Natural faecal fluorophores and the potential of chlorophyll based markers to optimise fluorescence as a real-time solution for the detection of faecal contamination on carcasses.

More accurate and sensitive visualisation of faecal contamination in the abattoir would significantly reduce the risk posed by harbouring pathogenic micro-organisms. We carried out a preliminary investigation of the range of fluorophores found naturally in faeces from typical ruminant diets. Sixteen ewes were offered either: i) fresh forage (FF), ii) grass silage (GS), iii) grass hay (GH) or iv) concentrate and barley straw (CB). Animals offered FF diets had a greater concentration (P<0.001) of chlorophyll based compounds in their faeces and subsequent fluorescent emission spectra. In a second experiment we investigated a range of fluorescent markers against a basal concentrate and barley straw diet. Ten Cheviot sheep were split into five treatment groups during a duplicate 5 × 5 Latin square design. Four of the groups received a chlorophyll based marker at a rate of 2g/d: i) Mg-Chlorophyllin (MgC), ii) Fe-Chlorophyllin (FeC), iii) Zn-Chlorophyllin (ZnC) or iv) Spirulina (Chlorophyll a extract from blue green algae, Sp). The last group received no supplement as the control (Con). The appearance of chlorophyllin markers and their derivatives in faeces was similar with mean concentrations of 3.1 and 7.2 µg/g DM, respectively. The most intense fluorescent signal was shown with MgC followed by ZnC, FeC, Sp and Con at 685 nm. The use of markers in pre-slaughter diets would improve the accuracy of faecal detection as a result of greater fluorescence and specific emission wavelengths which do not overlap with natural meat components to help with visualisation.

The control of chlorophyll catabolism and the status of yellowing as a biomarker of leaf senescence.

The pathway of chlorophyll catabolism during leaf senescence is known in a fair amount of biochemical and cell biological detail. In the last few years, genes encoding a number of the catabolic enzymes have been characterized, including the key ring-opening activities, phaeophorbide a oxygenase (PaO) and red chlorophyll catabolite reductase (RCCR). Recently, a gene that modulates disassembly of chlorophyll-protein complexes and activation of pigment ring-opening has been isolated by comparative mapping in monocot species, positional cloning exploiting rice genomics resources and functional testing in Arabidopsis. The corresponding gene in pea has been identified as Mendel's I locus (green/yellow cotyledons). Mutations in this and other chlorophyll catabolic genes have significant consequences, both for the course of leaf senescence and senescence-like stress responses, notably hypersensitivity to pathogen challenge. Loss of chlorophyll can occur via routes other than the PaO/RCCR pathway, resulting in changes that superficially resemble senescence. Such 'pseudosenescence' responses tend to be pathological rather than physiological and may differ from senescence in fundamental aspects of biochemistry and regulation.

The effect of gibberellic acid on the response of leaf extension to low temperature.

The effect of cooling on leaf extension rate (LER) and on relative elemental growth rate (REGR) was measured in both gibberellic acid (GA)-responsive dwarf barley and in the same barley variety treated with GA. Seedlings were maintained at 20 degrees C while their leaf extension zone (LEZ) temperature was reduced either in steps to -6 degrees C in short-term cooling experiments, or to 10 degrees C for 48 h in long-term cooling experiments. Short-term cooling resulted in a biphasic response in LER, with a clear inflection point identified. Below this point, the activation energy for leaf extension becomes higher. The short-term response of LER to cooling was altered by the application of GA, which resulted in a lower base temperature (Tb), inflection point temperature and activation energy for leaf extension. Both GA-treated and untreated seedlings were less sensitive to cooling maintained for a prolonged period, with LER making a partial recover over the initial 5 h. Although long-term cooling reduced maximum REGR, it resulted in a longer LEZ and an increase in the length of mature interstomatal cells in GA-treated and untreated seedlings. These changes in overall physiology appear to enhance the ability of the leaves to continue expansion at suboptimal temperatures. In both GA-treated and cold-acclimated tissue, the occurrence of a longer LEZ was associated with a lower temperature sensitivity in LER.

Functional bioinformatics for Arabidopsis thaliana.

MOTIVATION: The genome of Arabidopsis thaliana, which has the best understood plant genome, still has approximately one-third of its genes with no functional annotation at all from either MIPS or TAIR. We have applied our Data Mining Prediction (DMP) method to the problem of predicting the functional classes of these protein sequences. This method is based on using a hybrid machine-learning/data-mining method to identify patterns in the bioinformatic data about sequences that are predictive of function. We use data about sequence, predicted secondary structure, predicted structural domain, InterPro patterns, sequence similarity profile and expressions data. RESULTS: We predicted the functional class of a high percentage of the Arabidopsis genes with currently unknown function. These predictions are interpretable and have good test accuracies. We describe in detail seven of the rules produced.

Molecular tagging of a senescence gene by introgression mapping of a stay-green mutation from Festuca pratensis.

* Intergeneric hybrids between Lolium multiflorum and Festuca pratensis (Lm/Fp) and their derivatives exhibit a unique combination of genetic and cytogenetic characteristics: chromosomes undergo a high frequency of homoeologous recombination at meiosis; the chromosomes of the two species can easily be discriminated by genomic in situ hybridization (GISH); recombination occurs along the entire length of homoeologous bivalents; a high frequency of marker polymorphism is observed between the two species. * This combination of characters has been used to transfer and isolate a F. pratensis chromosome segment carrying a mutant 'stay-green' gene conferring a disrupted leaf senescence phenotype into L. multiflorum. * The genetic location within the introgressed F. pratensis segment of the senescence gene has been mapped using amplified fragment length polymorphisms (AFLPs), and F. pratensis-specific AFLP markers closely flanking the green gene have been cloned. * The use of these cloned sequences as markers for the stay-green locus in marker-assisted selection programmes has been tested. The potential application of Lm/Fp introgressions as a tool for the map-based cloning of introgressed Fp genes is discussed.

Forage breeding and management to increase the beneficial fatty acid content of ruminant products.

The declining consumption of ruminant products has been partly associated with their high proportion (but not necessarily content) of saturated fatty acids. Recent studies have focused on the less prominent fact that they are also important sources of beneficial fatty acids, including n-3 fatty acids and conjugated linoleic acids. alpha-Linolenic acid (18 : 3n-3) is of particular interest because it also contributes to improved flavour of beef and lamb. Many recent studies showed large effects of special concentrates on levels of fatty acids in milk and meat. However, the 'rumen protection' treatments, needed to ensure a worthwhile level of fatty acid in products, are expensive. Herbage lipids are the cheapest and safest source of these fatty acids and so breeding to increase delivery of fatty acids from plants into ruminant products is an important long-term strategy. Plant lipids usually contain high levels of polyunsaturated fatty acids, particularly 18 : 2n-6 and 18 : 3n-3 which are the precursors of beneficial fatty acids. Whilst some plants are particularly rich in individual fatty acids (e.g. 18 : 3n-3 in linseed), there are also useful levels in grass and clover (Trifolium Spp.). Levels of fatty acids in forages in relation to species and varieties are considered, as well as management and conservation methods. Relationships between levels of fatty acids and existing traits and genetic markers are identified. The effects of forage treatments on the fatty acid content of ruminant products are reviewed. The higher levels of polyunsaturated fatty acids in milk from cows fed clover silages show that the level of fatty acids in herbage is not the only factor affecting levels of fatty acids in ruminant products. Further effort is needed to characterise susceptibility of unsaturated fatty acids to oxidative loss during field wilting and biohydrogenation losses in the rumen, and the relative importance of plant and microbial processes in these losses. The pathways of lipolysis and lipid oxidation are reviewed and other plant factors which offer potential to breed for reduced losses are considered.

Both light-dependent protochlorophyllide oxidoreductase A and protochlorophyllide oxidoreductase B are down-regulated in the slender mutant of barley.

The gibberellin-insensitive overgrowth mutant of barley, slender, exhibits altered expression of a number of nuclear genes in comparison with the wild type. There is a particularly marked reduction in slender seedlings of transcript encoding protochlorophyllide oxidoreductase (POR), the enzyme which catalyses the penultimate and only light-requiring step in chlorophyll biosynthesis. The expression of the two barley genes encoding light-dependent POR, PORA and PORB was investigated. Expression of both genes was found to be reduced in slender seedlings relative to the wild type, in both etiolated and light-grown leaf tissue; this was most marked in the zone of rapid cell extension. Western blot analysis showed that POR protein was also less abundant in etiolated and in light-grown slender than in the equivalent wild-type leaf tissue, although the effect was less pronounced than at the transcript level. Protochlorophyllide content in etiolated slender seedlings was reduced in comparison with wild-type seedlings, though chlorophyll content in light-grown leaf blades was unaffected. The reduction in POR expression in slender barley may reflect a novel response to the constitutive activation of gibberellin signalling in this mutant. Despite the consequences of the mutation for POR gene expression, slender seedlings develop apparently normal chloroplasts in the light, and etioplasts with well-defined prolamellar bodies when grown in continuous darkness. This suggests that the POR content of wild-type barley seedlings is well in excess of the minimum required for normal plastid development.

Annuality, perenniality and cell death.

This essay considers annuality and perenniality as quantitative traits and discusses the application of established and new genetic tools to the analysis of plant life histories. Annual/perennial status is a function of meristem determinacy in combination with the processes of cell death and disposal employed by plants to generate well-adapted anatomies and morphologies. Creeping perennials, like clover or bracken, seem to move around in the environment. They do this by extending into unoccupied space while the oldest tissues behind the growing and mature regions senesce, die and decompose. Trees do essentially the same thing, except that they develop vertically and the old dead tissue does not disappear but instead persists as wood. A root system is a kind of upended vertical perennial. The balance between exploratory growth and the wave of tissue death that succeeds it is a major determinant of perenniality. So although perenniality and annuality may appear to be dramatically different traits, extremes of behaviour can arise by a relatively minor change in the relationship between growth and death. This conclusion is supported by evidence from genome dosage studies, from the practical experiences of breeding perennial-type traits into annual backgrounds and from molecular cladistics. Applications of methods for the genetic analysis of quantitative characters are described, including the exploitation of introgression mapping in Lolium-Festuca and quantitative trait locus mapping in cereals and other species.

De novo evolution of satellite DNA on the rye B chromosome.

The most distinctive region of the rye B chromosome is a subtelomeric domain that contains an exceptional concentration of B-chromosome-specific sequences. At metaphase this domain appears to be the physical counterpart of the subtelomeric heterochromatic regions present on standard rye chromosomes, but its conformation at interphase is less condensed. In this report we show that the two sequence families that have been previously found to make up the bulk of the domain have been assembled from fragments of a variety of sequence elements, giving rise to their ostensibly foreign origin. A single mechanism, probably based on synthesis-dependent strand annealing (SDSA), is responsible for their assembly. We provide evidence for sequential evolution of one family on the B chromosome itself. The extent of these rearrangements and the complexity of the higher-order organization of the B-chromosome-specific families indicate that instability is a property of the domain itself, rather than of any single sequence. Indirect evidence suggests that particular fragments may have been selected to confer different properties on the domain and that rearrangements are frequently selected for their effect on DNA structure. The current organization appears to represent a transient stage in the evolution of a conventional heterochromatic region from complex sequences.

UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics.

The UK Crop Plant Bioinformatics Network (UK CropNet) was established in 1996 in order to harness the extensive work in genome mapping in crop plants in the UK. Since this date we have published five databases from our central UK CropNet WWW site (http://synteny.nott.ac.uk/) with a further three to follow shortly. Our resource facilitates the identification and manipulation of agronomically important genes by laying a foundation for comparative analysis among crop plants and model species. In addition, we have developed a number of software tools that facilitate the visualisation and analysis of our data. Many of our tools are made freely available for use with both crop plant data and with data from other species.

Identification of three cDNA clones expressed in the leaf extension zone and with altered patterns of expression in the slender mutant of barley: a tonoplast intrinsic protein, a putative structural protein and protochlorophyllide oxidoreductase.

Three cDNA clones have been isolated on the basis of altered patterns of expression in the leaf extension zone of the developmental mutant, slender barley, compared with the wild type. mRNAs corresponding to two of the cDNAs, 7s and 8s, are increased in slender compared with normal. 7s encodes a putative gamma-TIP and is expressed throughout the elongation zone. gamma-TIPs form transmembrane channels which allow the passive transfer of water. Although expression of 7s was increased in slender leaf tissue, the increase was much less extreme than that shown by Phillips and Huttly (1994) following the application of GA to an extreme dwarf of Arabidopsis. 8s is maximally expressed in the region of early cell elongation and has 66% encoded protein identity with MFS18, a cDNA encoding a putative cell wall structural protein isolated from male flowers of maize. Both 8s and MFS18 encode small (128 amino acids) basic proteins rich in glycine, alanine, proline and serine. mRNA corresponding to the third cDNA, 24n, is present at a greatly reduced level in slender compared with normal and encodes protochlorophyllide oxidoreductase (POR). POR catalyses the conversion of protochlorophyllide into chlorophyllide. The reduced level of POR mRNA is not correlated with a similar reduction in expanded leaf blade chlorophyll levels. Western analysis identified two POR proteins present in light-grown seedlings. Whilst the larger of the proteins is present throughout most of the leaf, the smaller protein mimics the mRNA results, being both maximally present in the elongation tissue and present at a reduced level in slender. An antagonistic relationship between chlorophyll biosynthesis and extension growth is suggested.

Subcellular Visualization of Gene Transcripts Encoding Key Proteins of the Chlorophyll Accumulation Process in Developing Chloroplasts.

The coordination of the synthesis of chlorophyll (Chl) and light-harvesting Chl proteins was determined by observing the sequence of appearance of the specific mRNAs for the nuclear genes CHLH, Por, and Lhcb1*2 (AB180). CHLH encodes a magnesium protoporphyrin chelatase subunit that is involved in the first committed step in Chl biosynthesis; Por encodes protochlorophyllide oxidoreductase, which catalyzes the penultimate and only light-dependent step in Chl biosynthesis; and Lhcb1*2 encodes light-harvesting Chl a/b binding protein of the type-1 light-harvesting complex of photosystem II. Using digoxigenin-labeled antisense and sense RNA probes and a highly sensitive in situ hybridization technique, we have visualized the first appearance of the specific mRNAs in postmitotic mesophyll cells of developing 7-d-old wheat leaves (Triticum aestivum cv Maris dove). The transcripts for CHLH and POR are detectable in the youngest (18 h postmitotic) leaf tissue containing dividing cells; light-harvesting complex of photosystem II transcripts appear 12 h later. This is consistent with a requirement for accumulation of Chl before synthesis of Chl a/b binding protein can proceed at a high rate. All of the transcripts are most abundant in mesophyll cells. In the first leaf the POR message is initially restricted to the palisade, but 12 h later it is also present in the spongy mesophyll cells. All three transcripts aggregated around the surface of the chloroplasts, suggesting that translation may occur preferentially in the vicinity of the target organelle for the primary translation products.

Temperature shock proteins in plants.

Plant tissue generally responds rapidly to sudden increases in temperature by curtailing or abolishing normal protein synthesis and producing new polypeptides known as heat shock proteins (HSP). Some of the methods used for monitoring the expression of heat shock genes are described, and the characteristics of the heat shock response in higher plants are discussed with special reference to tropical cereals. The possible role for heat shock proteins in conferring thermo-tolerance upon plant tissue is considered. The behaviour of plant tissue subjected to temperature decreases has been much less intensively studied, and varies greatly according to species and the nature of the cold treatment. No homology has yet been detected between the heat shock and the cold shock response in any plant system. Cold-induced changes in gene expression observed in a wide range of plant species are discussed with particular reference to parallel changes in cold-hardiness. Marked contrasts have been observed between the response of temperate grasses and that of tropical cereals to cold treatment, and these are discussed in relation to growth and survival at suboptimal temperatures.

Camphor revisited: involvement of a unique monooxygenase in metabolism of 2-oxo-delta 3-4,5,5-trimethylcyclopentenylacetic acid by Pseudomonas putida.

Previously, Pseudomonas putida was shown to degrade (+)-camphor, and cleavage of the first ring of the bicyclic structure involved two monooxygenases (a hydroxylase and a ring oxygen-inserting enzyme), a dehydrogenase, and spontaneous cleavage of an unstable oxygenation product (lactone). Cleavage of the second ring was not demonstrated but was assumed also to occur by ring oxygen insertion, since the predicted oxygenation product was extracted from whole-cell incubation systems. Our investigation established that metabolism of the first ring cleavage intermediate, 2-oxo-delta 3-4,5,5-trimethylcyclopentenylacetic acid, occurred through the sequential action of two inducible enzymes, a coenzyme A ester synthetase and an oxygenase. The oxygenase was purified to homogeneity and had a molecular weight of 106,000. This enzyme carried a single molecule of flavin adenine dinucleotide and consisted of two identical subunits. Iron was not present at a significant level. The oxygenase was specific for NADPH as the electron donor and absolutely specific for the coenzyme A ester of 2-oxo-delta 3-4,5,5-trimethylcyclopentenylacetic acid as the substrate. The reaction stoichiometry was compatible with this enzyme being a monooxygenase, and a mass spectral analysis of the methyl ester of the product confirmed the insertion of a single oxygen atom. The enzyme appeared to be analogous to, although distinct from. 2,5-diketocamphane 1,2-monooxygenase in catalyzing a "biological Baeyer-Villiger" reaction with the formation of a lactone. Structural analogy suggested that this lactone, like the first, was also unstable and susceptible to spontaneous ring opening, although this was not experimentally established.

Metabolism of cyclohexaneacetic acid and cyclohexanebutyric acid by Arthrobacter sp. strain CA1.

A strain of Arthrobacter was isolated by enrichment culture with cyclohexaneacetate as the sole source of carbon and grew with a doubling time of 4.2 h. In addition to growing with cyclohexaneacetate, the organism also grew with cyclohexanebutyrate at concentrations not above 0.05%, and with a variety of alicyclic ketones and alcohols. Oxidation of cyclohexaneacetate proceeded through formation of the coenzyme A (CoA) ester followed by initiation of a beta-oxidation cycle. beta-Oxidation was blocked before the second dehydrogenation step due to the formation of a tertiary alcohol, and the side chain was eliminated as acetyl-CoA by the action of (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase. The cyclohexanone thus formed was degraded by a well-described route that involves ring-oxygen insertion by a biological Baeyer-Villiger oxygenase. All enzymes of the proposed metabolic sequence were demonstrated in cell-free extracts. Arthrobacter sp. strain CA1 synthesized constitutive beta-oxidative enzymes, but further induction of enzymes active toward cyclohexaneacetate and its metabolites could occur during growth with the alicyclic acid. Other enzymes of the sequence, (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase and enzymes of cyclohexanone oxidation, were present at negligible levels in succinate-grown cells but induced by growth with cyclohexaneacetate. The oxidation of cyclohexanebutyrate was integrated into the pathway for cyclohexaneacetate oxidation by a single beta-oxidation cycle. Oxidation of the compound could be divided into two phases. Initial oxidation to (1-hydroxycyclohexan-1-yl)acetate could be catalyzed by constitutive enzymes, whereas the further degradation of (1-hydroxycyclohexan-1-yl)acetate was dependent on induced enzyme synthesis which could be inhibited by chloramphenicol with the consequent accumulation of cyclohexaneacetate and (1-hydroxycyclohexan-1-yl)acetate.