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Biomedical subjects

Philip J White

Publications and source records attributed to Philip J White.

At least 19 recordsLinked to original sources
PubMed2006

How do plants respond to nutrient shortage by biomass allocation?

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.

Acclimatization↗
PubMed2006

Biofortification of UK food crops with selenium.

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.

Crops, Agricultural↗
PubMed2006

A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes.

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.

Alleles↗
PubMed2005

Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species.

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.

Journal Article↗
PubMed2005

Biofortifying crops with essential mineral elements.

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.

Crops, Agricultural↗
PubMed2005

A cellular hypothesis for the induction of blossom-end rot in tomato fruit.

BACKGROUND: The incidence of blossom-end rot (BER) is generally associated with a calcium (Ca) deficiency in the distal portion of tomato fruits. The visible symptom is a necrotic lesion, which is presumed to be a consequence of cell death and the subsequent leakage of solutes into the extracellular space. Environmental factors that affect either fruit cell expansion or Ca delivery to the distal portion of the fruit influence the occurrence of BER. However, since no absolute, critical fruit Ca concentration for the occurrence of BER has been identified, it is now important to define the role of Ca in fruit cell physiology and to seek the cause of BER at the cellular level. HYPOTHESIS: Here, it is suggested that BER is initiated by a cellular dysfunction in the distal portion of a young fruit during rapid cell expansion. It is proposed that insufficient Ca(2+) is available for critical apoplastic and cytoplasmic functions when the cellular Ca demand imposed by vacuolation exceeds the Ca delivery to an expanding cell. A local Ca deficiency, therefore, may result in aberrant intracellular Ca(2+) signals, a weakening of cell walls and a loss of cellular integrity. Ultimately it may lead to cell death and the visible symptoms of BER. Several experimental strategies are suggested to confirm the occurrence of aberrant Ca(2+) concentrations in cells contributing to BER. PERSPECTIVE: Many genetic and genomic resources are becoming available for tomato. Ultimately, these will allow genes affecting the occurrence of BER to be identified. Such knowledge will inform breeding strategies to eliminate BER. In the meanwhile, increasing the apoplastic Ca concentration in susceptible fruit tissue should provide a simple and reliable, practical solution for the prevention of BER in tomatoes. It is suggested that current horticultural practices, such as the manipulation of the mineral composition of the feed or the growth environment, are not completely effective in reducing BER because they affect apoplastic Ca concentration in fruit tissue indirectly. Therefore, spraying Ca directly onto young fruits is recommended for the prevention of BER.

Calcium↗
PubMed2004

Cesium toxicity in Arabidopsis.

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.

Arabidopsis↗
PubMed2004

Genetic responses to phosphorus deficiency.

BACKGROUND: Phosphorus (P) is an essential macronutrient for plants. Plants take up P as phosphate (Pi) from the soil solution. Since little Pi is available in most soils, P fertilizers are applied to crops. However, the use of P fertilizers is unsustainable and may cause pollution. Consequently, there is a need to develop more P-use-efficient (PUE) crops and precise methods to monitor crop P-status. SCOPE: Manipulating the expression of genes to improve the PUE of crops could reduce their P fertilizer requirement. This has stimulated research towards the identification of genes and signalling cascades involved in plant responses to P deficiency. Genes that respond to P deficiency can be grouped into 'early' genes that respond rapidly and often non-specifically to P deficiency, or 'late' genes that impact on the morphology, physiology or metabolism of plants upon prolonged P deficiency. SUMMARY: The use of micro-array technology has allowed researchers to catalogue the genetic responses of plants to P deficiency. Genes whose expression is altered by P deficiency include various transcription factors, which are thought to coordinate plant responses to P deficiency, and other genes involved in P acquisition and tissue P economy. Several common cis-regulatory elements have been identified in the promoters of these genes, suggesting that their expression might be coordinated. It is suggested that knowledge of the genes whose expression changes in response to P deficiency might allow the development of crops with improved PUE, and could be used in diagnostic techniques to monitor P deficiency in crops either directly using 'smart' indicator plants or indirectly through transcript profiling. The development of crops with improved PUE and the adoption of diagnostic technology could reduce production costs, minimize the use of a non-renewable resource, reduce pollution and enhance biodiversity.

Arabidopsis↗
PubMed2004

Phylogenetic variation in the shoot mineral concentration of angiosperms.

The calcium (Ca) concentration of plant shoot tissues varies systematically between angiosperm orders. The phylogenetic variation in the shoot concentration of other mineral nutrients has not yet been described at an ordinal level. The aims of this study were (1) to quantify the shoot mineral concentration of different angiosperm orders, (2) to partition the phylogenetic variation in shoot mineral concentration between and within orders, (3) to determine if the shoot concentration of different minerals are correlated across angiosperm species, and (4) to compare experimental data with published ecological survey data on 81 species sampled from their natural habitats. Species, selected pro rata from different angiosperm orders, were grown in a hydroponic system under a constant external nutrient regime. Shoots of 117 species were sampled during vegetative growth. Significant variation in shoot carbon (C), calcium (Ca), potassium (K), and magnesium (Mg) concentration occurred between angiosperm orders. There was no evidence for systematic differences in shoot phosphorus (P) or organic-nitrogen (N) concentration between orders. At a species level, there were strong positive correlations between shoot Ca and Mg concentration, between shoot P and organic-N concentration, and between shoot K concentration and shoot fresh weight:dry weight ratio. Shoot C and cation concentration correlated negatively at a species level. Species within the Poales and the Caryophyllales had distinct shoot mineralogies in both the designed experiment and in the ecological survey.

Calcium↗
PubMed2003

Calcium in plants.

Calcium is an essential plant nutrient. It is required for various structural roles in the cell wall and membranes, it is a counter-cation for inorganic and organic anions in the vacuole, and the cytosolic Ca2+ concentration ([Ca2+]cyt) is an obligate intracellular messenger coordinating responses to numerous developmental cues and environmental challenges. This article provides an overview of the nutritional requirements of different plants for Ca, and how this impacts on natural flora and the Ca content of crops. It also reviews recent work on (a) the mechanisms of Ca2+ transport across cellular membranes, (b) understanding the origins and specificity of [Ca2+]cyt signals and (c) characterizing the cellular [Ca2+]cyt-sensors (such as calmodulin, calcineurin B-like proteins and calcium-dependent protein kinases) that allow plant cells to respond appropriately to [Ca2+]cyt signals.

Biological Transport↗
PubMed2003

The nitrogen and nitrate economy of butterhead lettuce (Lactuca sativa var capitata L).

Quantifying and simulating the relationships between crop growth, total-nitrogen (total-N) and nitrate-N (NO3--N) concentration can improve crop nutritional husbandry. In this study, the relationship between shoot relative growth rate (RGR) and shoot total-N, organic-N and NO3--N concentration of hydroponically-grown lettuce (Lactuca sativa var. capitata L. cv. Kennedy) was described and simulated. Plants were grown hydroponically for up to 74 d. Nitrogen was supplied throughout (control; T1), or removed at 35 d (T2) and 54 d (T3), respectively, after sowing. The organic-N and NO3--N concentration declined in the shoots of control plants with growth, until commercial maturity approached when organic-N and NO3--N concentration increased. There were sub-linear relationships between both total-N and organic-N concentration, and shoot RGR, in the N-limited treatments, i.e. shoot RGR approached an asymptote at high shoot N concentration. The proportional effects of total-N and organic-N concentration on shoot RGR were independent of plant age. A dynamic simulation model ('Nicolet'), derived previously under different conditions, was used to simulate the growth, dry matter content, organic-N, and NO3--N concentration of lettuce grown under the extreme N-stress conditions experienced by the plants. In view of the largely successful fitting of the model to experimental data, the model was used to interpret the results. Suggestions for model improvement are made.

Hydroponics↗
PubMed2003

Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants.

Our aim was to generate and prove the concept of "smart" plants to monitor plant phosphorus (P) status in Arabidopsis. Smart plants can be genetically engineered by transformation with a construct containing the promoter of a gene up-regulated specifically by P starvation in an accessible tissue upstream of a marker gene such as beta-glucuronidase (GUS). First, using microarrays, we identified genes whose expression changed more than 2.5-fold in shoots of plants growing hydroponically when P, but not N or K, was withheld from the nutrient solution. The transient changes in gene expression occurring immediately (4 h) after P withdrawal were highly variable, and many nonspecific, shock-induced genes were up-regulated during this period. However, two common putative cis-regulatory elements (a PHO-like element and a TATA box-like element) were present significantly more often in the promoters of genes whose expression increased 4 h after the withdrawal of P compared with their general occurrence in the promoters of all genes represented on the microarray. Surprisingly, the expression of only four genes differed between shoots of P-starved and -replete plants 28 h after P was withdrawn. This lull in differential gene expression preceded the differential expression of a new group of 61 genes 100 h after withdrawing P. A literature survey indicated that the expression of many of these "late" genes responded specifically to P starvation. Shoots had reduced P after 100 h, but growth was unaffected. The expression of SQD1, a gene involved in the synthesis of sulfolipids, responded specifically to P starvation and was increased 100 h after withdrawing P. Leaves of Arabidopsis bearing a SQD1::GUS construct showed increased GUS activity after P withdrawal, which was detectable before P starvation limited growth. Hence, smart plants can monitor plant P status. Transferring this technology to crops would allow precision management of P fertilization, thereby maintaining yields while reducing costs, conserving natural resources, and preventing pollution.

Arabidopsis↗
PubMed2003

Variation in the shoot calcium content of angiosperms.

This study describes the variation in the mean relative shoot Ca content within the angiosperms at the ordinal level. Data were derived from studies in the literature in which the shoot Ca content of two or more species had been compared, and from a hydroponic experiment in which plants were selected to represent the relative number of species within each angiosperm order. Across all angiosperms, most of the variation in shoot Ca content occurred at and above the level of the order. Relative shoot Ca contents and variances correlated between literature and experimental data. In general, orders of commelinoid monocots had lower Ca contents than other monocot or eudicot orders. These results are used to illustrate how physiological and ecological hypotheses can be formulated using literature data.

Calcium↗
PubMed2002

Genes for calcium-permeable channels in the plasma membrane of plant root cells.

In plant cells, Ca(2+) is required for both structural and biophysical roles. In addition, changes in cytosolic Ca(2+) concentration ([Ca(2+)](cyt)) orchestrate responses to developmental and environmental signals. In many instances, [Ca(2+)](cyt) is increased by Ca(2+) influx across the plasma membrane through ion channels. Although the electrophysiological and biochemical characteristics of Ca(2+)-permeable channels in the plasma membrane of plant cells are well known, genes encoding putative Ca(2+)-permeable channels have only recently been identified. By comparing the tissue expression patterns and electrophysiology of Ca(2+)-permeable channels in the plasma membrane of root cells with those of genes encoding candidate plasma membrane Ca(2+) channels, the genetic counterparts of specific Ca(2+)-permeable channels can be deduced. Sequence homologies and the physiology of transgenic antisense plants suggest that the Arabidopsis AtTPC1 gene encodes a depolarisation-activated Ca(2+) channel. Members of the annexin gene family are likely to encode hyperpolarisation-activated Ca(2+) channels, based on their corresponding occurrence in secretory or elongating root cells, their inhibition by La(3+) and nifedipine, and their increased activity as [Ca(2+)](cyt) is raised. Based on their electrophysiology and tissue expression patterns, AtSKOR encodes a depolarisation-activated outward-rectifying (Ca(2+)-permeable) K(+) channel (KORC) in stelar cells and AtGORK is likely to encode a KORC in the plasma membrane of other Arabidopsis root cells. Two candidate gene families, of cyclic-nucleotide gated channels (CNGC) and ionotropic glutamate receptor (GLR) homologues, are proposed as the genetic correlates of voltage-independent cation (VIC) channels.

Amino Acid Sequence↗
PubMed2002

The deposition of suberin lamellae determines the magnitude of cytosolic Ca2+ elevations in root endodermal cells subjected to cooling.

A transient increase in cytosolic Ca2+ concentration ([Ca2+]cyt) is thought to be a prerequisite for an appropriate physiological response to both chilling and salt stress. The [Ca2+]cyt is raised by Ca2+ influx to the cytosol from the apoplast and/or intracellular stores. It has been speculated that different signals mobilise Ca2+ from different stores, but little is known about the origin(s) of the Ca2+ entering the cytosol in response to specific environmental challenges. We have utilised the developmentally regulated suberisation of endodermal cells, which is thought to prevent Ca2+ influx from the apoplast, to ascertain whether Ca2+ influx is required to increase [Ca2+]cyt in response to chilling or salt stress. Perturbations in [Ca2+]cyt were studied in transgenic Arabidopsis thaliana, expressing aequorin fused to a modified yellow fluorescent protein solely in root endodermal cells, during slow cooling of plants from 20 to 0.5 degrees C over 5 min and in response to an acute salt stress (0.333 m NaCl). Only in endodermal cells in the apical 4 mm of the Arabidopsis root did [Ca2+]cyt increase significantly during cooling, and the magnitude of the [Ca2+]cyt elevation elicited by cooling was inversely related to the extent of suberisation of the endodermal cell layer. No [Ca2+]cyt elevations were elicited by cooling in suberised endodermal cells. This is consistent with the hypothesis that suberin lamellae isolate the endodermal cell protoplast from the apoplast and, thereby, prevent Ca2+ influx. By contrast, acute salt stress increased [Ca2+]cyt in endodermal cells throughout the root. These results suggest that [Ca2+]cyt elevations, upon slow cooling, depend absolutely on Ca2+ influx across the plasma membrane, but [Ca2+]cyt elevations in response to acute salt stress do not. They also suggest that Ca2+ release from intracellular stores contributes significantly to increasing [Ca2+]cyt upon acute salt stress.

Aequorin↗
PubMed2002

Arabidopsis thaliana root non-selective cation channels mediate calcium uptake and are involved in growth.

Calcium is a critical structural and regulatory nutrient in plants. However, mechanisms of its uptake by root cells are poorly understood. We have found that Ca2+ influx in Arabidopsis root epidermal protoplasts is mediated by voltage-independent rapidly activating Ca2+-permeable non-selective cation channels (NSCCs). NSCCs showed the following permeability (P) sequence: PCa (1.00) = PBa (0.93) > PZn (0.51), PCa/PNa = 0.19, PCa/PK = 0.14. They were inhibited by quinine, Gd3+, La3+ and the His modifier diethylpyrocarbonate, but not by the Ca2+ or K+ channel antagonists, verapamil and tetraethylammonium (TEA+). Single channel conductance measured in 20 mm external Ca2+ was 5.9 pS. Calcium-permeable NSCCs co-existed with hyperpolarisation-activated Ca2+ channels (HACCs), which activated 40-60 min after forming the whole-cell configuration. HACCs activated at voltages <-130 to -150 mV, showed slow activation kinetics and were regulated by cytosolic Ca2+ ([Ca2+]cyt). Using aequorin-expressing plants, a linear relationship between membrane potential (Vm) and resting [Ca2+]cyt was observed, indicating the involvement of NSCCs. Intact root 45Ca2+ influx was reduced by Gd3+ (NSCC blocker) but was verapamil and TEA+ insensitive. In the root elongation zone, both root net Ca2+ influx (measured by Ca2+-selective vibrating microelectrode) and NSCC activity were increased compared to the mature epidermis, suggesting the involvement of NSCC in growth. A Ca2+ acquisition system based on NSCC and HACC co-existence is proposed. In mature epidermal cells, NSCC-mediated Ca2+ influx dominates whereas in specialised root cells (root hairs and elongation zone cells) where elevated [Ca2+]cyt activates HACCs, HACC-mediated Ca2+ influx predominates.

Antiporters↗
PubMed2002

Recent advances in fruit development and ripening: an overview.

This article provides an overview of the Journal of Experimental Botany Special Issue on Fruit Development and Ripening. It reports that significant progress is being made in identifying genes controlling the development of dry dehiscent fruits in the model plant species Arabidopsis thaliana. In plants with fleshy fruits, a major focus has been the dissection of biochemical and genetic regulatory cascades controlling ripening, using tomato as a model species. Intermediates of the ethylene-signalling cascade, potential cross-talk between ethylene and auxin signals, and the role of ethylene-independent signals have all been described in this climacteric fruit. The recent isolation of the NOR and LeMADS-RIN genes, which participate in ethylene-independent signalling in tomato, and the discovery that a homologue of the RIN gene is expressed in strawberry, a non-climacteric fruit, suggests that common regulatory cascades may operate in all fruits. Transcriptional profiling during the development and ripening of both climacteric (tomato) and non-climacteric (strawberry) fruit has supported these observations, and also identified a number of novel genes involved in the biochemistry of fruit development and ripening. The use of phylogenies based on chloroplast gene sequences has allowed an insight into the evolution of fruit forms and fruit biochemistry, which may be useful for the manipulation of commercial species. Several molecular approaches, including positional cloning, QTL mapping and genetic engineering, are helping to define the biochemical and molecular bases of texture, flavour, colour, and aroma. As the understanding of the biology of fruit ripening has improved, so has the ability to improve the organoleptic and nutritional qualities of fruits through crop management, breeding or biotechnology.

Abscisic Acid↗