Gas chromatography-mass spectrometry based metabolite profiling of biological samples is rapidly ... more Gas chromatography-mass spectrometry based metabolite profiling of biological samples is rapidly becoming one of the cornerstones of functional genomics and systems biology. Thus, the technology needs to be available to many laboratories and open exchange of information is required such as those achieved for transcript and protein data. The key-step in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations with composite structure. Collections of mass spectra, which comprise frequently observed identified and non-identified metabolites, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here, we describe a platform for mass spectral and retention time index libraries that will enable this process (MSRI; www.csbdb.mpimpgolm.mpg.de/gmd.html). This resource should ameliorate many of the problems that each laboratory will face both for the initial establishment of metabolome analysis and for its maintenance at a constant sample throughput.
Plant cell wall biomass is an abundant and renewable organic resource. Of the polymers it enclose... more Plant cell wall biomass is an abundant and renewable organic resource. Of the polymers it encloses, cellulose and hemicellulose are regarded as a raw material for the production of fuels and other products. Nonetheless, current usage of lignocellulosic biomass is still below its full potential due to a series of limiting factors mainly related to the cell wall recalcitrance to saccharification, a severe constraint to maximum biomass usability in downstream processing.
As a strategy to optimise bio-energy and bio-refining applications, an increasing amount of effort is being put into the advancement of our knowledge concerning the cell wall compositional roots of recalcitrance. Fourier transform mid-infrared spectroscopy (FTIR) represents a very useful tool on this enterprise, as it allows for a high-throughput, non-destructive and low unit cost procedure for the examination of cell wall biomass. Furthermore, the use of Attenuated Total Reflection (ATR) in conjunction with infrared spectroscopy (IR) enables cell wall biomass samples to be examined in solid state without extensive preparation. Nonetheless, the analysis of purified cell wall preparations instead of the intact plant biomass is highly recommended, as it minimises or even eradicates interference from biomass components which are not part of the cell wall. Further information regarding the fundamentals of FTIR may be found elsewhere.
Datasets generated from FTIR spectroscopy can be extensive and complex. In these situations, data-driven modelling techniques are often used as exploratory approaches to identify the most distinctive features of the collected spectra. Here we suggest the use of Principal Component Analysis (PCA), a frequently employed method to transform a large set of variables into a smaller set of new variables (principal components), effectively reducing dataset dimensionality.
When the aim is a complete and detailed biomass characterisation, the FTIR-PCA method here described does not exclude the need for parallel wet gravimetric and analytical procedures. However, it does lead to a rapid identification of the major compositional shifts across large sets of samples; thus contributing to steer research pathways, minimise time-draining analytical procedures and reduce overall research costs.
Little is known about how plant biochemistry influences the grazing behavior of animals consuming... more Little is known about how plant biochemistry influences the grazing behavior of animals consuming heterogeneous plant communities. The biochemical profiles of grassland species are mostly restricted to major nutritional characteristics, although recent developments in analytical techniques and data analysis have made possible the detailed analysis of minor components that may influence animal feeding preferences, performance, and health. In the present study, gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF/MS) was used to profile the abundances of metabolites in nine specific heathland plant groups and in three mixed forage diets containing 10, 20, or 30% heather (Calluna vulgaris) and also in plasma and feces from sheep offered one of the three diets. Statistical and chemometric approaches, that is, principal component analysis (PCA) and hierarchical cluster analysis (HCA), were used to discriminate between these diets and between individual animals maintai...
Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass cro... more Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we pr...
Currently, rapid methods are needed for feed analysis. This study examined the potential of Fouri... more Currently, rapid methods are needed for feed analysis. This study examined the potential of Fouriertransform infrared (FTIR) spectroscopy to predict the nutritional value of a wide range of feeds for ruminants, as an alternative to the in situ technique. Moreover, we investigated whether universal equations could be developed that would allow the low-cost determination of crude protein (CP) concentrations and their kinetics of degradation into the rumen. Protein nutritional values of 663 samples comprising 80 different feed types were determined in terms of concentrations of CP, watersoluble CP (CP WS ), total-tract mobile bag CP digestibility (CP TTD ), and in situ CP degradability, including the rumen soluble fraction (CP A ), the degradable but not soluble fraction (CP B ), rate of CP B degradation (CP C ), effective degradability (CP ED ), and potential degradability (CP PD ). Infrared spectra of dry samples were collected by attenuated total reflectance from 4000 to 600 cm −1 . Models were developed by partial least squares (PLS) regression in a randomly selected subset of samples, and the precision of the equations was confirmed by using an external validation set. Analysis by FTIR spectroscopy was sufficiently sensitive to allow the accurate prediction of sample CP concentration (R 2 = 0.92) and to classify feeds according to their CP WS concentrations using universal models (R 2 = 0.78) that included all sample types. Moreover, substantial improvements in predictions were observed when samples were subdivided in groups. Models for forages led to accurate predictions of CP WS and fractions CP A and CP B (R 2 > 0.83), whereas models for CP TTD and CP ED could be used for screening purposes (R 2 > 0.67). This study showed that models for protein-rich concentrates alone could also be used for screening according to the feed concentrations of CP WS , CP TTD , CP ED , CP A , and CP B , but models for energy-rich concentrates gave relatively poor predictions. The general difficulty ob-served in predicting CP C is because of a low correlation between FTIR spectra and the kinetics of CP degradation, which may be the result of large variation in the reference method (i.e., in situ degradation studies) and perhaps also because of the presence of compounds that can modify the CP degradation pattern in the rumen.
Polyphenol oxidase (PPO) may have multiple functions in tissues depending on its cellular or tiss... more Polyphenol oxidase (PPO) may have multiple functions in tissues depending on its cellular or tissue localization. Here we use PPO RNAi transformants of red clover (Trifolium pratense) to determine the role PPO plays in normal development of plants, and especially in N 2 -fixing nodules. In red clover, PPO was not essential for either growth or nodule production, or for nodule function in plants grown under optimal, N-free conditions. However, absence of PPO resulted in a more reduced environment in all tissues, as measured by redox potential, and caused subtle developmental changes in nodules. Leaves and, to a lesser extent nodules, lacking PPO tended to accumulate phenolic compounds. A comparison of nodules of two representative contrasting clones by microscopy revealed that nodules lacking PPO were morphologically and anatomically subtly altered, and that phenolics accumulated in different cells and tissues. Developing nodules lacking PPO were longer, and there were more cell layers within the squashed cell layer (SCL), but the walls of these cells were less thickened and the cells were less squashed. Within the N 2 -fixing zone, bacteroids appeared more granular and were less tightly packed together, and were similar to developmentally compromised bacteroids elicited by catalase mutant rhizobia reported elsewhere.
Scrapie and bovine spongiform encephalopathy (BSE) are major global concerns and the emergence of... more Scrapie and bovine spongiform encephalopathy (BSE) are major global concerns and the emergence of variant Creutzfeldt-Jakob disease (vCJD) has caused turmoil for blood transfusion services and hospitals worldwide. Recent reports of iatrogenic CJD (iCJD) cases following blood transfusions from Transmissible Spongiform Encephalopathies (TSE)-infected donors have fuelled this concern. Major diagnostic tests for BSE and scrapie are conducted post-mortem from animals in late stages of the disease. Although the lymphoreticular system is involved in the earlier pathogenesis of some forms of sheep scrapie and vCJD, which presents great opportunity for diagnostic development, other TSE diseases (some strains of scrapie, sporadic CJD (sCJD) and bovine BSE) do not present such a diagnostic opportunity. Thus, there is an urgent need for premortem tests that differentiate between healthy and diseased individuals at early stages of illness, in accessible samples such as blood and urine using less invasive procedures. This review reports on the current state of progress in the development and use of prion and non-prion biomarkers in the diagnosis of TSE diseases. Some of these efforts have concentrated on improving the sensitivity of PrP Sc detection to allow in vivo diagnosis at low abundances of PrP Sc whilst others have sought to identify non-prion protein biomarkers of TSE disease, many of which are still at early stages of development. In this review we comment upon the limitations of prion based tests and review current research on the development of tests for TSE that rely on non-prion disease markers in body fluids that may allow preclinical disease diagnosis.
Nitrogen availability has profound ecological consequences in nutrientlimited systems. In terrest... more Nitrogen availability has profound ecological consequences in nutrientlimited systems. In terrestrial settings these would include the upland heaths, sand dunes and blanket bogs of temperate latitudes. Understanding the physiological consequences of nitrogen enrichment is a first critical step in predicting possible consequences. Results are presented from a metabolic fingerprinting study using Fourier transform-infrared spectroscopy (FTIR) to detect biochemical differences in the lichen Cladonia portentosa collected from 25 sites across mainland Britain varying in their nitrogen input. Partial least-squares regression analysis of the FTIR data demonstrated that changes in broad biochemical classes were consistently correlated with mean annual wet inorganic nitrogen deposition loads. These results demonstrated a direct coupling of a broad range of metabolic processes in C. portentosa to nitrogen deposition.
Gabaculine (2,3-dihydro 3-amino benzoic acid) is a potent inhibitor of tetrapyrrole biosynthesis ... more Gabaculine (2,3-dihydro 3-amino benzoic acid) is a potent inhibitor of tetrapyrrole biosynthesis in organisms that use the C 5 pathway for the synthesis of d-aminolaevulinic acid. Glutamate semialdehyde aminotransferase (GSA-AT), the enzyme catalysing the formation of this key precursor of tetrapyrroles, is normally inhibited by concentrations of gabaculine in the order of 5 lM. However, in Synechococcus 6301 strain GR6, a cyanobacterium that is resistant to 100 lM gabaculine, this enzyme has undergone two changes in structure: a deletion of three amino acids from positions 5 to 7 and the substitution of isoleucine for methionine at position 248. To establish the eect in vivo of these speci®c changes in the gene for GSA-AT (hemL), a suicide vector (pHS7) containing an antibiotic cassette was constructed to achieve the replacement, by homologous recombination, of the wild-type hemL gene in the chromosome by a modi®ed form of the gene. Recombinant strains of Synechococcus 7942 obtained using pHS7-hemL GR6 were indistinguishable from Synechococcus 6301 GR6 in terms of the resistance of growth and of chlorophyll accumulation to high concentrations of gabaculine, while a wild-type recombinant produced using pHS7-hemL WT had retained its sensitivity. Southern hybridisation using gene probes for hemL, amp r and cm r con®rmed that chromosomal integration of the plasmids had occurred in both WT and GR6 recombinants. Growth and chlorophyll accumulation in equivalent strains with the hemL gene containing either the deletion or the transition characteristic of Synechococcus 6301 GR6 were inhibited by 10 lM gabaculine. Consequently, resistance in vivo to high concentrations of this compound is dependent on both the changes in gene/enzyme structure. This investigation has established the eectiveness of the suicide vector pHS7 for studying the eect in vivo of speci®c changes in the hemL gene. It has also demonstrated that replacement of the wild-type gene by that from Synechococcus 6301 GR6 is sucient to confer resistance in vivo to high concentrations of gabaculine.
This study explored the potential of partial least squares (PLS) and Fourier-transform infrared s... more This study explored the potential of partial least squares (PLS) and Fourier-transform infrared spectroscopy (FTIR) to predict rumen dry matter (DM) and neutral detergent fiber (NDF) degradation parameters of a wide range of feeds for ruminants, as an alternative to the in situ method. In total, 663 samples comprising 80 different feed types were analyzed. In situ DM and NDF degradabilities were determined as follows: effective degradability (ED), rumen soluble fraction (A), degradable but not soluble fraction (B), rate of degradation of the B fraction (C), and indigestible NDF (iNDF). Infrared spectra of dry samples were collected by attenuated total reflectance from 600 to 4000 cm −1 . Feeds were randomly classified into 2 subsets of samples with representation of all feed types; one subset was used to develop regression models using partial least squares, and the second subset was used to conduct an external validation of the models. This study indicated that universal models containing all feed types and specific models containing concentrate feeds could provide only a relatively poor estimation of in situ DM degradation parameters because of compositional heterogeneity. More research, such as a particle size distribution analysis, is required to determine whether this lack of accuracy was due to limitations of the FTIR approach, or simply due to methodological error associated with the in situ method. This latter hypothesis may explain the low accuracy observed in the prediction of degradation rates if there was physical leakage of fine particles from the mesh bags used during in situ studies. In contrast, much better predictions were obtained when models were developed for forage feeds alone. Models for forages led to accurate predictions of DM A , DM B , NDF ED , and NDF concentration (R 2 = 0.91, 0.89, 0.85, and 0.79, standard error = 4.34, 5.97, 4.59, and 4.41% of DM, respectively), and could be used for screening of DM ED , NDF C , and iNDF.
Polyphenol oxidase (PPO) genes and their corresponding enzyme activities occur in many plants; na... more Polyphenol oxidase (PPO) genes and their corresponding enzyme activities occur in many plants; natural PPO substrates and enzyme/substrate localization are less well characterized. Leaf and root PPO activities in Arabidopsis and five legumes were compared with those of high-PPO red clover (Trifolium pratense L.). Red clover PPO enzyme activity decreased leaves > stem > nodules > peduncle = petiole > embryo; PPO1 and PPO4 genes were expressed early in leaf emergence, whereas PPO4 and PPO5 predominated in mature leaves. PPO1 was expressed in embryos and nodules. PPO substrates, phaselic acid and clovamide, were detected in leaves, and clovamide was detected in nodules. Phaselic acid and clovamide, along with caffeic and chlorogenic acids, were suitable substrates for PPO1, PPO4, and PPO5 genes expressed in alfalfa (Medicago sativa L.) leaves. PPO enzyme presence and activity were colocalized in leaves and nodules by cytochemistry. Substrates and PPO activity were localized in developing squashed cell layer of nodules, suggesting PPO may have a developmental role in nodules.
The effect of the tetrapyrrole biosynthesis inhibitor gabaculine on the expression of specific ge... more The effect of the tetrapyrrole biosynthesis inhibitor gabaculine on the expression of specific genes involved in phycocyanin biosynthesis was investigated in cultures of Synechococcus PCC6301 in nitrogen chlorosis, and during recovery to nitrogen sufficiency.
Glutamate-l-semialdehyde (GSA) aminotransferase catalyses the final step in the C5 pathway conver... more Glutamate-l-semialdehyde (GSA) aminotransferase catalyses the final step in the C5 pathway converting glutamate to the tetrapyrrole precursor δ-aminolaevulinic acid. This enzyme is sensitive to gabaculine (2,3-dihydro-3-amino benzoic acid) and to 4-amino-5-fluoropentanoic acid (AFPA), which are irreversible, mechanism-based inhibitors of pyridoxal phosphatedependent enzymes. Spontaneous mutants of Synechococcus PCC6301 resistant to these inhibitors contain altered enzyme that displays corresponding resistance to high concentrations of the inhibitor. The enzyme from strain GR6, resistant to both inhibitors, contains a three-amino-acid deletion at positions 5-7 and a Met#%) Ile substitution. The enzyme from strain K40 resistant to AFPA but not to gabaculine, contains a Ser"'$ Thr substitution. GSA aminotransferases containing either the deletion or the substitution that are characteristic of the GR6 mutant were produced in Escherichia coli using the expression vector pMalc2. These engineered mutant enzymes were characterized in terms of their catalytic parameters and sensitivities to gabaculine and AFPA. Furthermore, maltose binding protein\aminotransferase fusion proteins were characterized spectrophotometrically to monitor the interaction of bound cofactor with diamino-and dioxocompounds related to the substrate and both inhibitors. Results were compared with those for similarly produced recombinant wild-type, K40 and GR6 GSA aminotransferases. The engineered products with either the N-terminal deletion or the Met#%) Ile substitution displayed catalytic efficiencies that were intermediate between the wild-type and GR6 or K40 enzymes. However, with respect to their absorption spectra, sensitivity to inhibitors and the reactivity of bound cofactor, they were essentially wild-type. These in vitro studies demonstrate that both changes in enzyme structure are necessary to obtain the distinctive properties of the GR6 aminotransferase, including resistance to high concentrations of gabaculine and AFPA.
Consecutive batch cultures (CBC), involving nine serial transfers at 3, 5 and 7 d intervals (21, ... more Consecutive batch cultures (CBC), involving nine serial transfers at 3, 5 and 7 d intervals (21, 45 and 63 d, respectively) were established to enrich for plant fibre degrading co-cultures of anaerobic fungi and methanogens from rumen digesta. Microbial diversity and fermentation end-products were measured at appropriate intervals over each CBC time-course. While methanogenic populations remained diverse, anaerobic fungal diversity was related to transfer interval and appeared to decrease with increasing transfer number. Acetate was the principal aqueous fermentation end-product with minimal quantities of lactate and formate detected. Methane and carbon dioxide were detected in the gaseous head-space of all co-cultures and the total amounts of gas generated per transfer was greater with transfer intervals of 5 and 7 d compared with a 3 d interval, although the 3 d interval tended to be more efficient per unit time. In conclusion, rapidly growing, methane producing co-cultures of anaerobic fungi and methanogens from rumen digesta were easy to establish on lignocellulose (barley straw) and maintain over considerable time periods. These results suggest such co-cultures have potential in industrial scale anaerobic digestion (AD) of highly fibrous substrates, which are resistant to degradation in conventional AD plants.
BACKGROUND AND AIMS: Species and hybrids of the genus Miscanthus contain attributes that make the... more BACKGROUND AND AIMS: Species and hybrids of the genus Miscanthus contain attributes that make them front-runners among current selections of dedicated bioenergy crops. A key trait for plant biomass conversion to biofuels and biomaterials is cell-wall quality; however, knowledge of cell-wall composition and biology in Miscanthus species is limited. This study presents data on cell-wall compositional changes as a function of development and tissue type across selected genotypes, and considers implications for the development of miscanthus as a sustainable and renewable bioenergy feedstock. METHODS: Cell-wall biomass was analysed for 25 genotypes, considering different developmental stages and stem vs. leaf compositional variability, by Fourier transform mid-infrared spectroscopy and lignin determination. In addition, a Clostridium phytofermentans bioassay was used to assess cell-wall digestibility and conversion to ethanol. KEY RESULTS: Important cell-wall compositional differences between miscanthus stem and leaf samples were found to be predominantly associated with structural carbohydrates. Lignin content increased as plants matured and was higher in stem tissues. Although stem lignin concentration correlated inversely with ethanol production, no such correlation was observed for leaves. Leaf tissue contributed significantly to total above-ground biomass at all stages, although the extent of this contribution was genotype-dependent. CONCLUSIONS: It is hypothesized that divergent carbohydrate compositions and modifications in stem and leaf tissues are major determinants for observed differences in cell-wall quality. The findings indicate that improvement of lignocellulosic feedstocks should encompass tissue-dependent variation as it affects amenability to biological conversion. For gene-trait associations relating to cell-wall quality, the data support the separate examination of leaf and stem composition, as tissue-specific traits may be masked by considering only total above-ground biomass samples, and sample variability could be mostly due to varying tissue contributions to total biomass.
The efficiency of proteins of legume forages in ruminant nutrition is poor because of their exten... more The efficiency of proteins of legume forages in ruminant nutrition is poor because of their extensive degradation in the rumen. The objective of this study was to evaluate the variation available for protein degradation in tannin-free (alfalfa and white clover) and tannin-rich (Lotus sp.) legume species. Protein and dry matter degradation were measured by in sacco incubation of forage samples in the rumen of fistulated cows, for 2, 8 or 48 h. Condensed tannin content was measured on Lotus samples. Variation in protein degradation was low among alfalfa and white clover cultivars, but the degradation was more important for alfalfa than for clover cultivars. Protein degradation was less important in Lotus sp. than in alfalfa or clover, and the variation among Lotus cultivars was mainly related to condensed tannin content.
Gas chromatography-mass spectrometry based metabolite profiling of biological samples is rapidly ... more Gas chromatography-mass spectrometry based metabolite profiling of biological samples is rapidly becoming one of the cornerstones of functional genomics and systems biology. Thus, the technology needs to be available to many laboratories and open exchange of information is required such as those achieved for transcript and protein data. The key-step in metabolite profiling is the unambiguous identification of metabolites in highly complex metabolite preparations with composite structure. Collections of mass spectra, which comprise frequently observed identified and non-identified metabolites, represent the most effective means to pool the identification efforts currently performed in many laboratories around the world. Here, we describe a platform for mass spectral and retention time index libraries that will enable this process (MSRI; www.csbdb.mpimpgolm.mpg.de/gmd.html). This resource should ameliorate many of the problems that each laboratory will face both for the initial establishment of metabolome analysis and for its maintenance at a constant sample throughput.
Plant cell wall biomass is an abundant and renewable organic resource. Of the polymers it enclose... more Plant cell wall biomass is an abundant and renewable organic resource. Of the polymers it encloses, cellulose and hemicellulose are regarded as a raw material for the production of fuels and other products. Nonetheless, current usage of lignocellulosic biomass is still below its full potential due to a series of limiting factors mainly related to the cell wall recalcitrance to saccharification, a severe constraint to maximum biomass usability in downstream processing.
As a strategy to optimise bio-energy and bio-refining applications, an increasing amount of effort is being put into the advancement of our knowledge concerning the cell wall compositional roots of recalcitrance. Fourier transform mid-infrared spectroscopy (FTIR) represents a very useful tool on this enterprise, as it allows for a high-throughput, non-destructive and low unit cost procedure for the examination of cell wall biomass. Furthermore, the use of Attenuated Total Reflection (ATR) in conjunction with infrared spectroscopy (IR) enables cell wall biomass samples to be examined in solid state without extensive preparation. Nonetheless, the analysis of purified cell wall preparations instead of the intact plant biomass is highly recommended, as it minimises or even eradicates interference from biomass components which are not part of the cell wall. Further information regarding the fundamentals of FTIR may be found elsewhere.
Datasets generated from FTIR spectroscopy can be extensive and complex. In these situations, data-driven modelling techniques are often used as exploratory approaches to identify the most distinctive features of the collected spectra. Here we suggest the use of Principal Component Analysis (PCA), a frequently employed method to transform a large set of variables into a smaller set of new variables (principal components), effectively reducing dataset dimensionality.
When the aim is a complete and detailed biomass characterisation, the FTIR-PCA method here described does not exclude the need for parallel wet gravimetric and analytical procedures. However, it does lead to a rapid identification of the major compositional shifts across large sets of samples; thus contributing to steer research pathways, minimise time-draining analytical procedures and reduce overall research costs.
Little is known about how plant biochemistry influences the grazing behavior of animals consuming... more Little is known about how plant biochemistry influences the grazing behavior of animals consuming heterogeneous plant communities. The biochemical profiles of grassland species are mostly restricted to major nutritional characteristics, although recent developments in analytical techniques and data analysis have made possible the detailed analysis of minor components that may influence animal feeding preferences, performance, and health. In the present study, gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF/MS) was used to profile the abundances of metabolites in nine specific heathland plant groups and in three mixed forage diets containing 10, 20, or 30% heather (Calluna vulgaris) and also in plasma and feces from sheep offered one of the three diets. Statistical and chemometric approaches, that is, principal component analysis (PCA) and hierarchical cluster analysis (HCA), were used to discriminate between these diets and between individual animals maintai...
Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass cro... more Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we pr...
Currently, rapid methods are needed for feed analysis. This study examined the potential of Fouri... more Currently, rapid methods are needed for feed analysis. This study examined the potential of Fouriertransform infrared (FTIR) spectroscopy to predict the nutritional value of a wide range of feeds for ruminants, as an alternative to the in situ technique. Moreover, we investigated whether universal equations could be developed that would allow the low-cost determination of crude protein (CP) concentrations and their kinetics of degradation into the rumen. Protein nutritional values of 663 samples comprising 80 different feed types were determined in terms of concentrations of CP, watersoluble CP (CP WS ), total-tract mobile bag CP digestibility (CP TTD ), and in situ CP degradability, including the rumen soluble fraction (CP A ), the degradable but not soluble fraction (CP B ), rate of CP B degradation (CP C ), effective degradability (CP ED ), and potential degradability (CP PD ). Infrared spectra of dry samples were collected by attenuated total reflectance from 4000 to 600 cm −1 . Models were developed by partial least squares (PLS) regression in a randomly selected subset of samples, and the precision of the equations was confirmed by using an external validation set. Analysis by FTIR spectroscopy was sufficiently sensitive to allow the accurate prediction of sample CP concentration (R 2 = 0.92) and to classify feeds according to their CP WS concentrations using universal models (R 2 = 0.78) that included all sample types. Moreover, substantial improvements in predictions were observed when samples were subdivided in groups. Models for forages led to accurate predictions of CP WS and fractions CP A and CP B (R 2 > 0.83), whereas models for CP TTD and CP ED could be used for screening purposes (R 2 > 0.67). This study showed that models for protein-rich concentrates alone could also be used for screening according to the feed concentrations of CP WS , CP TTD , CP ED , CP A , and CP B , but models for energy-rich concentrates gave relatively poor predictions. The general difficulty ob-served in predicting CP C is because of a low correlation between FTIR spectra and the kinetics of CP degradation, which may be the result of large variation in the reference method (i.e., in situ degradation studies) and perhaps also because of the presence of compounds that can modify the CP degradation pattern in the rumen.
Polyphenol oxidase (PPO) may have multiple functions in tissues depending on its cellular or tiss... more Polyphenol oxidase (PPO) may have multiple functions in tissues depending on its cellular or tissue localization. Here we use PPO RNAi transformants of red clover (Trifolium pratense) to determine the role PPO plays in normal development of plants, and especially in N 2 -fixing nodules. In red clover, PPO was not essential for either growth or nodule production, or for nodule function in plants grown under optimal, N-free conditions. However, absence of PPO resulted in a more reduced environment in all tissues, as measured by redox potential, and caused subtle developmental changes in nodules. Leaves and, to a lesser extent nodules, lacking PPO tended to accumulate phenolic compounds. A comparison of nodules of two representative contrasting clones by microscopy revealed that nodules lacking PPO were morphologically and anatomically subtly altered, and that phenolics accumulated in different cells and tissues. Developing nodules lacking PPO were longer, and there were more cell layers within the squashed cell layer (SCL), but the walls of these cells were less thickened and the cells were less squashed. Within the N 2 -fixing zone, bacteroids appeared more granular and were less tightly packed together, and were similar to developmentally compromised bacteroids elicited by catalase mutant rhizobia reported elsewhere.
Scrapie and bovine spongiform encephalopathy (BSE) are major global concerns and the emergence of... more Scrapie and bovine spongiform encephalopathy (BSE) are major global concerns and the emergence of variant Creutzfeldt-Jakob disease (vCJD) has caused turmoil for blood transfusion services and hospitals worldwide. Recent reports of iatrogenic CJD (iCJD) cases following blood transfusions from Transmissible Spongiform Encephalopathies (TSE)-infected donors have fuelled this concern. Major diagnostic tests for BSE and scrapie are conducted post-mortem from animals in late stages of the disease. Although the lymphoreticular system is involved in the earlier pathogenesis of some forms of sheep scrapie and vCJD, which presents great opportunity for diagnostic development, other TSE diseases (some strains of scrapie, sporadic CJD (sCJD) and bovine BSE) do not present such a diagnostic opportunity. Thus, there is an urgent need for premortem tests that differentiate between healthy and diseased individuals at early stages of illness, in accessible samples such as blood and urine using less invasive procedures. This review reports on the current state of progress in the development and use of prion and non-prion biomarkers in the diagnosis of TSE diseases. Some of these efforts have concentrated on improving the sensitivity of PrP Sc detection to allow in vivo diagnosis at low abundances of PrP Sc whilst others have sought to identify non-prion protein biomarkers of TSE disease, many of which are still at early stages of development. In this review we comment upon the limitations of prion based tests and review current research on the development of tests for TSE that rely on non-prion disease markers in body fluids that may allow preclinical disease diagnosis.
Nitrogen availability has profound ecological consequences in nutrientlimited systems. In terrest... more Nitrogen availability has profound ecological consequences in nutrientlimited systems. In terrestrial settings these would include the upland heaths, sand dunes and blanket bogs of temperate latitudes. Understanding the physiological consequences of nitrogen enrichment is a first critical step in predicting possible consequences. Results are presented from a metabolic fingerprinting study using Fourier transform-infrared spectroscopy (FTIR) to detect biochemical differences in the lichen Cladonia portentosa collected from 25 sites across mainland Britain varying in their nitrogen input. Partial least-squares regression analysis of the FTIR data demonstrated that changes in broad biochemical classes were consistently correlated with mean annual wet inorganic nitrogen deposition loads. These results demonstrated a direct coupling of a broad range of metabolic processes in C. portentosa to nitrogen deposition.
Gabaculine (2,3-dihydro 3-amino benzoic acid) is a potent inhibitor of tetrapyrrole biosynthesis ... more Gabaculine (2,3-dihydro 3-amino benzoic acid) is a potent inhibitor of tetrapyrrole biosynthesis in organisms that use the C 5 pathway for the synthesis of d-aminolaevulinic acid. Glutamate semialdehyde aminotransferase (GSA-AT), the enzyme catalysing the formation of this key precursor of tetrapyrroles, is normally inhibited by concentrations of gabaculine in the order of 5 lM. However, in Synechococcus 6301 strain GR6, a cyanobacterium that is resistant to 100 lM gabaculine, this enzyme has undergone two changes in structure: a deletion of three amino acids from positions 5 to 7 and the substitution of isoleucine for methionine at position 248. To establish the eect in vivo of these speci®c changes in the gene for GSA-AT (hemL), a suicide vector (pHS7) containing an antibiotic cassette was constructed to achieve the replacement, by homologous recombination, of the wild-type hemL gene in the chromosome by a modi®ed form of the gene. Recombinant strains of Synechococcus 7942 obtained using pHS7-hemL GR6 were indistinguishable from Synechococcus 6301 GR6 in terms of the resistance of growth and of chlorophyll accumulation to high concentrations of gabaculine, while a wild-type recombinant produced using pHS7-hemL WT had retained its sensitivity. Southern hybridisation using gene probes for hemL, amp r and cm r con®rmed that chromosomal integration of the plasmids had occurred in both WT and GR6 recombinants. Growth and chlorophyll accumulation in equivalent strains with the hemL gene containing either the deletion or the transition characteristic of Synechococcus 6301 GR6 were inhibited by 10 lM gabaculine. Consequently, resistance in vivo to high concentrations of this compound is dependent on both the changes in gene/enzyme structure. This investigation has established the eectiveness of the suicide vector pHS7 for studying the eect in vivo of speci®c changes in the hemL gene. It has also demonstrated that replacement of the wild-type gene by that from Synechococcus 6301 GR6 is sucient to confer resistance in vivo to high concentrations of gabaculine.
This study explored the potential of partial least squares (PLS) and Fourier-transform infrared s... more This study explored the potential of partial least squares (PLS) and Fourier-transform infrared spectroscopy (FTIR) to predict rumen dry matter (DM) and neutral detergent fiber (NDF) degradation parameters of a wide range of feeds for ruminants, as an alternative to the in situ method. In total, 663 samples comprising 80 different feed types were analyzed. In situ DM and NDF degradabilities were determined as follows: effective degradability (ED), rumen soluble fraction (A), degradable but not soluble fraction (B), rate of degradation of the B fraction (C), and indigestible NDF (iNDF). Infrared spectra of dry samples were collected by attenuated total reflectance from 600 to 4000 cm −1 . Feeds were randomly classified into 2 subsets of samples with representation of all feed types; one subset was used to develop regression models using partial least squares, and the second subset was used to conduct an external validation of the models. This study indicated that universal models containing all feed types and specific models containing concentrate feeds could provide only a relatively poor estimation of in situ DM degradation parameters because of compositional heterogeneity. More research, such as a particle size distribution analysis, is required to determine whether this lack of accuracy was due to limitations of the FTIR approach, or simply due to methodological error associated with the in situ method. This latter hypothesis may explain the low accuracy observed in the prediction of degradation rates if there was physical leakage of fine particles from the mesh bags used during in situ studies. In contrast, much better predictions were obtained when models were developed for forage feeds alone. Models for forages led to accurate predictions of DM A , DM B , NDF ED , and NDF concentration (R 2 = 0.91, 0.89, 0.85, and 0.79, standard error = 4.34, 5.97, 4.59, and 4.41% of DM, respectively), and could be used for screening of DM ED , NDF C , and iNDF.
Polyphenol oxidase (PPO) genes and their corresponding enzyme activities occur in many plants; na... more Polyphenol oxidase (PPO) genes and their corresponding enzyme activities occur in many plants; natural PPO substrates and enzyme/substrate localization are less well characterized. Leaf and root PPO activities in Arabidopsis and five legumes were compared with those of high-PPO red clover (Trifolium pratense L.). Red clover PPO enzyme activity decreased leaves > stem > nodules > peduncle = petiole > embryo; PPO1 and PPO4 genes were expressed early in leaf emergence, whereas PPO4 and PPO5 predominated in mature leaves. PPO1 was expressed in embryos and nodules. PPO substrates, phaselic acid and clovamide, were detected in leaves, and clovamide was detected in nodules. Phaselic acid and clovamide, along with caffeic and chlorogenic acids, were suitable substrates for PPO1, PPO4, and PPO5 genes expressed in alfalfa (Medicago sativa L.) leaves. PPO enzyme presence and activity were colocalized in leaves and nodules by cytochemistry. Substrates and PPO activity were localized in developing squashed cell layer of nodules, suggesting PPO may have a developmental role in nodules.
The effect of the tetrapyrrole biosynthesis inhibitor gabaculine on the expression of specific ge... more The effect of the tetrapyrrole biosynthesis inhibitor gabaculine on the expression of specific genes involved in phycocyanin biosynthesis was investigated in cultures of Synechococcus PCC6301 in nitrogen chlorosis, and during recovery to nitrogen sufficiency.
Glutamate-l-semialdehyde (GSA) aminotransferase catalyses the final step in the C5 pathway conver... more Glutamate-l-semialdehyde (GSA) aminotransferase catalyses the final step in the C5 pathway converting glutamate to the tetrapyrrole precursor δ-aminolaevulinic acid. This enzyme is sensitive to gabaculine (2,3-dihydro-3-amino benzoic acid) and to 4-amino-5-fluoropentanoic acid (AFPA), which are irreversible, mechanism-based inhibitors of pyridoxal phosphatedependent enzymes. Spontaneous mutants of Synechococcus PCC6301 resistant to these inhibitors contain altered enzyme that displays corresponding resistance to high concentrations of the inhibitor. The enzyme from strain GR6, resistant to both inhibitors, contains a three-amino-acid deletion at positions 5-7 and a Met#%) Ile substitution. The enzyme from strain K40 resistant to AFPA but not to gabaculine, contains a Ser"'$ Thr substitution. GSA aminotransferases containing either the deletion or the substitution that are characteristic of the GR6 mutant were produced in Escherichia coli using the expression vector pMalc2. These engineered mutant enzymes were characterized in terms of their catalytic parameters and sensitivities to gabaculine and AFPA. Furthermore, maltose binding protein\aminotransferase fusion proteins were characterized spectrophotometrically to monitor the interaction of bound cofactor with diamino-and dioxocompounds related to the substrate and both inhibitors. Results were compared with those for similarly produced recombinant wild-type, K40 and GR6 GSA aminotransferases. The engineered products with either the N-terminal deletion or the Met#%) Ile substitution displayed catalytic efficiencies that were intermediate between the wild-type and GR6 or K40 enzymes. However, with respect to their absorption spectra, sensitivity to inhibitors and the reactivity of bound cofactor, they were essentially wild-type. These in vitro studies demonstrate that both changes in enzyme structure are necessary to obtain the distinctive properties of the GR6 aminotransferase, including resistance to high concentrations of gabaculine and AFPA.
Consecutive batch cultures (CBC), involving nine serial transfers at 3, 5 and 7 d intervals (21, ... more Consecutive batch cultures (CBC), involving nine serial transfers at 3, 5 and 7 d intervals (21, 45 and 63 d, respectively) were established to enrich for plant fibre degrading co-cultures of anaerobic fungi and methanogens from rumen digesta. Microbial diversity and fermentation end-products were measured at appropriate intervals over each CBC time-course. While methanogenic populations remained diverse, anaerobic fungal diversity was related to transfer interval and appeared to decrease with increasing transfer number. Acetate was the principal aqueous fermentation end-product with minimal quantities of lactate and formate detected. Methane and carbon dioxide were detected in the gaseous head-space of all co-cultures and the total amounts of gas generated per transfer was greater with transfer intervals of 5 and 7 d compared with a 3 d interval, although the 3 d interval tended to be more efficient per unit time. In conclusion, rapidly growing, methane producing co-cultures of anaerobic fungi and methanogens from rumen digesta were easy to establish on lignocellulose (barley straw) and maintain over considerable time periods. These results suggest such co-cultures have potential in industrial scale anaerobic digestion (AD) of highly fibrous substrates, which are resistant to degradation in conventional AD plants.
BACKGROUND AND AIMS: Species and hybrids of the genus Miscanthus contain attributes that make the... more BACKGROUND AND AIMS: Species and hybrids of the genus Miscanthus contain attributes that make them front-runners among current selections of dedicated bioenergy crops. A key trait for plant biomass conversion to biofuels and biomaterials is cell-wall quality; however, knowledge of cell-wall composition and biology in Miscanthus species is limited. This study presents data on cell-wall compositional changes as a function of development and tissue type across selected genotypes, and considers implications for the development of miscanthus as a sustainable and renewable bioenergy feedstock. METHODS: Cell-wall biomass was analysed for 25 genotypes, considering different developmental stages and stem vs. leaf compositional variability, by Fourier transform mid-infrared spectroscopy and lignin determination. In addition, a Clostridium phytofermentans bioassay was used to assess cell-wall digestibility and conversion to ethanol. KEY RESULTS: Important cell-wall compositional differences between miscanthus stem and leaf samples were found to be predominantly associated with structural carbohydrates. Lignin content increased as plants matured and was higher in stem tissues. Although stem lignin concentration correlated inversely with ethanol production, no such correlation was observed for leaves. Leaf tissue contributed significantly to total above-ground biomass at all stages, although the extent of this contribution was genotype-dependent. CONCLUSIONS: It is hypothesized that divergent carbohydrate compositions and modifications in stem and leaf tissues are major determinants for observed differences in cell-wall quality. The findings indicate that improvement of lignocellulosic feedstocks should encompass tissue-dependent variation as it affects amenability to biological conversion. For gene-trait associations relating to cell-wall quality, the data support the separate examination of leaf and stem composition, as tissue-specific traits may be masked by considering only total above-ground biomass samples, and sample variability could be mostly due to varying tissue contributions to total biomass.
The efficiency of proteins of legume forages in ruminant nutrition is poor because of their exten... more The efficiency of proteins of legume forages in ruminant nutrition is poor because of their extensive degradation in the rumen. The objective of this study was to evaluate the variation available for protein degradation in tannin-free (alfalfa and white clover) and tannin-rich (Lotus sp.) legume species. Protein and dry matter degradation were measured by in sacco incubation of forage samples in the rumen of fistulated cows, for 2, 8 or 48 h. Condensed tannin content was measured on Lotus samples. Variation in protein degradation was low among alfalfa and white clover cultivars, but the degradation was more important for alfalfa than for clover cultivars. Protein degradation was less important in Lotus sp. than in alfalfa or clover, and the variation among Lotus cultivars was mainly related to condensed tannin content.
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Papers by Gordon Allison
As a strategy to optimise bio-energy and bio-refining applications, an increasing amount of effort is being put into the advancement of our knowledge concerning the cell wall compositional roots of recalcitrance. Fourier transform mid-infrared spectroscopy (FTIR) represents a very useful tool on this enterprise, as it allows for a high-throughput, non-destructive and low unit cost procedure for the examination of cell wall biomass. Furthermore, the use of Attenuated Total Reflection (ATR) in conjunction with infrared spectroscopy (IR) enables cell wall biomass samples to be examined in solid state without extensive preparation. Nonetheless, the analysis of purified cell wall preparations instead of the intact plant biomass is highly recommended, as it minimises or even eradicates interference from biomass components which are not part of the cell wall. Further information regarding the fundamentals of FTIR may be found elsewhere.
Datasets generated from FTIR spectroscopy can be extensive and complex. In these situations, data-driven modelling techniques are often used as exploratory approaches to identify the most distinctive features of the collected spectra. Here we suggest the use of Principal Component Analysis (PCA), a frequently employed method to transform a large set of variables into a smaller set of new variables (principal components), effectively reducing dataset dimensionality.
When the aim is a complete and detailed biomass characterisation, the FTIR-PCA method here described does not exclude the need for parallel wet gravimetric and analytical procedures. However, it does lead to a rapid identification of the major compositional shifts across large sets of samples; thus contributing to steer research pathways, minimise time-draining analytical procedures and reduce overall research costs.
As a strategy to optimise bio-energy and bio-refining applications, an increasing amount of effort is being put into the advancement of our knowledge concerning the cell wall compositional roots of recalcitrance. Fourier transform mid-infrared spectroscopy (FTIR) represents a very useful tool on this enterprise, as it allows for a high-throughput, non-destructive and low unit cost procedure for the examination of cell wall biomass. Furthermore, the use of Attenuated Total Reflection (ATR) in conjunction with infrared spectroscopy (IR) enables cell wall biomass samples to be examined in solid state without extensive preparation. Nonetheless, the analysis of purified cell wall preparations instead of the intact plant biomass is highly recommended, as it minimises or even eradicates interference from biomass components which are not part of the cell wall. Further information regarding the fundamentals of FTIR may be found elsewhere.
Datasets generated from FTIR spectroscopy can be extensive and complex. In these situations, data-driven modelling techniques are often used as exploratory approaches to identify the most distinctive features of the collected spectra. Here we suggest the use of Principal Component Analysis (PCA), a frequently employed method to transform a large set of variables into a smaller set of new variables (principal components), effectively reducing dataset dimensionality.
When the aim is a complete and detailed biomass characterisation, the FTIR-PCA method here described does not exclude the need for parallel wet gravimetric and analytical procedures. However, it does lead to a rapid identification of the major compositional shifts across large sets of samples; thus contributing to steer research pathways, minimise time-draining analytical procedures and reduce overall research costs.