EU safety regulations – Dont mar legislation with pseudoscience

328. Dietrich DR, Dekant W, Greim H, Heslop-Harrison P, Berry C, Boobis A, Hengstler JG, Sharpe R. 2016. EU safety regulations: Don’t mar legislation with pseudoscience. Nature 535: 355 (21 July 2016) doi:10.1038/535355c

We are concerned that some of the European Union’s processes for setting safety regulations for chemicals are being influenced by media and pseudoscience scaremongering. Pseudoscience has no place in such decisions, which should be based purely on well-defined and transparent evidence.

For example, endocrine disruptors are being blamed for obesity and type 2 diabetes (J. Legler et al. J. Clin. Endocrinol. Metab. 100, 12781288; 2015) despite the absence of supporting evidence for this, and despite food and sugar over-consumption being established as a proven cause. As a consequence, the European Commission’s criteria for regulating endocrine-disrupting compounds as a threat to human health are based on correlational, not causal, studies (see go.nature.com/29rjlik).

Conflicts of interest can contribute to the problem, beyond the commercial motivation of industry. Some non-governmental organizations might need to maintain public concerns to boost charitable donations. Decision-makers might prefer to disregard evidence-based data that contradict a precautionary viewpoint. And some scientists put securing research funds above objective appraisal of the evidence.

Acting on hazard identification alone relieves the scaremongering party of the burden of proof, when harm is simply assumed. As a result, regulations can become unnecessarily restrictive. They may even be damaging, for example if an agricultural ban were to be imposed on triazole fungicides because of their endocrine-disrupting potential. The risk to humans at such levels of exposure would be negligible (J. E. Chambers et al. Crit. Rev. Toxicol. 44, 176210; 2014). It makes no sense to override such evidence with a blanket ban on potentially hazardous chemicals that ignores the public’s demonstrable low level of exposure.

http://www.nature.com/nature/journal/v535/n7612/extref/535355c-s1.pdf

 

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Molecular Cytogenetics Group – an infographic of what we do

Infographic: what we do in the Molecular Cytogenetics Research Group

Infographic: what we do in the Molecular Cytogenetics Research Group

Infographic: what we do in the Molecular Cytogenetics Research Group

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Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

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324. Ali N, Heslop-Harrison JS, Ahmad H, Graybosch RA, Hein GL, Schwarzacher T. 2016. Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance. Heredity (2016) 117, 114–123; published online 1 June 2016 doi:10.1038/hdy.2016.36

Author version: N_Ali_et al 2016 Multiple Alien Introgressions in Wheat

Publisher site: http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy201636a.pdf

Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridization were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of twenty experimental lines, ten carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, seven lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV-resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien-wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: 1) at or near to the centromere, 2) intercalary between markers UL-Thin5 and Xgwm1130, and 3) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridized to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm.

KEYWORDS

Fluorescent in situ hybridization, molecular markers, wheat, Thinopyrum intermedium, rye, Wheat streak mosaic virus

 

Author version: N_Ali_et al 2016 Multiple Alien Introgressions in Wheat

Publisher site: http://www.nature.com/hdy/journal/vaop/ncurrent/pdf/hdy201636a.pdf

 

 

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Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida flowers: sequenced by a consortium including the MolCyt,.com lab

Petunia hybrida flowers: sequenced by a consortium including the MolCyt.com lab

325b. Bombarely, Moser M, Amrad A, Bao M, Bapaume L, Barry CS,  Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D’Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus S, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. 2016. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants 2: article number 16074.

http://dx.doi.org/10.1038/nplants.2016.74

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization, the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.

 

See also related / supplementary manuscript from Molecular Cytogenetics lab.

 

 

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Analysis of Petunia vein clearing virus (PVCV) sequences, retroelements and tandem repeats in Petunia axillaris N and P. inflata S6

PetuniaNaturePVCVchromosomes.jpg325a. Schwarzacher T, Heslop-Harrison JS, Richert-Pöggeler KR. 2016. Analysis of Petunia vein clearing virus (PVCV) sequences, retroelements and tandem repeats in Petunia axillaris N and P. inflata S6. Supplementary manuscript 2. Nature Plants 2: article number 16074.

Link to manuscript: Petunia_PVCV_Repeats_SchwarzacherEtAl2016

Within the genome sequence assemblies of P. axillaris (PaxiN) and P. inflata (PinfS6) and unassembled reads, we analysed the occurrence of endogenous Petunia vein clearing virus (PVCV) sequences, other endogenous pararetrovirus (EPRV) sequences, LTR-retroelements, and tandem repeats. Petunia genomes show substantial diversity in their pararetroviral sequences as revealed in searches using the polymerase motif. Homologies to two genera of Caulimoviridae, Petu- and Florendoviruses, with more than 60% amino acid identity, were present in both species. Almost complete PVCV copies, fragments, and degenerate copies, sometimes in tandem arrays, were found. PVCV motifs were more frequent in P. axillaris, with the results seen in the assemblies confirmed by in situ hybridization of PVCV fragments to metaphase chromosomes indicating that P. axillaris is likely a more permissive host for EPRVs. LTR-retroelements are localised near centromeres; about 6500 full length elements were found in the PinfS6 assembly while 4500 were in PaxiN. Apart from rDNA, microsatellites and telomeric sequences, no highly abundant tandem repeats were identified in the assembly or raw reads. Repeat cluster analysis indicates that LTR-retroelements are associated with simple sequence repeats and low complexity DNA families and that repeats within Petunia are very diverse, with none having amplified to form a major proportion of the genome. The repeat landscape of Petunia is different from other species of Solanaceae, in particular the x=12 crown group including Solanum and Nicotiana, with a relative low proportion of total repeats for a genome size of 1.4Gb, x=7, and a high degree of genome plasticity.

Link to manuscript: Petunia_PVCV_Repeats_SchwarzacherEtAl2016

Supplementary manuscript 2 from

325b. Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS,  Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D’Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus S, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. 2016. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. Nature Plants 2: article number 16074. doi:10.1038/nplants.2016.74

http://dx.doi.org/10.1038/nplants.2016.74

 

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Regulation should follow robust scientific assessments not opinions

Risk Delegation with EU Commissioner Vytenis Andriukaitis [From the left: Prof. Richard Sharp (back), Prof. Helmut Greim (middle) ,Prof. Sir Colin Berry (front), Prof. Pat Heslop-Harrison (back), Dr. Vytenis Andriukaitis, Commissioner of Health & Food Safety (middle), Prof. Daniel Dietrich (front), Prof. Wolfgang Dekant (back), and Prof. Alan Boobis (front)]

Risk Delegation with EU Commissioner Vytenis Andriukaitis [From the left: Prof. Richard Sharp (back), Prof. Helmut Greim (middle) ,Prof. Sir Colin Berry (front), Prof. Pat Heslop-Harrison (back), Dr Vytenis Andriukaitis, Commissioner of Health & Food Safety (middle), Prof. Daniel Dietrich (front), Prof. Wolfgang Dekant (back), and Prof. Alan Boobis (front)]

University of Leicester scientist in battle to ‘stem onslaught of pseudoscience’

Geneticist at European Commission alarmed at impact of ‘dogma’ in regulation and the negative impact on the environment and European industry

A University of Leicester scientist has joined leading scientists from across Europe in raising an alarm over the ‘pseudoscience’ concerning regulation of compounds used in agriculture, healthcare and industry.

Professor Pat Heslop-Harrison, from the Department of Genetics, was among scientists meeting Dr Vytenis Andriukaitis, European Commissioner of Health and Food Safety, earlier this month. The scientists highlighted the fact that some people are being ‘deliberately selective’ in presentations of risks, including those from glyphosate herbicides, new plant breeding technologies and endocrine disrupting chemicals or EDCs. Pat Heslop-Harrison brought his knowledge of environmental and agricultural genetics and risk analysis to the meeting, while others in the delegation had particular expertise in toxicology, endocrinology and human pathology. The characterization of risk determines the likelihood that effects will occur under real exposure conditions. For chemicals, whether of natural or synthetic origin, sound regulation requires comparison of exposure with potency, and risk characterization is required to enable the potential benefit of a chemical to be assessed against its potential to inflict harm. Professor Heslop-Harrison was joined by well-established and respected scientists Prof. Sir Colin Berry, Prof. Alan Boobis, Prof. Wolfgang Dekant, Prof. Daniel Dietrich, Prof. Helmut Greim and Prof. Richard Sharpe.

Professor Heslop-Harrison said: “In the discussion, the concern was raised that public perceptions about scientific assessments are currently distorted by people, often from NGOs and well-funded pressure groups, calling for increased regulation or bans. The reality is that there is no robust, consistent scientific evidence to support many of these dogmatic stances, and indeed most of the robust evidence points in the opposite direction for some of the chemicals and techniques now being considered as subject to extra regulation.

“The European Parliament and European Commission have access to robust scientific advice, but this is not always being used in legislation because of these strongly expressed opinions and (sometimes blatantly present) advocacy activities.”

In particular, the scientists in the delegation argued that the presentation of the issues to the public and to the Commission by some groups has been deliberately selective and courses of action have been proposed that are not supported by a scientific evidence base. For EDCs, glyphosate and gene editing techniques for plant breeding for example, the regulation proposed runs counter to the huge database and detailed understanding of all aspects of the substances from their mode of action, to breakdown in the environment, to their effect in humans. The group further highlighted that the current level of knowledge about EDCs and hormone action is such that it allows scientists and the regulatory bodies to identify compounds with potential endocrine activity, natural or synthetic, and to address their potential to cause harm to humans or to the environment via well-established processes.

The group emphasised that management of chemicals and techniques should be based on robust scientific evidence, as is common to all legal procedures (not least including criminal law). This regulation ensure safe use of compounds in a range of applications. In the use of such scientific evidence, this will ensure protection of human health and the environment, while maintaining the sustainability and competitiveness of the European economy.

Pat Heslop-Harrison can be contacted through phh4(a)le.ac.uk or by mobile phone +44/0  7413 292 7five4 .

 

A second press-release from those of us involved in the meeting with Commissioner Andriukaitis is at http://www.prnewswire.co.uk/news-releases/well-known-scientists-ready-to-stem-the-onslaught-of-pseudoscience-in-the-eu-578980091.html

An earlier molcyt.com blogpost is at https://molcyt.org/2016/05/11/scientists-ready-to-stem-the-onslaught-of-pseudoscience-in-the-eu/

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Scientists ready to stem the onslaught of pseudoscience in the EU

EU Commissioner for Health and Food Safety, Vytenis Andriukaitis (left) discussing risk assessment with Pat Heslop-Harrison

EU Commissioner for Health and Food Safety, Dr Vytenis Andriukaitis (left) discussing risk assessment with Pat Heslop-Harrison

BRUSSELS, May 11, 2016 /PRNewswire/

A meeting was held between Dr Vytenis Andriukaitis, Commissioner of Health & Food Safety and well established and respected scientists (Prof. Sir Colin Berry, Prof. Alan Boobis, Prof. Wolfgang Dekant, Prof. Daniel Dietrich, Prof. Helmut Greim, Prof. Pat Heslop-Harrison and Prof. Richard Sharpe) in the fields of human risk assessment and endocrine active compounds (“endocrine disrupting chemicals” or EDCs). Amongst the topics discussed by the group was how the presentation of the issue of EDCs to the public and to the Commission by some scientists has been deliberately selective and has proposed courses of action that: (1) are not supported by a robust scientific evidence base, and (2) run counter to the huge database and detailed understanding of the therapeutic effects of (endocrine active) hormones in human patients. The group emphasized that management of EDCs should be based on robust scientific evidence, as is common to all legal procedures (e.g. criminal law).

In discussion, the concern was raised that public perceptions about EDCs are currently dominated by certain scientists, NGOs and well-funded pressure groups, who categorically assert that EDCs contribute to human cancer, reproductive disorders, obesity and type 2 diabetes. The reality is that there is no robust, consistent scientific evidence to support such a dogmatic stance, and indeed most of the robust evidence points in the opposite direction. The group highlighted that the current level of knowledge about EDC and hormone action is such that it allows scientists and the regulatory bodies to identify compounds with potential endocrine activity and to address their potential to cause harm to humans or to the environment via well-established processes.

Pressure groups have advocated that EDCs should be treated as a “special case” when considering their potential to do harm, on the basis that EDCs (and hormones in general) can have unexpected effects at low level exposures and that they do not have thresholds of effect, with the result that their exposure-response curves are non-monotonic. The reality is that these assumptions are not supported by robust (i.e. reproducible) scientific data and are unlikely to occur in humans, because there is extensive knowledge on the human effects of endocrine active substances from the speciality of clinical endocrinology. Endocrine disorders, extending from diabetes through Graves disease to osteoporosis, that result from hormone levels that are too high or too low are managed by treatment with endocrine-active compounds, which has built a huge level of understanding of the relationships between levels of exposure and resulting health effects in humans. For all of these hormone-mediated functions in humans, thresholds are observed, there are no non-monotonic exposure response curves and no ‘unexpected’ effects at low-level exposures.

In the recent consensus document regarding EDCs developed at the BfR in Berlin (April 12-13, 2016; seehttp://www.bfr.bund.de/en/home.html) it was emphasized that identification of EDCs is only the first step in the risk assessment of EDCs, but that potency and consideration of likely human exposure are necessary for any adequate evaluation of the human or environmental effects of EDCs. As EDCs comprise both natural and synthetic (i.e. manufactured) compounds, sugar in our foods which, when ingested will immediately trigger the release of the hormone insulin, will, if the opinion of some observers is consistently applied, have to be identified as an EDC and be subject to potential regulation. The natural component of sweet mustard (bisphenol F), that has nearly identical endocrine mediated activities as the bisphenol A that was banned from certain uses in France and Germany, would also have to be subject to restriction as would the many estrogenic chemicals present in many plants and vegetables (and presumably thus the plants themselves). This would clearly be nonsensical.

In view of the conclusions reported in the thoughtful consensus document (http://www.bfr.bund.de/en/home.html) and the importance of potency and human exposures in assessing the effects of EDCs, the scientists who met Commissioner Andriukaitis are confident that the current regulatory criteria for all potential EDCs can be developed by the Commission with the input of experienced toxicologists, endocrinologists and risk assessment professionals to enable the safe use of many compounds in a range of applications. In so doing, this will be achieved in a manner that ensures protection of human health and the environment, whilst maintaining the sustainability and competitiveness of the European economy.

From: Concerned Toxicologists for Better Science and Regulation

Contacts:

Prof. Daniel Dietrich, +49-7531-883518, Daniel.Dietrich@uni-konsanz.de, University of Konstanz; Germany

Prof. Helmut Greim, +49-8161-715600, helmut.greim@lrz.tu-muenchen.de, TU Munich, Germany

Prof. Alan Boobis, +44-(0)20-7594-6806, a.boobis@imperial.ac.uk, Imperial College London, UK

Prof. Richard Sharp, +44-(0)131-242-6387, r.sharpe@ed.ac.uk, University of Edinburgh, UK


For environmental and genetic perspective, contact Prof. Pat Heslop-Harrison +44(0) 7413 292 754 phh4@le.ac.uk University of Leicester, UK

Risk Delegation with EU Commissioner Vytenis Andriukaitis [From the left: Prof. Richard Sharp (back), Prof. Helmut Greim (middle) ,Prof. Sir Colin Berry (front), Prof. Pat Heslop-Harrison (back), Dr. Vytenis Andriukaitis, Commissioner of Health & Food Safety (middle), Prof. Daniel Dietrich (front), Prof. Wolfgang Dekant (back), and Prof. Alan Boobis (front)]

Risk Delegation with EU Commissioner Vytenis Andriukaitis [From the left: Prof. Richard Sharp (back), Prof. Helmut Greim (middle) ,Prof. Sir Colin Berry (front), Prof. Pat Heslop-Harrison (back), Dr. Vytenis Andriukaitis, Commissioner of Health & Food Safety (middle), Prof. Daniel Dietrich (front), Prof. Wolfgang Dekant (back), and Prof. Alan Boobis (front)]

 

 

 

 

 
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Characterization and diversity of novel PIF/Harbinger DNA transposons in Brassica genomes

331. Nouroz F, Noreen S, Heslop-Harrison J.S. 2016. Characterization and diversity of novel PIF/Harbinger DNA transposons in Brassica genomes. Pakistani Journal of Botany 48(1): 167-178. www.pakbs.org/pjbot/PDFs/48(1)/21.pdf

Among DNA transposons, PIF/Harbinger is most recently identified superfamily characterized by 3 bp target site duplications (TSDs), flanked by 14-45 bp terminal inverted repeats (TIRs) and displaying DDD or DDE domain displaying transposase. Their autonomous elements contain two open reading frames, ORF1 and ORF2 encoding superfamily specific transposase and DNA-binding domain. Harbinger DNA transposons are recently identified in few plants. In present study, computational and molecular approaches were used for the identification of 8 Harbinger transposons, of which only 2 were complete with putative transposase, while rest 6 lack transposase and are considered as defective or non-autonomous elements. They ranged in size from 0.5-4 kb with 3 bp TSDs, 15-42 bp TIRs and internal AT rich regions. The PCR amplification of Brassica Harbinger transposase revealed diversity and ancient nature of these elements. The amplification polymorphism of some non-autonomous Harbingers showed species specific distribution. Phylogenetic analyses of transposase clustered them into two clades (monocot and dicot) and five sub-clades. The Brassica, Arabidopsis and Malus transposase clustered into genera specific sub-clades; although a lot of homology in transposase was observed. The multiple sequence alignment of Brassica and related transposase showed homology in five conserved blocks. The DD35E triad and sequences showed similarity to already known Pong-like or Arabidopsis ATISI12 Harbinger transposase in contrast to other transposase having DD47E or DD48E motifs. The present study will be helpful in the characterization of Harbingers, their structural diversity in related genera and Harbinger based molecular markers for varietal/lines identification.

www.pakbs.org/pjbot/PDFs/48(1)/21.pdf

Locally archived at https://lra.le.ac.uk/handle/2381/37674

 

 

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Saffron crocus, cooking and Iran on the radio

crocus_saffron_pgiprotection.jpgThe spice Saffron is valued worldwide for its flavor, aroma and color. I’ve just broadcast an interview with Robin Young produced by Jill Ryan for NPR’s Here and Now program which let me tell you something about my enjoyment of saffron both as a consumer and scientist.

dsc01717paellaprawnssaffronnimesmarketSaffron is unusual in that it is equally at home in savory or sweet dishes, and as a drink made with hot water or cold vodka. Saffron is the most valuable agricultural product in the world: in a typical store, the weight of one penny (one cent piece, about 2.5g or a bit under a tenth of an ounce) will cost almost $25. That weight will come from about 200 flowers! But you only need a few strands per serving, costing a few cents – and most people who have enjoyed the real thing will be sure that it is worth it._phh5404saffron_rice.jpg

Saffron spice is the stigmas of the saffron Crocus flower: the three bright orange strands that normally capture the pollen. All _phh6001SaffronCrocusFlowerflowers have these stigmas, but the saffron crocus is unique in having stigmas with the sensory values. The whole flowers are picked, and the individual strands separated and dried. Different countries use slightly different drying temperatures and conditions, as well as soils and altitude, so saffron can vary in colour and aroma. Much is produced on family farms, and the whole family will be involved in picking from the early morning to drying later in the day. Most of the world’s saffron – something like 150 tons per year – is produced in Iran, where the climate and soils are favorable, as well as having people to pick by hand and separate the spice. Other saffron is produced in Kashmir (India/China/Pakistan border region), Greece and Spain, with smaller amounts from growers in many other countries.

Unfortunately, with such a high value product, fraud is an problem. Many types of fraud are possible: you can have the saffron repackaged so it looks like it comes from one country when it was actually produced elsewhere. Much worse though, is where the fraudsters copy the look or color. They will use things like corn silks or jute rope fibres, and colour from plants like safflower (a type of thistle) or tumeric (a type of ginger), or even synthetic dyes like Sudan yellow. As a consumer, you can look carefully at the saffron strands and check they look like the real thing. Smelling might be a problem where it is packaged, and shops would be less keen on tasting too, but you will soon recognize the flower petal-vanilla smell and tartly, slightly peppery taste. Be suspicious of buying powdered saffron, or if the price is too low: it can be kept for at least a couple of years, and nobody will pick hundreds of flowers for a few cents. Look for origin marks on packaging, and the reputation of the company selling it. We recently looked at 10 samples of saffron from supermarkets and those sold in small prepacks with clear labelling were all saffron. Those in packets with unclear labels or mentioning safflower and ‘saffron rice color’ had no aroma and were not saffron.dscn0071SaffronStigmasSpiceOnPaperLR

My scientific laboratory is part of the Saffronomics project. We are a consortium ranging from growers and producers through traders to scientists. As a group, we are developing ways to detect fraud in saffron, ranging from DNA and gene expression studies through to optical spectroscopy and isotope-ratio mass spectrometry. My own lab is interested in the diversity of the saffron crop – there is very little at the genetic level – and the origin from it’s closest wild relatives, some of the Crocuses which are often grown in gardens. The saffron crocus itself is sterile because it has three sets of chromosomes rather than the two of fertile plants and animals. We are also interested in development of high-value agricultural products and crops contributing to sustainable rural livelihoods. We have had several collaborations with researchers from Iran and I have much appreciated their input into our biodiversity and molecular genome studies. I am happy their farmers will have the chance now to export saffron to the US and hope development of this market will let new people enjoy the flavor and aroma of saffron.

LogoSaffronomics

 

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Preparation and fluorescent analysis of plant metaphase chromosomes

Chromosome Preparations: Schwarzacher 2016. www.molcyt.com

Chromosome Preparations: Schwarzacher 2016. http://www.molcyt.com

TS. Schwarzacher T. 2016. Preparation and fluorescent analysis of plant metaphase chromosomes. Chapter 7. In: Plant Cell Division: Methods and Protocols, ed Caillaud M-C; Methods in Molecular Biology 1370: 87-103. doi: 10.1007/978-1-4939-3142-2_7. Humana Press, Springer, New York. Local Copy: Chromosome Preparation. Trude Schwarzacher. www.molcyt.com

Good preparations are essential for informative analysis of both somatic and meiotic chromosomes, cytogenetics, and cell divisions. Fluorescent chromosome staining allows even small chromosomes to be visualized and counted, showing their morphology. Aneuploidies and polyploidies can be established for species, populations, or individuals while changes occurring in breeding lines during hybridization or tissue culture and transformation protocols can be assessed. The process of division can be followed during mitosis and meiosis including pairing and chiasma distribution, as well as DNA organization and structure during the evolution of chromosomes can be studied. This chapter presents protocols for pretreatment and fixation of material, including tips of how to grow plants to get good and healthy meristem with many divisions. The chromosome preparation technique is described using proteolytic enzymes, but acids can be used instead. Chromosome slide preparations are suitable for fluorochrome staining for fast screening (described in the chapter) or fluorescent in situ hybridization (see Schwarzacher and Heslop-Harrison, In situ hybridization. BIOS Scientific Publishers, Oxford, 2000).

KEYWORDS: Chromosome; DAPI; Fluorochromes; Heterochromatin; Meiosis; Metaphase; Proteolytic enzyme

Local Copy: Chromosome Preparation. Trude Schwarzacher. www.molcyt.com

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Saffron Crocus, quality and fraud in New York Times

_PHH2244SaffronStigmasPDOjarsProducts.jpgElaine Sciolino discusses saffron in the New York Times. Saffronomics partners Jean Thiercelin and Pat Heslop-Harrison are quoted, with the outcome of the project in developing methods to detect fraud and measure quality. In the article, the special qualities of saffron are discussed and many examples of the use in sweet and savoury foods explain the value in cooking. The high price encourages fraud and mis-labelling, but even at 20 Euro’s ($20, £15) a gram, the cost per serving is still not so great. Our work on the lack of genetic diversity in saffron and its relationships to wild crocus  was published in 2015 in Annals of Botany: this lack of diversity means that DNA-marker tests can be used to identify plant-based contamination but not the origin of saffron nor adulteration with dyes.

The full article is here http://mobile.nytimes.com/2015/12/30/dining/saffron-iran.html

 

 

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The molecular cytogenetic characterization of pistachio (Pistacia vera) suggests the arrest of recombination in the largest heteropycnotic pair HC1

Pistachio chromosomes: Sola-Campoy et al. 2015 PLoS One.

Pistachio chromosomes: Sola-Campoy et al. 2015 PLoS One.

TS. Sola-Campoy PJ, Robles F, Schwarzacher T, Ruiz Rejón C, de la Herrán R, Navajas-Pérez R (2015) The molecular cytogenetic characterization of Pistachio (Pistacia vera L.) suggests the arrest of recombination in the largest heteropycnotic pair HC1. PLoS ONE 10(12): e0143861. doi:10.1371/journal.pone.0143861. Local copy here.

This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.

 

TS. Sola-Campoy PJ, Robles F, Schwarzacher T, Ruiz Rejón C, de la Herrán R, Navajas-Pérez R (2015) The molecular cytogenetic characterization of Pistachio (Pistacia vera L.) suggests the arrest of recombination in the largest heteropycnotic pair HC1. PLoS ONE 10(12): e0143861. doi:10.1371/journal.pone.0143861. Local copy here.

 

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Banana research at the botanic garden

Banana fruit bunch with male flower

Banana fruit bunch with male flower

324. Heslop-Harrison, P. 2015. Banana research at the botanic garden. University of Leicester Botanic Garden Newsletter 12: 4. November 2015.

Dessert bananas and the cooking bananas or plantains are among the oldest crops in the world. Most crops were domesticated through a long pathway of selection and crossing but, for banana, virtually all the two thousand varieties which are grown throughout the tropics were collected as spontaneous mutants in the wild with the extraordinary property of having large fleshy fruit without any seeds. Most varieties of banana are also unusual in having three sets of chromosomes, a condition known as triploid.

The wild progenitors of the domesticated banana are from south-east Asia and are currently known as Musa acuminata (with a genome designated as ‘A’, green on the map below) and Musa balbisiana (with a ‘B’ genome, orange on the map below). About 15% of the world’s banana production is for the export trade, and is based on a single variety, ‘Cavendish’. This sweet banana has the genome constitution AAA. Banana varieties that are hybrids with AAB and ABB genome constitutions are a staple food for a billion people in Asia and Africa, and in Leicester we are fortunate that many of these plantains and cooking bananas (eaten fried or steamed and mashed as a vegetable) are easily available in the market and speciality shops.

In many parts of Asia, banana leaves are also used as disposable plates or as wrappers for steaming rice or banana fruit. Interestingly, there is now the possibility that these two currently recognized A and B species will be merged into one; this would probably mean resurrecting one of the original names given by Linneaus, Musa paradisiaca L. or Musa sapientum L.

Traditionally, bananas are propagated by side suckers to the main stem but, in commercial plantations, most plants are now multiplied through tissue culture to ensure disease-free planting material. In our research group, we study the diversity and evolution of bananas at the DNA level, and are looking for new diversity to improve current varieties. The amount of DNA in plant genomes varies widely, from less than 100 Mbp in some carnivorous plants such as Genlisea, to more than 17,000 Mbp in wheat and pines. Bananas are at the lower end of the range, with about 550 Mbp. We were involved in the international consortium that sequenced all the DNA in banana in 2012, and thus we have a reference for all the genes and regulatory sequences present in the species.

This is vital if breeding programmes are to produce new disease-resistant varieties. Disease is a major problem in banana production in the topics: bananas suffer from fungi, bacteria, viruses, insects and nematodes. About a third of the cost of growing the bananas is spent on crop protection chemicals, and all fruit bunches are covered with blue bags to deter insects from damaging the fruit and allowing entry of secondary fungal. Eradication of disease in some areas costs millions of pounds and requires destruction of millions of plants. Very careful agronomy can control diseases, such as burning plants at the first sign of infection, or dipping machetes in bleach between harvesting each plant, but such measures required huge amounts of training and labour. Some diseases cannot be controlled with agronomy or chemicals, and means banana production is lost to an area. Our current work is looking at the diversity present in the whole banana genome at various positions related to diseases, we are also looking how the variation can be exploited in generating new varieties of banana which are disease resistant.

324. Heslop-Harrison, P. 2015. Banana research at the botanic garden. University of Leicester Botanic Garden Newsletter 12: 4. November 2015.

 

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Repetitive DNA in eukaryotic genomes

Biscotti et al. 2015. Repetitive DNA in the eukaryotic genome. Chromosome Research

Biscotti et al. 2015. Repetitive DNA in the eukaryotic genome. Chromosome Research

322. Biscotti MA, Olmo E, Heslop-Harrison JS. 2015. Repetitive DNA in eukaryotic genomes. Chromosome Research 23(3): 415-420. DOI: 10.1007/s10577-015-9499-z

Biscotti Repetitive DNA Author Version

Link to Repetitive DNA summary Diagram Molcyt.com DNA

Repetitive DNA — sequence motifs repeated hundreds or thousands of times in the genome— makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest contrasting modes of evolution of repetitive DNA of different types, including selfish sequences that propagate themselves and may even be transferred horizontally between species rather than by descent, through to sequences that have a tendency to amplification because of their sequence motifs, to those that have structural significance because of their bulk rather than precise sequence. Functional consequences of repeats include generation of variability by movement and insertion in the genome (giving useful genetic markers), the definition of centromeres, expression under stress conditions and regulation of gene expression via RNA moieties. Molecular cytogenetics and bioinformatic studies in a comparative context are now enabling understanding of the nature and behaviour of this major genomic component.

repetitive DNA, tandem repeats, genomics, junk DNA, transposons, satellite DNA, retrotransposons, review

Biscotti MA, Olmo E, Heslop-Harrison JS. 2015. Repetitive DNA in eukaryotic genomes. Chromosome Research 23(3): 415-420. DOI: 10.1007/s10577-015-9499-z

Biscotti Repetitive DNA Author Version

Link to Repetitive DNA summary Diagram Molcyt.com DNA

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Innovative science and blue-sky research

Seagull in blue sky - what research needs

Seagull in blue sky – what research needs

321. Braben DW, Heslop-Harrison JS and 48 others. 2015. Letter: Innovative science, Blue Sky research, scientific enterprise and prosperity. The Times (London) 23 September 2015. p. 28.  (http://www.thetimes.co.uk/tto/opinion/letters/article4564669.ece ££)

The Times (London) September 23, 2015 Wednesday Edition 1;
Letter on Innovative science
SECTION: EDITORIAL; OPINION; LEADING ARTICLES; Pg. 28

Sir, “Blue sky” research is vital to scientific enterprise and prosperity, yet it is increasingly hard to find funding for truly innovative projects. First, universities must approve all proposals that are submitted. Funding agencies then subject all proposals they receive to peer review, a process by which a few researchers, usually acting anonymously, assess the proposal’s chances of achieving its goals, whether it offers the best value for money, is relevant to a priority and has an impact on a socioeconomic problem. Only about 25 per cent of proposals win funding. These processes force researchers to exploit existing knowledge, discourage open ended studies, and are hugely time consuming. They are also new: before 1970, few researchers wrote proposals. Now they are effectively mandatory.

Globally, the 20th century was dominated by some 500 Nobel prizewinning academics who explored new concepts, leading to such discoveries as nuclear power, penicillin, lasers, magnetic resonance imaging and monoclonal antibodies.

We must find ways of giving unconstrained support to the tiny number of scientists with radical agendas. BP’s Venture Research initiative for supporting such people ran from 1980 to 1993 and created at least 14 major discoveries from the 37 groups supported. Almost all had been rejected by peer review. Its cost, including BP and university overheads, was about £20 million over 13 years. Identifying people to lead such initiatives will be difficult – but it must be done.

Donald W Braben, UCL; Peter Edwards FRS, University of Oxford; Dame Anne Glover, University of Aberdeen; John Hall, Nobel Laureate, University of Colorado; Dudley Herschbach, Nobel Laureate, Harvard University; Sir Harry Kroto FRS, Nobel Laureate, Florida State University; John Mattick, Garvan Institute of Medical Research, Sydney; Sir Richard J Roberts FRS, Nobel Laureate, New England Biolabs; Ken Seddon, Queen’s University Belfast; Pat Heslop-Harrison, University or Leicester; Plus 40 other senior scientists www.thetimes.co.uk/letters

http://www.thetimes.co.uk/tto/opinion/letters/article4564669.ece ££

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