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Biomedical subjects

Howard Thomas

Publications and source records attributed to Howard Thomas.

16 recordsLinked to original sources

Cross-species identification of Mendel's I locus.

A key gene involved in plant senescence, mutations of which partially disable chlorophyll catabolism and confer stay-green leaf and cotyledon phenotypes, has been identified in Pisum sativum, Arabidopsis thaliana, and Festuca pratensis by using classical and molecular genetics and comparative genomics. A stay-green locus in F. pratensis is syntenically equivalent to a similar stay-green locus on rice chromosome 9. Functional testing in Arabidopsis of a homolog of the rice candidate gene revealed (i) senescence-associated gene expression and (ii) a stay-green phenotype after RNA interference silencing. Genetic mapping in pea demonstrated cosegregation with the yellow/green cotyledon polymorphism (I/i) first reported by Gregor Mendel in 1866.

Amino Acid Sequence↗

Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines.

Introgression in Festulolium is a potentially powerful tool to isolate genes for a large number of traits which differ between Festuca pratensis Huds. and Lolium perenne L. Not only are hybrids between the two species fertile, but the two genomes can be distinguished by genomic in situ hybridisation and a high frequency of recombination occurs between homoeologous chromosomes and chromosome segments. By a programme of introgression and a series of backcrosses, L. perenne lines have been produced which contain small F. pratensis substitutions. This material is a rich source of polymorphic markers targeted towards any trait carried on the F. pratensis substitution not observed in the L. perenne background. We describe here the construction of an F. pratensis BAC library, which establishes the basis of a map-based cloning strategy in L. perenne. The library contains 49,152 clones, with an average insert size of 112 kbp, providing coverage of 2.5 haploid genome equivalents. We have screened the library for eight amplified fragment length polymorphism (AFLP) derived markers known to be linked to an F. pratensis gene introgressed into L. perenne and conferring a staygreen phenotype as a consequence of a mutation in primary chlorophyll catabolism. While for four of the markers it was possible to identify bacterial artificial chromosome (BAC) clones, the other four AFLPs were too repetitive to enable reliable identification of locus-specific BACs. Moreover, when the four BACs were partially sequenced, no obvious coding regions could be identified. This contrasted to BACs identified using cDNA sequences, when multiple genes were identified on the same BAC.

Blotting, Southern↗

Bringing medicinal plants into cultivation: opportunities and challenges for biotechnology.

Consumption of herbal medicines is widespread and increasing. Harvesting from the wild, the main source of raw material, is causing loss of genetic diversity and habitat destruction. Domestic cultivation is a viable alternative and offers the opportunity to overcome the problems that are inherent in herbal extracts: misidentification, genetic and phenotypic variability, extract variability and instability, toxic components and contaminants. The use of controlled environments can overcome cultivation difficulties and could be a means to manipulate phenotypic variation in bioactive compounds and toxins. Conventional plant-breeding methods can improve both agronomic and medicinal traits, and molecular marker assisted selection will be used increasingly. There has been significant progress in the use of tissue culture and genetic transformation to alter pathways for the biosynthesis of target metabolites. Obstacles to bringing medicinal plants into successful commercial cultivation include the difficulty of predicting which extracts will remain marketable and the likely market preference for what is seen as naturally sourced extracts.

Biotechnology↗

The colors of autumn leaves as symptoms of cellular recycling and defenses against environmental stresses.

The color changes that occur during foliar senescence are directly related to the regulation of nutrient mobilization and resorption from leaf cells, often under conditions of biotic and abiotic stress. Chlorophyll is degraded through a metabolic pathway that becomes specifically activated in senescence. Chlorophyll catabolic enzymes and genes have been identified and characterized and aspects of their regulation analyzed. Particular genetic interventions in the pathway lead to disruptions in protein mobilization and increased sensitivity to light-dependent cell damage and death. The chemistry and metabolism of carotenoid and anthocyanin pigments in senescing leaves are considered. Bright autumn colors observed in the foliage of some woody species have been hypothesized to act as a defense signal to potential insect herbivores. Critical consideration of the biochemical and physiological features of normal leaf senescence leads to the conclusion that accumulating or unmasking compounds with new colors are unlikely to represent a costly investment on the part of the tree. The influences of human evolutionary and social history on our own perception of autumn coloration are discussed. The possibility that insect herbivores may respond to volatiles emitted during leaf senescence, rather than to bright colors, is also presented. Finally, some new approaches to the analysis of protein recycling in senescence are briefly considered.

Animals↗

Analysis of the chlorophyll catabolism pathway in leaves of an introgression senescence mutant of Lolium temulentum.

Pigments, proteins and enzyme activity related to chlorophyll catabolism were analysed in senescing leaves of wild-type (WT) Lolium temulentum and compared with those of an introgression line carrying a mutant gene from stay-green (SG) Festuca pratensis. During senescence of WT leaves chlorophylls a and b were continuously catabolised to colourless products and no other derivatives were observed, whereas in SG leaves there was an accumulation of dephytylated and oxidised catabolites including chlorophyllide a, phaeophorbide a and 13(2) OH-chlorophyllide a. Dephytylated products were absent from SG leaf tissue senescing under a light-dark cycle. Retention of pigments in SG was accompanied by significant stabilisation of light harvesting chlorophyll-proteins compared with WT, but soluble proteins such as Rubisco were degraded during senescence at a similar rate in the two genotypes. The activity of phaeophorbide a oxygenase measured in SG tissue at 3d was less than 12% of that in WT tissue at the same time-point during senescence and of the same order as that in young pre-senescent WT leaves, indicating that the metabolic lesion in SG concerns a deficiency at the ring-opening step of the catabolic pathway. In senescent L. temulentum tissue two terminal chlorophyll catabolites were identified with chromatographic characteristics that suggest they may represent hitherto undescribed catabolite structures. These data are discussed in relation to current understanding of the genetic and metabolic control of chlorophyll catabolism in leaf senescence.

Cellular Senescence↗

Leaf senescence is delayed in maize expressing the Agrobacterium IPT gene under the control of a novel maize senescence-enhanced promoter.

We have genetically modified maize plants to delay leaf senescence. A senescence-enhanced promoter from maize (P(SEE1)) was used to drive expression of the Agrobacterium cytokinin biosynthesis gene IPT in senescing leaf tissue. Three maize lines expressing IPT from P(SEE1), Sg1, Sg2 and Sg3, were analysed in detail, representing mild, intermediate and extreme expression, respectively, of the delayed-senescence phenotype. Backcross populations segregating for the presence or absence of the P(SEE1Xba)IPTNOS transgene also simultaneously segregated for the senescence phenotype. At the time of ear leaf emergence, individuals of lines Sg1 and Sg2 segregating for the presence of the transgene carried about three fewer senescing leaves than control (transgene-minus) segregants, and IPT transcript levels were higher in leaves at incipient senescence than in young leaves. Leaves of transgenic Sg3 plants were significantly greener than controls and progressed directly from fully green to bleached and dead without an intervening yellowing phase. IPT transcript abundance in this line was not related to the initiation of senescence. Extended greenness was accompanied by a delay in the loss of photosynthetic capacity with leaf age. The delayed-senescence trait was associated with relatively minor changes in morphology and development. The phenotype was particularly emphasized in plants grown in low soil nitrogen. The reduced ability of the extreme transgenic line Sg3 to recycle internal nitrogen from senescing lower leaves accounted for significant chlorosis in emerging younger leaves when plants were grown in low nutrient conditions. This study demonstrates that the agronomically important delayed-senescence ('stay-green') trait can be engineered into a monocot crop, and is the first example outside Arabidopsis of senescence modification using a homologous senescence-enhanced promoter.

Journal Article↗

Quantitative versus morphological assessment of liver fibrosis: semi-quantitative scores are more robust than digital image fibrosis area estimation.

BACKGROUND/AIM: Digital image analysis (DIA) allows quantitative assessment of fibrosis on liver biopsy. Accurate determination of a threshold greyscale level representing fibrous tissue is critical. This method has not been fully evaluated in clinical practice. METHODS: Digital images of stained liver biopsy sections were captured by microscopy and converted to greyscale. A novel method of determining the threshold greyscale value at which to measure fibrosis area was developed (peak proportion area change (PPAC)). Reproducibility was tested in comparison with standard interactive thresholding and with semi-quantitative scoring using the Histological activity index (HAI) system by a histopathologist. Fibrosis areas for different sections from the same biopsy core were also compared by each method. RESULTS: Comparison between PPAC and interactive thresholding method demonstrated superior reproducibility of the PPAC method: r > 0.7, P < 0.001 compared with r = 0.19-0.64 (not all reaching significance). On a single section, reproducibility was similar for PPAC and the modified HAI system. When different sections from the same core were compared, the HAI system was more robust. CONCLUSIONS: The PPAC method is superior to standard interactive thresholding. However, variability in DIA scores between sections invalidates the technique for clinical use and semi-quantitative scoring systems remain the gold standard for fibrosis assessment.

Fibrosis↗

Defining senescence and death.

This article evaluates features of leaf and flower senescence that are shared with, or are different from, those of other terminal events in plant development. Alterations of plastid structure and function in senescence are often reversible and it is argued that such changes represent a process of transdifferentiation or metaplasia rather than deterioration. It may be that the irreversible senescence of many flowers and some leaves represents the loss of ancestral plasticity during evolution. Reversibility serves to distinguish senescence fundamentally from programmed cell death (PCD), as does the fact that viability is essential for the initiation and progress of cell senescence. Senescence (particularly its timing and location) requires new gene transcription, but the syndrome is also subject to significant post- transcriptional and post-translational regulation. The reversibility of senescence must relate to the plastic, facultative nature of underlying molecular controls. Senescence appears to be cell-autonomous, though definitive evidence is required to substantiate this. The vacuole plays at least three key roles in the development of senescing cells: it defends the cell against biotic and abiotic damage, thus preserving viability, it accumulates metabolites with other functions, such as animal attractants, and it terminates senescence by becoming autolytic and facilitating true cell death. The mechanisms of PCD in plants bear a certain relation to those of apoptosis, and some processes, such as nucleic acid degradation, are superficially similar to aspects of the senescence syndrome. It is concluded that, in terms of physiological components and their controls, senescence and PCD are at best only distantly related.

Apoptosis↗

Hepatic stem cells.

The liver in an adult healthy body maintains a balance between cell gain and cell loss. Though normally proliferatively quiescent, hepatocyte loss such as that caused by partial hepatectomy, uncomplicated by virus infection or inflammation, invokes a rapid regenerative response to restore liver mass. This restoration of moderate cell loss and 'wear and tear' renewal is largely achieved by hepatocyte self-replication. Furthermore, hepatocyte transplants in animals have shown that a certain proportion of hepatocytes can undergo significant clonal expansion, suggesting that hepatocytes themselves are the functional stem cells of the liver. More severe liver injury can activate a potential stem cell compartment located within the intrahepatic biliary tree, giving rise to cords of bipotential so-called oval cells within the lobules that can differentiate into hepatocytes and biliary epithelial cells. A third population of stem cells with hepatic potential resides in the bone marrow; these haematopoietic stem cells can contribute to the albeit low renewal rate of hepatocytes, make a more significant contribution to regeneration, and even completely restore normal function in a murine model of hereditary tyrosinaemia. How these three stem cell populations integrate together to achieve a homeostatic balance is not known. This review focuses on two major aspects of liver stem cell biology: firstly, the identity of the liver stem cells, and secondly, their potential value in the treatment of major liver disease.

Animals↗

Ageing in plants.

Ageing in green plants differs in some fundamental ways from the process in animals. The seasonal cycle and persistence of a plant is governed by a combination of the determinate or indeterminate status of meristems (growth centres) and the cell death and disposal strategies employed by plants to generate well-adapted anatomies and morphologies. The degree of perenniality depends on the balance between exploratory growth and the wave of tissue death that succeeds it, and extremes of longevity can arise by relatively minor changes in the quantitative relationship between growth and death. The senescence and elimination of organs and tissues are related to the internal reallocation of resources but are programmed phases in the integrated development of the whole plant and do not represent a kind of ageing by stress or starvation. Meristems of long-lived plants accumulate genetic damage but selection mechanisms exist within the organism to control genetic load, and even to exploit somatic mutations that confer adaptive benefits. It is concluded that most plants do not age in the strict gerontological sense and that extremely long-lived forms like trees and clonal creeping perennials are sustained by selection and correction at the level of semi-autonomous cell lineages.

Aging↗

What stay-green mutants tell us about nitrogen remobilization in leaf senescence.

Leaf senescence has an important role in the plant's nitrogen economy. Chlorophyll catabolism is a visible symptom of protein mobilization. Genetic and environmental factors that interfere with yellowing tend to modify protein degradation as well. The chlorophyll-protein relationship is much closer for membrane proteins than it is for soluble or total leaf proteins. In stay-greens, genotypes with a specific defect in the chlorophyll catabolism pathway, soluble protein degradation during senescence may be close to normal, but light-harvesting and reaction centre thylakoid membrane proteins are much more stable. Genes for the chlorophyll catabolism pathway and its control are important in the regulation of protein mobilization. Genes for three steps in the pathway are reported to have been isolated. The gene responsible for the stay-green phenotype in grasses and legumes has not yet been cloned but a fair amount is known about it. Pigment metabolism in senescing leaves of the Festuca-Lolium stay-green mutant is clearly disturbed and is consistent with a blockage at the ring-opening (PaO) step in chlorophyll breakdown. PaO is de novo synthesized in senescence and thought to be the key enzyme in the chlorophyll a catabolic pathway. The stay-green mutation is likely to be located in the PaO gene, or a specific regulator of it. These genes may well be in the various senescence-enhanced cDNA collections that have been generated, but functional handles on them are currently lacking. When the stay-green locus from Festuca pratensis was introgressed into Lolium temulentum, a gene encoding F. pratensis UDPG-pyrophosphorylase was shown to have been transferred on the same chromosome segment. A strategy is described for cloning the stay-green gene, based on subtractive PCR-based analyses of intergeneric introgressions and map-based cloning.

Base Sequence↗

CHLOROPHYLL DEGRADATION.

Although the loss of green color in senescent leaves and ripening fruits is a spectacular natural phenomenon, research on chlorophyll breakdown has been largely neglected until recently. This review summarizes knowledge about the fate of chlorophyll in degreening tissues that has been gained during the past few years. Structures of end- and intermediary products of degradation as well as the biochemistry of the porphyrin-cleaving reaction have been elucidated. The intracellular localization of the catabolic pathway is particularly important in the regulation of chlorophyll breakdown. None of the genes encoding the related catabolic enzymes has so far been isolated, which makes chlorophyll degradation an area of opportunity for future research.

Journal Article↗