Publications by authors named "Lenka Havlickova"

16 Publications

  • Page 1 of 1

Genome structural evolution in Brassica crops.

Nat Plants 2021 Jun 27;7(6):757-765. Epub 2021 May 27.

Department of Biology, University of York, York, UK.

The cultivated Brassica species include numerous vegetable and oil crops of global importance. Three genomes (designated A, B and C) share mesohexapolyploid ancestry and occur both singly and in each pairwise combination to define the Brassica species. With organizational errors (such as misplaced genome segments) corrected, we showed that the fundamental structure of each of the genomes is the same, irrespective of the species in which it occurs. This enabled us to clarify genome evolutionary pathways, including updating the Ancestral Crucifer Karyotype (ACK) block organization and providing support for the Brassica mesohexaploidy having occurred via a two-step process. We then constructed genus-wide pan-genomes, drawing from genes present in any species in which the respective genome occurs, which enabled us to provide a global gene nomenclature system for the cultivated Brassica species and develop a methodology to cost-effectively elucidate the genomic impacts of alien introgressions. Our advances not only underpin knowledge-based approaches to the more efficient breeding of Brassica crops but also provide an exemplar for the study of other polyploids.
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http://dx.doi.org/10.1038/s41477-021-00928-8DOI Listing
June 2021

A Reductase Gene Dissected by Associative Transcriptomics Enhances Plant Adaption to Freezing Stress.

Front Plant Sci 2020 26;11:971. Epub 2020 Jun 26.

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

Cold treatment (vernalization) is required for winter crops such as rapeseed ( L.). However, excessive exposure to low temperature (LT) in winter is also a stress for the semi-winter, early-flowering rapeseed varieties widely cultivated in China. Photosynthetic efficiency is one of the key determinants, and thus a good indicator for LT tolerance in plants. So far, the genetic basis underlying photosynthetic efficiency is poorly understood in rapeseed. Here the current study used Associative Transcriptomics to identify genetic loci controlling photosynthetic gas exchange parameters in a diversity panel comprising 123 accessions. A total of 201 significant Single Nucleotide Polymorphisms (SNPs) and 147 Gene Expression Markers (GEMs) were detected, leading to the identification of 22 candidate genes. Of these, Cab026133.1, an ortholog of the gene AT2G29300.2 encoding a tropinone reductase (), was further confirmed to be closely linked to transpiration rate. Ectopic expressing in plants significantly increased the transpiration rate and enhanced LT tolerance under freezing conditions. Also, a much higher level of alkaloids content was observed in the transgenic plants, which could help protect against LT stress. Together, the current study showed that AT is an effective approach for dissecting LT tolerance trait in rapeseed and that is a good target gene for the genetic improvement of LT tolerance in plant.
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http://dx.doi.org/10.3389/fpls.2020.00971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333310PMC
June 2020

Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits.

Plant J 2020 08 22;103(5):1885-1893. Epub 2020 Jul 22.

Department of Biology, University of York, Heslington, York, YO10 5DD, UK.

The development of more productive crops will be key to addressing the challenges that climate change, population growth and diminishing resources pose to global food security. Advanced 'omics techniques can help to accelerate breeding by facilitating the identification of genetic markers for use in marker-assisted selection. Here, we present the validation of a new Associative Transcriptomics platform in the important oilseed crop Brassica juncea. To develop this platform, we established a pan-transcriptome reference for B. juncea, to which we mapped transcriptome data from a diverse panel of B. juncea accessions. From this panel, we identified 355 050 single nucleotide polymorphism variants and quantified the abundance of 93 963 transcripts. Subsequent association analysis of functional genotypes against a number of important agronomic and quality traits revealed a promising candidate gene for seed weight, BjA.TTL, as well as additional markers linked to seed colour and vitamin E content. The establishment of the first full-scale Associative Transcriptomics platform for B. juncea enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.
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http://dx.doi.org/10.1111/tpj.14876DOI Listing
August 2020

Effect of Capsular Tension Ring Implantation on Postoperative Rotational Stability of a Toric Intraocular Lens.

J Refract Surg 2020 Mar;36(3):186-192

Purpose: To analyze clinical outcomes of cataract surgery with implantation of a toric intraocular lens (IOL) and to evaluate the effect of capsular tension ring (CTR) presence or absence on the rotational stability of implanted IOLs and postoperative refraction.

Methods: This cohort study included 64 eyes of 41 patients who underwent uneventful cataract surgery with implantation of a toric IOL (enVista toric MX60T; Bausch & Lomb, Rochester, NY) to correct preoperative corneal astigmatism. In 30 eyes, a CTR (11 SR model; Videris s.r.o., Prague, Czech Republic) was co-implanted. Analyzed parameters were refraction, visual acuity, and misalignment of toric lenses.

Results: The mean patient age was 67 years (range: 42 to 89 years) and the mean follow-up period was 5 months. Mean manifest astigmatism improved from -1.53 ± 1.15 diopters (D) preoperatively to -0.40 ± 0.61 D postoperatively (P < .001). Postoperative uncorrected distance visual acuity was 0.10 ± 0.13 logMAR (20/25 Snellen). Mean absolute IOL misalignment was 3.70° with CTR and 3.85° without CTR (P = .683). In eyes with an axial length of 24 mm or greater, IOL axis matched the planned axis in 90.5% of eyes with CTR and 81.8% of eyes without CTR (P = .964). Four eyes (6.25%) needed additional surgical IOL rotation.

Conclusions: In eyes after cataract surgery with implantation of a toric IOL, there were no significant differences in the rotational stability of the lens with respect to the presence or absence of CTR. In eyes with an axial length of 24 mm or greater, better IOL alignment was observed in the group with CTR. [J Refract Surg. 2020;36(3):186-192.].
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http://dx.doi.org/10.3928/1081597X-20200120-01DOI Listing
March 2020

Analysing the genetic architecture of clubroot resistance variation in by associative transcriptomics.

Mol Breed 2019 20;39(8):112. Epub 2019 Jul 20.

1Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic.

Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species ), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of . A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.
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http://dx.doi.org/10.1007/s11032-019-1021-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6647481PMC
July 2019

Species-Wide Variation in Shoot Nitrate Concentration, and Genetic Loci Controlling Nitrate, Phosphorus and Potassium Accumulation in L.

Front Plant Sci 2018 16;9:1487. Epub 2018 Oct 16.

Plant and Crop Sciences Division, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom.

Large nitrogen, phosphorus and potassium fertilizer inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertilizer use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of was characterized. Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localize with chromosomal regions associated with leaf P concentration. Orthologs of three ABC-transporters involved in suberin synthesis in roots also co-localize with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associated with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favorable alleles identified here may prove useful in marker-assisted selection strategies to improve fertilizer use efficiency in .
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http://dx.doi.org/10.3389/fpls.2018.01487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198146PMC
October 2018

AFLP reveals low genetic diversity of the bryozoan (Leidy, 1851) in the Czech Republic.

J Biol Res (Thessalon) 2017 Dec 25;24:12. Epub 2017 Nov 25.

Faculty of Agriculture, University of South Bohemia, 370 05 České Budějovice, Czech Republic.

Background: Non-native species have aroused scientific interest because of their ability to successfully colonise areas to which they have been introduced, despite their sometimes limited genetic variation compared to their native range. These species establish themselves with the aid of some pre-existing features favouring them in the new environment. (Leidy, 1851), the freshwater magnificent bryozoan, is non-native in Europe and Asia. This study was designed to determine the genetic diversity and population structure of colonies collected from the Protected Landscape Area (PLA) and UNESCO Biosphere Reserve Třeboňsko (the Czech Republic) in the 2009 and 2011-2014 periods using Amplified Fragment Length Polymorphism (AFLP).

Findings: The vast majority of the examined non-native colonies, except three colonies sampled in 2012, expressed very low levels of genetic variation, not differentiating from the USA native colony. The Bayesian clustering approach grouped the 28 accessions into two genetically different populations.

Conclusions: The data suggest relatively low gene diversity within all colonies, which might reflect the recent expansion of in the Czech Republic.
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http://dx.doi.org/10.1186/s40709-017-0069-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702124PMC
December 2017

Identification of Candidate Genes for Calcium and Magnesium Accumulation in L. by Association Genetics.

Front Plant Sci 2017 15;8:1968. Epub 2017 Nov 15.

Plant and Crop Sciences Division, University of Nottingham, Loughborough, United Kingdom.

Calcium (Ca) and magnesium (Mg) are essential plant nutrients and vital for human and animal nutrition. Biofortification of crops has previously been suggested to alleviate widespread human Ca and Mg deficiencies. In this study, new candidate genes influencing the leaf accumulation of Ca and Mg were identified in young plants using associative transcriptomics of ionomics datasets. A total of 247 and 166 SNP markers were associated with leaf Ca and Mg concentration, respectively, after false discovery rate correction and removal of SNPs with low second allele frequency. Gene expression markers at similar positions were also associated with leaf Ca and Mg concentration, including loci on chromosomes A10 and C2, within which lie previously identified transporter genes and . Further candidate genes were selected from seven loci and the mineral composition of whole shoots were characterized from lines mutated in orthologous genes. Four and two mutant lines had reduced shoot Ca and Mg concentration, respectively, compared to wild type plants. Three of these mutations were found to have tissue specific effects; notably reduced silique Ca in all three such mutant lines. This knowledge could be applied in targeted breeding, with the possibility of increasing Ca and Mg in plant tissue for improving human and livestock nutrition.
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http://dx.doi.org/10.3389/fpls.2017.01968DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694822PMC
November 2017

Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds.

Plant J 2018 Jan 2;93(1):181-192. Epub 2017 Dec 2.

Department of Biology, University of York, Heslington, York, YO10 5DD, UK.

An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 10 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single-nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high-erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor-effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take-one-out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ-tocopherol methyl transferase converting γ-tocopherol into α-tocopherol) associated with the observed trait variation. The establishment of the first full-scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.
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http://dx.doi.org/10.1111/tpj.13767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767744PMC
January 2018

Carbohydrate microarrays and their use for the identification of molecular markers for plant cell wall composition.

Proc Natl Acad Sci U S A 2017 06 12;114(26):6860-6865. Epub 2017 Jun 12.

Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom;

Genetic improvement of the plant cell wall has enormous potential to increase the quality of food, fibers, and fuels. However, the identification and characterization of genes involved in plant cell wall synthesis is far from complete. Association mapping is one of the few techniques that can help identify candidate genes without relying on our currently incomplete knowledge of cell wall synthesis. However, few cell wall phenotyping methodologies have proven sufficiently precise, robust, or scalable for association mapping to be conducted for specific cell wall polymers. Here, we created high-density carbohydrate microarrays containing chemically extracted cell wall polysaccharides collected from 331 genetically diverse cultivars and used them to obtain detailed, quantitative information describing the relative abundance of selected noncellulosic polysaccharide linkages and primary structures. We undertook genome-wide association analysis of data collected from 57 carbohydrate microarrays and identified molecular markers reflecting a diversity of specific xylan, xyloglucan, pectin, and arabinogalactan moieties. These datasets provide a detailed insight into the natural variations in cell wall carbohydrate moieties between genotypes and identify associated markers that could be exploited by marker-assisted breeding. The identified markers also have value beyond for functional genomics, facilitated by the close genetic relatedness to the model plant Together, our findings provide a unique dissection of the genetic architecture that underpins plant cell wall biosynthesis and restructuring.
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http://dx.doi.org/10.1073/pnas.1619033114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495229PMC
June 2017

Genome sequence and genetic diversity of European ash trees.

Nature 2017 01 26;541(7636):212-216. Epub 2016 Dec 26.

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.

Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.
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http://dx.doi.org/10.1038/nature20786DOI Listing
January 2017

Extensive homoeologous genome exchanges in allopolyploid crops revealed by mRNAseq-based visualization.

Plant Biotechnol J 2017 05 6;15(5):594-604. Epub 2016 Dec 6.

Department of Biology, University of York, Heslington, York, UK.

Polyploidy, the possession of multiple sets of chromosomes, has been a predominant factor in the evolution and success of the angiosperms. Although artificially formed allopolyploids show a high rate of genome rearrangement, the genomes of cultivars and germplasm used for crop breeding were assumed stable and genome structural variation under the artificial selection process of commercial breeding has remained little studied. Here, we show, using a repurposed visualization method based on transcriptome sequence data, that genome structural rearrangement occurs frequently in varieties of three polyploid crops (oilseed rape, mustard rape and bread wheat), meaning that the extent of genome structural variation present in commercial crops is much higher than expected. Exchanges were found to occur most frequently where homoeologous chromosome segments are collinear to telomeres and in material produced as doubled haploids. The new insights into genome structural evolution enable us to reinterpret the results of recent studies and implicate homoeologous exchanges, not deletions, as being responsible for variation controlling important seed quality traits in rapeseed. Having begun to identify the extent of genome structural variation in polyploid crops, we can envisage new strategies for the global challenge of broadening crop genetic diversity and accelerating adaptation, such as the molecular identification and selection of genome deletions or duplications encompassing genes with trait-controlling dosage effects.
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http://dx.doi.org/10.1111/pbi.12657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399007PMC
May 2017

Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics.

Sci Rep 2016 Jan 13;6:19335. Epub 2016 Jan 13.

Department of Biology, University of York, York, UK.

Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback.
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http://dx.doi.org/10.1038/srep19335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4725942PMC
January 2016

Detection of self-incompatible oilseed rape plants (Brassica napus L.) based on molecular markers for identification of the class I S haplotype.

Genet Mol Biol 2014 Sep;37(3):556-9

Biotechnological Centre, Faculty of Agriculture , University of South Bohemia , Ceské Budejovice , Czech Republic .

The selection of desirable genotypes with recessive characteristics, such as self-incompatible plants, is often difficult or even impossible and represents a crucial barrier in accelerating the breeding process. Molecular approaches and selection based on molecular markers can allow breeders to overcome this limitation. The use of self-incompatibility is an alternative in hybrid breeding of oilseed rape. Unfortunately, stable self-incompatibility is recessive and phenotype-based selection is very difficult and time-consuming. The development of reliable molecular markers for detecting desirable plants with functional self-incompatible genes is of great importance for breeders and allows selection at early stages of plant growth. Because most of these reliable molecular markers are based on discrimination of class I S-locus genes that are present in self-compatible plants, there is a need to use an internal control in order to detect possible PCR inhibition that gives false results during genotyping. In this study, 269 double haploid F2 oilseed rape plants obtained by microspore embryogenesis were used to verify the applicability of an improved PCR assay based on the detection of the class I SLG gene along with an internal control. Comparative analysis of the PCR genotyping results vs. S phenotype analysis confirmed the applicability of this molecular approach in hybrid breeding programs. This approach allows accurate detection of self-incompatible plants via a different amplification profile.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171774PMC
http://dx.doi.org/10.1590/s1415-47572014000400012DOI Listing
September 2014

Different stress responsive strategies to drought and heat in two durum wheat cultivars with contrasting water use efficiency.

BMC Genomics 2013 Nov 22;14:821. Epub 2013 Nov 22.

Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov,le Lecce Monteroni, I-73100 Lecce, Italy.

Background: Durum wheat often faces water scarcity and high temperatures, two events that usually occur simultaneously in the fields. Here we report on the stress responsive strategy of two durum wheat cultivars, characterized by different water use efficiency, subjected to drought, heat and a combination of both stresses.

Results: The cv Ofanto (lower water use efficiency) activated a large set of well-known drought-related genes after drought treatment, while Cappelli (higher water use efficiency) showed the constitutive expression of several genes induced by drought in Ofanto and a modulation of a limited number of genes in response to stress. At molecular level the two cvs differed for the activation of molecular messengers, genes involved in the regulation of chromatin condensation, nuclear speckles and stomatal closure. Noteworthy, the heat response in Cappelli involved also the up-regulation of genes belonging to fatty acid β-oxidation pathway, glyoxylate cycle and senescence, suggesting an early activation of senescence in this cv. A gene of unknown function having the greatest expression difference between the two cultivars was selected and used for expression QTL analysis, the corresponding QTL was mapped on chromosome 6B.

Conclusion: Ofanto and Cappelli are characterized by two opposite stress-responsive strategies. In Ofanto the combination of drought and heat stress led to an increased number of modulated genes, exceeding the simple cumulative effects of the two single stresses, whereas in Cappelli the same treatment triggered a number of differentially expressed genes lower than those altered in response to heat stress alone. This work provides clear evidences that the genetic system based on Cappelli and Ofanto represents an ideal tool for the genetic dissection of the molecular response to drought and other abiotic stresses.
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http://dx.doi.org/10.1186/1471-2164-14-821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046701PMC
November 2013

An evaluation of GC-MS and HPLC-FD methods for analysis of protein binders in paintings.

J Sep Sci 2006 Nov;29(17):2653-63

Department of Analytical Chemistry, Faculty of Science, Charles University in Prague, Albertov, Prague, Czech Republic.

Two chromatographic methods have been compared for analysis of protein-binding media used in paintings, namely, HPLC with fluorescence detection and GC-MS. The proteins were hydrolyzed to the corresponding amino acids (AAs) by gaseous HCl and the AAs were derivatized with methyl chloroformate, followed by GC-MS or by HPLC after derivatization with the AccQ fluorescence reagent. The hydrolysis, derivatization reactions and the chromatographic procedures have been optimized and applied to standard binding media, model and real samples of paintings. The methods have been compared and critically evaluated.
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http://dx.doi.org/10.1002/jssc.200600171DOI Listing
November 2006
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