In this way good quality trials can be undertaken which will yield reliable results and therefore add meaningful data to the body of knowledge appertaining to the effectiveness of acupuncture.
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Gregson S, Mushati P, White PJ, Mlilo M, Mundandi C, Nyamukapa C. Informal confidential voting interview methods and temporal changes in reported sexual risk behaviour for HIV transmission in sub-Saharan Africa. Sex Transm Infect 2005; 80 Suppl 2:ii36-42. [PMID: 15572638 PMCID: PMC1765846 DOI: 10.1136/sti.2004.012088] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES Reliable data on sexual behaviour trends are needed to evaluate HIV interventions in sub-Saharan Africa but are difficult to obtain due inter alia to social desirability bias. The objective of this paper is to assess whether the use of informal confidential voting interviews (ICVI) was associated with greater reporting of socially proscribed behavioural risk factors for HIV infection than were conventional interviewing methods. METHODS Comparison of changes in reports of risk behaviours for HIV infection in ICVI versus face to face interviews (FTFIs) between the first two rounds of a large scale, longitudinal, population based survey in Manicaland, Zimbabwe. Examination of factors that could contribute to observed changes in the effect of ICVI, including temporal changes in response error and social desirability, and factors affecting statistical power to detect differences between methods-that is, reductions in the prevalence of risk behaviours and sample size. RESULTS Enhanced reporting of HIV associated risk behaviours in ICVI interviews was not so apparent in the second round as in the first round of the survey, particularly for less frequently reported behaviours. Levels of reported HIV associated risk behaviour and sample sizes both declined between the two survey rounds. The level of response error was higher in ICVI interviews than in FTFI interviews but did not alter over time. CONCLUSION ICVI interviews can reduce social desirability bias in data on HIV associated risk behaviours. The extent and direction of change in net reduction in bias over time remains uncertain and will depend on local circumstances.
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Beresford NA, Broadley MR, Howard BJ, Barnett CL, White PJ. Estimating radionuclide transfer to wild species--data requirements and availability for terrestrial ecosystems. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2004; 24:A89-A103. [PMID: 15700700 DOI: 10.1088/0952-4746/24/4a/006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Assessment of the transfer of radionuclides to wild species is an important component in the estimation of predicted doses to biota. Reviews of available data for the many potential radionuclide-biota combinations which may be required for environmental assessments highlight many data gaps for terrestrial species. Here, we discuss different approaches which have been suggested to compensate for these data gaps. All of the reviewed approaches have merit; however, there is a requirement for transparency in methodology and data provenance which in some instances is currently missing. Furthermore, there is a need to validate the various methodologies to enable their use with confidence. The requirements of improving our ability to predict radionuclide transfer to wild species are discussed and recommendations made.
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Hampton CR, Bowen HC, Broadley MR, Hammond JP, Mead A, Payne KA, Pritchard J, White PJ. Cesium toxicity in Arabidopsis. PLANT PHYSIOLOGY 2004; 136:3824-37. [PMID: 15489280 PMCID: PMC527179 DOI: 10.1104/pp.104.046672] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2004] [Revised: 05/30/2004] [Accepted: 05/30/2004] [Indexed: 05/18/2023]
Abstract
Cesium (Cs) is chemically similar to potassium (K). However, although K is an essential element, Cs is toxic to plants. Two contrasting hypotheses to explain Cs toxicity have been proposed: (1) extracellular Cs+ prevents K+ uptake and, thereby, induces K starvation; and (2) intracellular Cs+ interacts with vital K(+)-binding sites in proteins, either competitively or noncompetitively, impairing their activities. We tested these hypotheses with Arabidopsis (Arabidopsis thaliana). Increasing the Cs concentration in the agar ([Cs](agar)) on which Arabidopsis were grown reduced shoot growth. Increasing the K concentration in the agar ([K](agar)) increased the [Cs](agar) at which Cs toxicity was observed. However, although increasing [Cs](agar) reduced shoot K concentration ([K](shoot)), the decrease in shoot growth appeared unrelated to [K](shoot) per se. Furthermore, the changes in gene expression in Cs-intoxicated plants differed from those of K-starved plants, suggesting that Cs intoxication was not perceived genetically solely as K starvation. In addition to reducing [K](shoot), increasing [Cs](agar) also increased shoot Cs concentration ([Cs](shoot)), but shoot growth appeared unrelated to [Cs](shoot) per se. The relationship between shoot growth and [Cs](shoot)/[K](shoot) suggested that, at a nontoxic [Cs](shoot), growth was determined by [K](shoot) but that the growth of Cs-intoxicated plants was related to the [Cs](shoot)/[K](shoot) quotient. This is consistent with Cs intoxication resulting from competition between K+ and Cs+ for K(+)-binding sites on essential proteins.
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