Sue M. Aspinall

A rapid and robust method of identifying transformed Arabidopsis thaliana seedlings following floral dip transformation

BackgroundThe floral dip method of transformation by immersion of inflorescences in a suspension of Agrobacterium is the method of choice for Arabidopsis transformation. The presence of a marker, usually antibiotic- or herbicide-resistance, allows identification of transformed seedlings from untransformed seedlings. Seedling selection is a lengthy process which does not always lead to easily identifiable transformants. Selection for kanamycin-, phosphinothricin- and hygromycin B-resistance commonly takes 7–10 d and high seedling density and fungal contamination may result in failure to recover transformants.ResultsA method for identifying transformed seedlings in as little as 3.25 d has been developed. Arabidopsis T1 seeds obtained after floral dip transformation are plated on 1% agar containing MS medium and kanamycin, phosphinothricin or hygromycin B, as appropriate. After a 2-d stratification period, seeds are subjected to a regime of 4–6 h light, 48 h dark and 24 h light (3.25 d). Kanamycin-resistant and phosphinothricin-resistant seedlings are easily distinguished from non-resistant seedlings by green expanded cotyledons whereas non-resistant seedlings have pale unexpanded cotyledons. Seedlings grown on hygromycin B differ from those grown on kanamycin and phosphinothricin as both resistant and non-resistant seedlings are green. However, hygromycin B-resistant seedlings are easily identified as they have long hypocotyls (0.8–1.0 cm) whereas non-resistant seedlings have short hypocotyls (0.2–0.4 cm).ConclusionThe method presented here is an improvement on current selection methods as it allows quicker identification of transformed seedlings: transformed seedlings are easily discernable from non-transformants in as little as 3.25 d in comparison to the 7–10 d required for selection using current protocols.

Localized hypermutation and associated gene losses in legume chloroplast genomes

Point mutations result from errors made during DNA replication or repair, so they are usually expected to be homogeneous across all regions of a genome. However, we have found a region of chloroplast DNA in plants related to sweetpea (Lathyrus) whose local point mutation rate is at least 20 times higher than elsewhere in the same molecule. There are very few precedents for such heterogeneity in any genome, and we suspect that the hypermutable region may be subject to an unusual process such as repeated DNA breakage and repair. The region is 1.5 kb long and coincides with a gene, ycf4, whose rate of evolution has increased dramatically. The product of ycf4, a photosystem I assembly protein, is more divergent within the single genus Lathyrus than between cyanobacteria and other angiosperms. Moreover, ycf4 has been lost from the chloroplast genome in Lathyrus odoratus and separately in three other groups of legumes. Each of the four consecutive genes ycf4-psaI-accD-rps16 has been lost in at least one member of the legume inverted repeat loss clade, despite the rarity of chloroplast gene losses in angiosperms. We established that accD has relocated to the nucleus in Trifolium species, but were unable to find nuclear copies of ycf4 or psaI in Lathyrus. Our results suggest that, as well as accelerating sequence evolution, localized hypermutation has contributed to the phenomenon of gene loss or relocation to the nucleus.

Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes

Tomato, Solanum lycopersicum (formerly Lycopersicon esculentum), has long been one of the classical model species of plant genetics. More recently, solanaceous species have become a model of evolutionary genomics, with several EST projects and a tomato genome project having been initiated. As a first contribution toward deciphering the genetic information of tomato, we present here the complete sequence of the tomato chloroplast genome (plastome). The size of this circular genome is 155,461 base pairs (bp), with an average AT content of 62.14%. It contains 114 genes and conserved open reading frames (ycfs). Comparison with the previously sequenced plastid DNAs of Nicotiana tabacum and Atropa belladonna reveals patterns of plastid genome evolution in the Solanaceae family and identifies varying degrees of conservation of individual plastid genes. In addition, we discovered several new sites of RNA editing by cytidine-to-uridine conversion. A detailed comparison of editing patterns in the three solanaceous species highlights the dynamics of RNA editing site evolution in chloroplasts. To assess the level of intraspecific plastome variation in tomato, the plastome of a second tomato cultivar was sequenced. Comparison of the two genotypes (IPA-6, bred in South America, and Ailsa Craig, bred in Europe) revealed no nucleotide differences, suggesting that the plastomes of modern tomato cultivars display very little, if any, sequence variation.

Phytoestrogen content of foods of animal origin: dairy products, eggs, meat, fish, and seafood.

Dietary phytoestrogens may be involved in the occurrence of chronic diseases. Reliable information on the phytoestrogen content in foods is required to assess dietary exposure and disease risk in epidemiological studies. However, existing analyses have focused on only one class of these compounds in plant-based foods, and there is only little information on foods of animal origin, leading to an underestimation of intake. This is the first comprehensive study of phytoestrogen content in animal food. We have determined the phytoestrogen content (isoflavones: biochanin A, daidzein, formononetin, genistein, and glycitein; lignans: secoisolariciresinol and matairesinol; coumestrol; equol; enterolactone; and enterodiol) in 115 foods of animal origin (including milk and milk-products, eggs, meat, fish, and seafood) and vegetarian substitutes using liquid chromatography-mass spectrometry (LC-MS) with (13)C-labeled internal standards. Phytoestrogens were detected in all foods analyzed; the average content was 20 microg/100 g of wet weight (isoflavones, 6 microg/100 g; lignans, 6 microg/100 g; equol, 3 microg/100 g; and enterolignans, 6 microg/100 g). In infant soy formula, 19 221 microg/100 g phytoestrogens were detected (compared to 59 microg/100 g in non-soy formula). Our study shows that all foods analyzed contained phytoestrogens and most foods (except for fish, seafood, and butter) contained mammalian phytoestrogens (enterolignans and equol). This is the first comprehensive study of phytoestrogen content of foods of animal origin and will allow for a more accurate estimation of exposure to dietary phytoestrogens.

Effect of processed and red meat on endogenous nitrosation and DNA damage

Haem in red meat (RM) stimulates the endogenous production of mutagenic nitroso compounds (NOC). Processed (nitrite-preserved red) meat additionally contains high concentrations of preformed NOC. In two studies, of a fresh RM versus a vegetarian (VEG) diet (six males and six females) and of a nitrite-preserved red meat (PM) versus a VEG diet (5 males and 11 females), we investigated whether processing of meat might increase colorectal cancer risk by stimulating nitrosation and DNA damage. Meat diets contained 420 g (males) or 366 g (females) meat/per day. Faecal homogenates from day 10 onwards were analysed for haem and NOC and associated supernatants for genotoxicity. Means are adjusted for differences in male to female ratios between studies. Faecal NOC concentrations on VEG diets were low (2.6 and 3.5 mmol/g) but significantly higher on meat diets (PM 175 ± 19 nmol/g versus RM 185 ± 22 nmol/g; Pu2009=u20090.75). The RM diet resulted in a larger proportion of nitrosyl iron (RM 78% versus PM 54%; Pu2009<u20090.0001) and less nitrosothiols (RM 12% versus PM 19%; Pu2009<u20090.01) and other NOC (RM 10% versus PM 27%; Pu2009<u20090.0001). There was no statistically significant difference in DNA breaks induced by faecal water (FW) following PM and RM diets (Pu2009=u20090.80). However, PM resulted in higher levels of oxidized pyrimidines (Pu2009<u20090.05). Surprisingly, VEG diets resulted in significantly more FW-induced DNA strand breaks than the meat diets (Pu2009<u20090.05), which needs to be clarified in further studies. Meats cured with nitrite have the same effect as fresh RM on endogenous nitrosation but show increased FW-induced oxidative DNA damage.

Phytoestrogen Content of Beverages, Nuts, Seeds, and Oils

Phytoestrogens are secondary plant metabolites that have received increasing attention for their bioactivity, in particular due to their structural and functional similarity to 17beta-estradiol. Although urinary and plasma phytoestrogens can be used as biomarkers for dietary intake, this is often not possible in large epidemiological studies or in the assessment of general exposure in free-living individuals. Accurate information about dietary phytoestrogens is therefore important, but there are very limited data concerning food contents. In this study was analyzed a comprehensive selection of tea, coffee, alcoholic beverages, nuts, seeds, and oils for their phytoestrogen content using a newly developed sensitive method based on LC-MS incorporating (13)C 3-labeled standards. Phytoestrogens were detected in all foods analyzed, although the contents in gin and bitter (beer) were below the limit of quantification (1.5 microg/100 g). Lignans were the main type of phytoestrogens detected. Tea and coffee contained up to 20 microg/100 g phytoestrogens and beer (except bitter) contained up to 71 microg/100 g, mainly lignans. As these beverages are commonly consumed, they are a main source of dietary lignans. The results published here will contribute to databases of dietary phytoestrogen content and allow a more accurate determination of phytoestrogen exposure in free-living individuals.

Phytoestrogen content of cereals and cereal-based foods consumed in the UK.

Dietary phytoestrogens may be involved in the occurrence of chronic diseases. Reliable information on the phytoestrogen content in foods is required to assess dietary exposure and disease risk in epidemiological studies. However, there is little information on isoflavone, lignan, and coumestrol content of cereals and cereal-based foods, leading to an underestimation of intake. This is the first study of phytoestrogens (isoflavones: biochanin A, daidzein, formononetin, genistein, glycitein; lignans: matairesinol, secoisplariciresinol; coumestrol) in a comprehensive selection of 101 cereals and cereal-based foods—including breads, breakfast cereals, biscuits, pasta and rice—consumed in the UK using a sensitive LCMS technique with 13 C-labelled internal standards. Phytoestrogens were detected in all foods analyzed; bread contained the highest amount of phytoestrogens—many as isoflavones—with an average content of 375 ± 67 μ g/100 g wet weight (excluding soya-linseed bread with 12,000 μ g/100 g). Most other foods contained less than 100 μ g/100 g, many as lignans. Our study shows that all foods analyzed contained phytoestrogens, with the highest amount found in breads, making them one of the main sources of dietary phytoestrogens in the UK. These results will allow a more accurate estimation of exposure to dietary phytoestrogens.

GUN1 (GENOMES UNCOUPLED1) Encodes a Pentatricopeptide Repeat (PPR) Protein Involved in Plastid Protein Synthesis-Responsive Retrograde Signaling to the Nucleus

Plastid-to-nucleus signaling coordinates the expression of nuclear and plastid genes required for the assembly of functional chloroplasts. We have isolated new alleles of gun1 (genomes uncoupled1) by screening EMS-mutagenised lines of Arabidopsis thaliana containing the GFP reporter gene under the control of a tobacco RbcS promoter for GFP expression in the presence of norflurazon, a carotenoid biosynthesis inhibitor, or lincomycin, an inhibitor of plastid translation. gun1 mutants were able to express photosynthesis- related nuclear genes in the presence of lincomycin, unlike other gun (gun2-gun5) mutants. Microarray analysis identified CA1 (CARBONIC ANHYDRASE1) as the gene most responsive to lincomycin in wild-type seedlings, and a CA1 promoter::GFP reporter gene was used to map the gun1 mutation to a 224 kb region on chromosome 2. Sequencing of candidate genes identified GUN1 as At2g31400, encoding a pentatricopeptide repeat (PPR) protein of 918 amino acid residues. gun1-100 contained a point mutation creating a stop codon at amino acid 56, whereas gun1-1 contained a point mutation resulting in an Ala259Val change. GUN1-GFP fusion proteins were targeted to chloroplast nucleoids following microprojectile bombardment of Arabidopsis and tobacco leaves.

Association between sucrose intake and risk of overweight and obesity in a prospective sub-cohort of the European Prospective Investigation into Cancer in Norfolk (EPIC-Norfolk)

Objective The objective of the present study was to investigate associations between sugar intake and overweight using dietary biomarkers in the Norfolk cohort of the European Prospective Investigation into Cancer and Nutrition (EPIC-Norfolk). Design Prospective cohort study. Setting EPIC-Norfolk in the UK, recruitment between 1993 and 1997. Subjects Men and women (n 1734) aged 39–77 years. Sucrose intake was assessed using 7 d diet diaries. Baseline spot urine samples were analysed for sucrose by GC-MS. Sucrose concentration adjusted by specific gravity was used as a biomarker for intake. Regression analyses were used to investigate associations between sucrose intake and risk of BMI>25·0 kg/m2 after three years of follow-up. Results After three years of follow-up, mean BMI was 26·8 kg/m2. Self-reported sucrose intake was significantly positively associated with the biomarker. Associations between the biomarker and BMI were positive (β=0·25; 95 % CI 0·08, 0·43), while they were inverse when using self-reported dietary data (β=−1·40; 95 % CI −1·81, −0·99). The age- and sex-adjusted OR for BMI>25·0 kg/m2 in participants in the fifth v. first quintile was 1·54 (95 % CI 1·12, 2·12; P trend=0·003) when using biomarker and 0·56 (95 % CI 0·40, 0·77; P trend<0·001) with self-reported dietary data. Conclusions Our results suggest that sucrose measured by objective biomarker but not self-reported sucrose intake is positively associated with BMI. Future studies should consider the use of objective biomarkers of sucrose intake.

Effect of dietary meat and fish on endogenous nitrosation, inflammation and genotoxicity of faecal water

N-3 polyunsaturated fatty acids have been associated with reduced colon tumorigenesis. However, their association with colorectal cancer incidence is not conclusive. We investigated the influence of isocaloric replacement of red meat with fatty fish on endogenous nitrosation, inflammation and genotoxicity of faecal water in apparently healthy human volunteers on controlled diets. Fourteen volunteers consumed a high red meat, a combined red meat/fish and a high fish diet for 8 days each. Faecal homogenates were analysed for haem, nitroso compounds (NOC) and calprotectin and associated supernatants for genotoxicity. Both faecal NOC and haem excretion decreased with more fish and less meat in the diet. Nitrosyl iron (FeNO) was the main contributor to total NOC on all diets. The proportion of other NOC increased with more fish and less meat in the diet (P = 0.01), resulting in a non-statistically significant decrease in the proportion of FeNO on the fish diet. There was no statistically significant difference in faecal calprotectin (P = 0.54) and faecal water-induced DNA strand breaks and oxidized purines and pyrimidines between the diets (P > 0.36). Increasing fish intake and reducing the intake of red meat does not seem to have an effect on inflammation and faecal water-induced (oxidative) DNA damage; however, it does reduce the formation of mutagenic and potentially carcinogenic NOC and may as such beneficially affect colorectal risk.