
James William AllwoodUniversity of Dundee · Leverhulme Research Centre for Forensic Science
James William Allwood
BSc Microbio PhD Plant Metabol
About
166
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Introduction
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September 1999 - June 2006
Publications
Publications (166)
Profiling of secondary metabolites within Fragaria sp. (strawberry), Rubus sp. (raspberries and blackberries), and Ribes sp. (blackcurrants and redcurrants) is of key importance with respect to the nutritional (antioxidant) benefits associated with a range of polyphenol classes within such fruits and how they vary between growth environment and sea...
Objective
The objective of this study was to investigate the genetic control of polyphenol accumulation in red raspberry ( Rubus idaeus L).
Methods
The levels of total anthocyanins and 37 individual polyphenol metabolites were measured over three years in a raspberry biparental mapping population. Quantitative trait loci (QTLs) for these traits we...
The metabolic profiles of different tissues and industrially relevant co-products of alginate extraction from Laminaria hyperborea samples harvested in different seasons were assessed using Hydrophilic Interaction Liquid Chromatography – Mass Spectrometry (HILIC-MS). Positive and negative mode MS data, predicted exact mass data and matching with da...
Disruption of microvascular architecture is a common pathogenic mechanism in the progression of Alzheimer's disease (AD). Given the anti-angiogenic activity of berry (poly)phenols, we investigated whether long-term feeding of Rubus idaeus (raspberries) could ameliorate cerebral microvascular pathology and improve cognition in the APP/PS-1 mouse mod...
In red raspberry, a condition known as ‘crumbly’ fruit causes the formation of misshapen fruits with drupelets reduced in number but enlarged in size. Complex fruits such as those of raspberry, formed by the aggregation of many fertilised ovaries, require a regulating mechanism to coordinate and synchronise their growth and development. The recepta...
Lonicera caeruleabrix is a perennial shrub native to North America, Europe and Asia. It produces dark blue berries known as honeyberries or haskap berries which are produced commercially in several territories including Canada, Japan, Russia and Poland. Plants are suited to UK environments, but it is yet to be widely commercially developed in the U...
This work aims to determine the effect of genotype x environment (GxE) interaction that influence blackcurrant (Ribes nigrum) fruit quality. We applied metabolomics-driven analysis on fruits from four cultivars grown in contrasting European-locations over two seasons. By integrating metabolomics and sensory analysis, we also defined specific metabo...
BACKGROUND: Berry pomaces obtained after commercial juice production contain phytochemicals which may find use as antioxidants, food additives and biomedical products. Oil extraction from seeds provides additional value but the availability of phytochemicals before and after oil extraction is not well established. OBJECTIVE: This pilot study define...
Honey is known to have antimicrobial, immunomodulatory and wound healing properties. The biological properties of honey have been attributed to phytochemicals derived from their source plants and research has focused on identifying the bioactive phytochemi-cals with therapeutic potential. In this study, we determined the ability of 5 honeys from Ka...
In this work, Hydrophilic Interaction Liquid Chromatography – Mass Spectrometry (HILIC-MS) was applied to assess the metabolic profiles of different tissues and industrially relevant co-products of alginate extraction from Laminaria hyperborea samples obtained in different seasons.
This is the first metabolomic analysis in L. hyperborea and it allo...
The influence of genotype and domestic processing on iron and zinc bioavailability in common bean germplasm was investigated using an in vitro digestion model. Raw beans exhibited diversity in iron content (50 to > 90 mg kg⁻¹) although zinc content was similar (30-40 mg kg⁻¹). Following preparation by different household cooking methods < 5% of the...
Background
Antimicrobial drug resistance is a major public health threat that can render infections including wound and skin infections untreatable. The discovery of new antimicrobials is critical. Approaches to discover novel antimicrobial therapies have included investigating the antimicrobial activity of natural sources such as honey. In this st...
Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global...
The metabolic profile of seaweeds can fluctuate depending on environmental factors and biotic/abiotic stresses. Osmundea pinnatifida is a red alga, known as Pepper Dulse in the UK, harvested from the wild and sold as seasoning due to its unique peppery taste. This paper highlights the seasonal variation in the compositional profile of biomass harve...
PurposeStudies on broccoli (Brassica oleracea var. italica) indicate beneficial effects against a range of chronic diseases, commonly attributed to their bioactive phytochemicals. Sulforaphane, the bioactive form of glucoraphanin, is formed by the action of the indigenous enzyme myrosinase. This study explored the role that digestion and cooking pr...
Oats (Avena sativa L.) are a healthy food, being high in dietary fibre (e.g. β-glucans), antioxidants, minerals, and vitamins. Understanding the effect of variety and crop management on nutritional quality is important. The response of four oat varieties to increased nitrogen levels was investigated across multiple locations and years with respect...
In this work, a new magnetic ligand fishing probe for discovery of DPP-IV inhibitory ligands was developed and it was tested as a proof of concept on the fruit extract of Vaccinium vitis-idaea (lingonberry). The ligands were shown to have appreciable dipeptidyl peptidase IV (DPP-IV) inhibitory activity (IC50: 31.8 μg mL-1).) Inhibition of DPP-IV is...
Diets rich in fruit and vegetables are associated with a decreased incidence of colorectal cancer (CRC) due, in part, to the bioactive (poly)phenolic components and their microbiota-mediated metabolites. This study investigated how such compounds, derived from ingested raspberries in the gastrointestinal tract, may exert protective effects by reduc...
Cichorium intybus L. has recently gained major attention due to large quantities of health-promoting compounds in its roots, such as inulin and sesquiterpene lactones (SLs). Chicory is the main dietary source of SLs, which have underexplored bioactive potential. In this study, we assessed the capacity of SLs to permeate the intestinal barrier to be...
Fruit quality, that remains crucial to human nutrition and health, is closely related to biochemical composition, mostly, although not only, due to low molecular-weight metabolites. Final fruit quality results from coordinated physiological processes during development from anthesis to growth and ripe stages. Fruit development and quality may be mo...
Phenolic components from the edible brown seaweed, Ascophyllum nodosum, have been associated with considerable antioxidant activity but also bioactivities related to human health. This study aims to select and identify the main phlorotannin components from this seaweed which have been previously associated with potential health benefits. Methods to...
Potato, S. tuberosum, is one of the most important global crops, but has high levels of waste due to tuber greening under light, which is associated with the accumulation of neurotoxic glycoalkaloids. However, unlike the situation in de-etiolating seedlings, the mechanisms underlying tuber greening are not well understood. Here, we have investigate...
A hydroxycinnamate-like component was identified in highbush blueberry (Vaccinium corymbosum) fruit, which had identical UV and mass spectrometric properties to an S-linked glutathionyl conjugate of chlorogenic acid synthesized using a peroxidase-catalyzed reaction. The conjugate was present in fruits from all highbush blueberry genotypes grown in...
The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotypin...
Despite considerable research the evidence around the antidiabetic properties of cinnamon remains equivocal, and this may be due to varietal differences which is an aspect that is understudied. This study systematically compared the anti-hyperglycaemic properties of the four major commercial cinnamon types used around the world (Chinese; Cinnamomum...
Respiration of bulky plant organs such as fleshy fruits depends on oxygen (O2) availability and often decreases with O2 concentration to avoid anoxia, but the relationship between O2 diffusional resistance and metabolic adjustments remains unclear. Melon fruit (Cucumis melo L.) was used to study relationships between O2 availability and metabolism...
Plant material rich in anthocyanins has been historically used in traditional medicines, but only recently have the specific pharmacological properties of these compounds been the target of extensive studies. In addition to their potential to modulate the development of various diseases, coloured anthocyanins are valuable natural alternatives commo...
Introduction
Oats (Avena sativa L.) are a whole grain cereal recognised for their health benefits and which are cultivated largely in temperate regions providing both a source of food for humans and animals, as well as being used in cosmetics and as a potential treatment for a number of diseases. Oats are known as being a cereal source high in diet...
The article Answering biological questions by analysis of the strawberry metabolome, written by Annika Haugeneder, Johanna Trinkl, Katja Härtl, Thomas Hoffman, James William Allwood and Wilfred Schwab, was originally published electronically on the publisher’s internet portal (currently SpringerLink) on 26 OCtober, 2018 without open access. After p...
Introduction
Blackcurrant (Ribes nigrum L.) is an excellent example of a “super fruit” with potential health benefits. Both genotype and cultivation environment are known to affect the chemical composition of blackcurrant, especially ascorbic acid and various phenolic compounds. Environmental conditions, like temperature, solar radiation and precip...
Fig. S1 Forskolin does not inhibit the effect of AICAR on glucose production or AMPK signalling. Primary mouse hepatocytes were incubated for 8 hours with forskolin (FSK; 100μM) in the presence or absence of metformin (Met; 250 μM) or AICAR (250 μM). The amount of glucose produced was measured as in Figure 1A. Data is expressed as mean ± SEM from t...
Clostridium difficile virulence is driven primarily by the processes of toxinogenesis and sporulation, however many in vitro experimental systems for studying C. difficile physiology have arguably limited relevance to the human colonic environment. We therefore created a more physiologically–relevant model of the colonic milieu to study gut pathoge...
Edible berries are considered to be among nature’s treasure chests as they contain a large number of (poly)phenols with potentially health-promoting properties. However, as berries contain complex (poly)phenol mixtures, it is challenging to associate any interesting pharmacological activity with a single compound. Thus, identification of pharmacolo...
Background
The qualitative and quantitative analysis of all low molecular weight metabolites within a biological sample, known as the metabolome, provides powerful insights into their roles in biological systems and processes. The study of all the chemical structures, concentrations, and interactions of the thousands of metabolites is called metabo...
Blackcurrant fruit collected at six stages of development were assessed for changes in gene expression using custom whole transcriptome microarrays and for variation in metabolite content using a combination of liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. Principal components analysis demonstrated that fruit dev...
Overview of changes in fruit chemistry during development. An illustration of the six stages of fruit development are shown at the top of the figure. Horizontal bars indicate the relative abundance of different groups of compounds during fruit development.
Significantly enriched gene ontology terms amongst transcripts assigned to six K means clusters dependent on changes in abundance during fruit development.
Comparison of relative abundance of transcripts as estimated by microarray analysis and qRT-PCR. Transcripts were chosen as representative of each of the K-means patterns of expression as indicated in Figure 5. Relative abundance was estimated from the average normalized fluorescence of the appropriate microarray or by the 2-ΔΔCt method (Livak and...
Transcripts encoding transcription factors exhibiting significant differences in abundance during fruit development.
Transcripts encoding proteins associated with hormone metabolism and signaling exhibiting significant differences in abundance during fruit development. Transcripts associated with metabolisms and signaling of cytokinin (A), auxin (B), gibberellin (C), ethylene (D), abscisic acid (E), brassinosteroid (F), jasmonate (G), and salicylate (H) are liste...
Primers used for qRT-PCR.
Transcripts exhibiting significant changes in abundance during fruit development.
Dry matter content of developing blackcurrant fruit. Dry matter content was estimated following lyophilisation of a single sample comprising 100 fresh fruit as dry weight × 100/fresh weight.
Relative proportion of differentially abundant transcripts associated with specific GO terms at different stages of fruit development. White bars indicate the proportion of significantly differentially abundant transcripts within each GO term identifier amongst all of the transcripts differentially abundant at different stages of fruit development:...
Change in relative abundance of chemicals at six different stages of fruit development.
Metabolomics-based approaches were applied to understand interactions of trimethoprim with Escherichia coli K-12 at sub-minimum inhibitory concentrations (MIC≈0.2, 0.03 and 0.003 mg L⁻¹). Trimethoprim inhibits dihydrofolate reductase and thereby is an indirect inhibitor of nucleic acid synthesis. Due to the basicity of trimethoprim, two pH levels (...
Growth curves of E. coli K-12 (at pH 7 in LB) exposed to different concentrations of trimethoprim.
Blue indicates control samples (0 mg L-1); red 8 mg L-1; green 2 mg L-1; purple 0.3 mg L-1; turquoise 0.2 mg L-1; orange 0.03 mg L-1 and light blue 0.003 mg L-1.
(PNG)
General scheme of sample preparation for FT-IR and GC-MS.
Sample preparation includes: (1) analysis by Bioscreen to determine the MIC of trimethoprim and produce the growth curves of E. coli K-12 at pH 5 and 7 with and without drug challenge. (2) FT-IR analysis of samples after washing with normal saline. (3) GC-MS analysis of samples after quenchi...
FT-IR spectra before and after CO2 removal and EMSC scaling.
(a) FT-IR spectra obtained from E. coli K-12 after exposure to four concentrations of trimethoprim (0.2, 0.03, 0.003 and 0 mg L-1) at two different pH values (5 and 7). (b) FT-IR spectra post CO2 removed at ≈ 2350 cm-1 and EMSC scaling.
(PNG)
List of metabolites detected by GC-MS.
Metabolites after extraction from control and stressed E. coli K-12 with trimethoprim at two different pH levels (5 and 7) are shown.
(XLSX)
FT-IR spectra obtained from E. coli K-12.
(a) After exposure to four concentrations of trimethoprim (0.2, 0.03, 0.003 and 0 mg L-1) at three different pH values (pH 5, 7 and 9). There were six biological replicates for each condition; each replicate was analysed three times, totalling 18 spectra for each condition (total number of spectra = 216). (...
Supporting methods and results.
Further description of methods and results.
(PDF)
Optical microscopic image of E. coli grown under different conditions.
Magnification: ×100. E. coli K-12 inoculated in LB medium at different pH levels: (a) pH 5; (b) pH 7; (c) pH 9.
(PNG)
Growth curves of E. coli K-12 exposed to different concentrations of trimethoprim.
(a) Chemical structure of trimethoprim (blue circles show the main ionization points on the structure in acidic media). Blue indicates growth curves of control samples (0 mg L-1); red 0.003 mg L-1; green 0.03 mg L-1and purple 0.2 mg L-1 at (b) pH 9, (c) pH 7 and (d)...
FT-IR multi-block PCA scores plot.
The plot shows the distribution of samples with different pH levels at different drug concentrations: (a) 0 mg L-1, (b) 0.003 mg L-1, (c) 0.03 mg L-1 and (d) 0.2 mg L-1.
(PNG)
KEGG metabolic pathway of E. coli K-12 MG1655.
The map highlights significant metabolites with their relative levels subjected to different concentrations of trimethoprim at different pH levels.
(PNG)
General scheme of sample preparation for LC-MS.
Sample preparation includes: (1) analysis by Bioscreen to produce the growth curves of E. coli K-12 at pH 5 and 7 after challenge with 0.8 mg L-1 of trimethoprim added at two time points: (I) at the beginning of the lag phase (time = 0 h) and (II) at the mid-exponential phase (time = 5 h). (2) LC-MS a...
Aim
Recently we have observed differences in the ability of metformin and AICAR to repress glucose production from hepatocytes using 8CPT‐cAMP. Previous results indicate that besides activating protein kinase A, 8CPT‐modified cAMP analogues suppress the Nitrobenzylthioinosine (NBMPR)‐sensitive equilibrative nucleoside transporter ENT1. We aimed to...
In the hunt for novel chemometric and biostatistical tools suitable for the automated mining of large metabolite profiling and fingerprinting data sets, the application of well‐established statistical tools appears to have been neglected. Using a data set that aims to understand the contributions that the metabolome can make to the prediction of th...
The reduction of the environmental footprint of crop production without compromising crop yield and their nutritional value is a key goal for improving the sustainability of agriculture. In 2009, the Balruddery Farm Platform was established at The James Hutton Institute as a long-term experimental platform for cross-disciplinary research of crops u...