All posts by Editor Pat Heslop-Harrison

About Editor Pat Heslop-Harrison

Pat Heslop-Harrison is Professor of Molecular Cytogenetics and Cell Biology at the University of Leicester. He is also Chief Editor of Annals of Botany.

Domestication – rabbits now catching up with plants

Wild rabbits: how do their genomes differ from domesticated rabbits?

Wild rabbits: how do their genomes differ from domesticated rabbits?

Domestication of species is critical for our farming and own nutrition, as well as being important for retrospective studies of evolutionary genetics and future applications in animal and plant breeding. The genes involved in the first stages of domestication in plants are relatively clear: a single, tasty, energy-rich, product over-produced with a high proportion easily harvested, quick and easy establishment when planted, and disease resistance (free: Special Issue Preface and full issue of Annals of Botany). It has been less clear what is needed from a newly domesticated animal: many are multi-purpose (wool, leather, milk, meat, draught/traction, as well as companions and guarding), but why haven’t more animals been domesticated? What traits are being selected? (In particular, not one of the nearly 1000 sub-Saharan vegetarian mammal species has been domesticated.) Remarkably, most of our current crop plants and animals were domesticated in a relatively short period about 10,000 years ago, so, particularly for animals, finding near-relatives for genetic studies has been difficult.

A new paper from Miguel Carneiro Porto, Portugal, and colleagues from Sweden and the US in Science this week (Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication – Carneiro et al. p. 1074; 29 August, on the Science website) uses genomic analysis of DNA in domestic and wild rabbit with whole-genome DNA sequencing information. They address some of the key questions about animal domestication. Another summary of the paper is given by Penny Sarchet in New Scientist today. Rabbit domestication is recent – only in the last 1400 years; wild populations exist for comparison, and there are multiple selected breeds, so it is a good system to work with compared to other animals. I met first Miguel Carneiro when he talked about a related paper at a meeting in Portugal in 2010 (2011 Mol Biol Evol, The Genetic Structure of Domestic Rabbits Carneiro et al.), but have not had other contact with him, although we have continuing collaboration with a nearby lab Prof Raquel Chaves at Vila Real, Portugal, on bovid genome structure and evolution.

Domesticated rabbits - friendly and little fear

Domesticated rabbits – friendly and little fear

Key points for me from the rabbit paper are that they found about 100 regions that were selected to be different and showed evidence for selective sweeps (genomic regions of reduced variation and segregation distortion or linkage disequilibrium) in the domesticated compared to wild rabbits. This means that many genes were selected simultaneously (new result) so domestication was difficult and involved only a dozen to a thousand individuals (those latter data are in the 2011 Mol Biol Evol paper) with the appropriate combination of genes. This high number also explains why domestication loci have been hard to find in animals – it is too many to study with crosses and genetic analysis, only with genome sequencing (a new result). The second really interesting new point is which genes are in these regions: they find genes affecting brain development and sensory organs are strongly over-represented in these regions. In other words, selection during domestication might have focused on tameness and lack of fear: as a farmer, you neither want the animal to hurt you, nor for the animal to die from stress. Secondarily, an animal uses a lot of energy and time to keep a look-out and flee – energy that humans would rather went into meat and milk! It is notable that gene loss is not significant during evolution: most of the changes are due to gene allele polymorphisms.

A wild rabbit on guard, using lots of energy and sensory perception. These genes are selected in domesticated rabbits.

A wild rabbit on guard, using lots of energy and sensory perception. Carneiro et al. 2014 show these genes are selected in domesticated rabbits.

I do mention sensory perception, ‘friendliness’ and fear in my lectures on animal domestication – zebras kill more people in zoos than any other animal because they bite and hold on to their keeper, while deer panic and have heart attacks or break a leg. But until now there have been minimal real data about the changes in this group of genes – I think this paper is a first. (I once heard a talk about reduced brain size in farmed trout fish, but forgot the author and never found a reference.) Given the large number of loci, possible introgression and crosses to wild rabbits every few dozen generations (although this was not noted in the study and should have been evident), and large regions around genes affected by the genomic sweep that include non-coding polymorphisms, the results make a lot of sense. They also explain why previous studies have had difficulty in showing genetic signatures of domestication in farmed animals – lots of loci, too long periods to study, more difficult population structures without wild relatives.

I did contact Miguel Carneiro about the introgression question: he replied “there is good solid data that domestic rabbits when released in the wild and in the native range (Iberia and France) are very unlikely to survive the first couple of days due to predation pressure, indicating that introgression in this direction is difficult.” So indeed, the reduced sensory perception and reduced fear response has an immediate and large consequence. He comments that the reverse of wild introgression into domestics is likely to have happened, but the genetic bottleneck signature in domestic rabbits perhaps suggests that this is not so frequent.

Lack of segregation of characters in crosses to look at rabbit (or indeed other animals,where wild x domestic crosses are possible) domestication characters suggests many genes are involved (unlike the small number of genes controlling, say, coat colour in rabbits, or growth-related genes like broiler vs egg-laying chickens). I would speculate that many different monasteries in France in the middle ages tried to keep wild rabbits, eventually with a few finding rare rabbits with a suitable combination of characters which were then progenitors to the current domestic breeds.

A cow tooth found in a milking parlour: cows loose their own milk teeth in their second lactation. Humans selected early breeding but not loss of other juvenile characters.

A cow tooth found in a milking parlour: cows loose their own milk teeth in their second lactation. Humans selected early breeding but not loss of other juvenile characters. Wild relatives would have their first calf years later.

The genomic loci give many suggestions where we should look to improve rabbits. I have blogged about the possible importance of aquaculture and fish or crustaceans as a part of improving agricultural sustainability already, but introduction of rabbits as a more exploited source of animal protein also has potential: they (or at least their bacterial gut microbiome) means they digest grasses and fibres. Thus, like cows but unlike pigs or chickens, they can use agricultural products that do not compete with human food uses. Since rabbit domestication is so recent, we can also anticipate what ‘second stage’ domestication traits we should be looking for – rather as we suggested earlier this year should be done in proso millet, Panicum miliaceum, which was domesticated in the first wave but has since declined in relative importance despite having extremely high water efficiency.

What wasn’t found in the the genes associated with rabbit domestication was remarkable. There is no mention of disease-resistance loci and nor of reproduction or breeding-related genes – I would expect these to be over-represented in selected regions (both of which are important traits for domestication of both plants and animals). Disease and reproduction are very important in other domestic animals: high population densities mean diseases spread quickly, while we need fast and easy breeding with no photoperiodic breeding response (not least so we can have eggs and milk all through the year and don’t need to keep cattle until they are 4 or 5 years old before breeding). It is possible these are single-gene loci which would be found but not necessarily stand-out in a genome-wide analysis. Or maybe these are characters where wild rabbits already have the domestication-required genes: they live in large inter-connected colonies (not unlike a farm already) and of course are a byword for reproductive success!

The ultimate friendly, domesticated rabbit

The ultimate friendly, domesticated rabbit.

Another summary of the rabbit genomics of domestication paper is given by Penny Sarchet in New Scientist.

Science 29 August 2014:
Vol. 345 no. 6200 pp. 1074-1079
DOI: 10.1126/science.1253714

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro, Carl-Johan Rubin, Federica Di Palma, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. Chang, Veronique Duranthon, Luca Fontanesi, Hervé Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel-Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand, Kerstin Lindblad-Toh, Leif Andersson

ABSTRACT
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

Bananas and their future on BBC Radio 4 The Food Programme @BBCFoodProg

Six banana varieties and banana products bought in Leicester, UKSix banana varieties and banana products bought in Leicester, UK

Six banana varieties and banana products bought in Leicester, UK

Bananas are our favourite fruit: you can hear lots about them on BBC Radio 4 The Food Programme, produced by award-winning BBC producer Emma Weatherill  and presented by Sheila Dillon, a University of Leicester graduate. A short version will be broadcast at 12.30pm today Sunday 8th August on BBC Radio 4 and the long version will be on Monday at 3.30pm on BBC Radio 4. You can listen to it via the iPlayer from this page. And from Monday afternoon you will be able to download a podcast of the programme from here (which might be useful for those of you living outside the UK.) In this piece, I will show some pictures of the things I talked about and amplify some of the points discussed.

Eating a banana curry from a banana leaf plate.

Eating a banana curry from a banana leaf plate.

As consumers in the UK, we are largely familiar with only one variety of banana – Cavendish. Can you imagine if we only knew about one model of one make of car? There are more than 1200 banana varieties known, each with its own distinctive flavour and texture. We also know about only one use, as a sweet dessert banana – this may be versatile as we eat them fresh, on toast, sliced in our cereal or in banana custard, but much of the world uses cooked bananas as a savoury starch instead of potato, or eats fried chips and even fermented beer. For the Radio programme, I was able to find six contrasting varieties of banana from Belgrave Road in Leicester, as well as different types of chips. The varieties shown and probably talked about in the programme include the ubiquitous Cavendish and the much smaller and fatter AAB Silk or Figue Pomme and smaller Prata (both very popular in West Africa and Brasil). These are more citrus and apple flavours, with some dry starchy mouthfeel in Silk as well. We also had three larger fruits of plantains: one was sweet enough to eat fresh, the others would be cooked or deep-fried, with the largest one being popular in West and Central Africa, Latin America, Brasil, India and Philippines. The medium sized one is and East Africa cooking banana, eaten as matoke, a steamed and mashed dish served with nearly every meal.

Harvesting bananas: the whole fruit bunch weights about 30kg and has 10 to 20 hands that we typically buy.

Harvesting bananas: the whole fruit bunch weights about 30kg and has 10 to 20 hands that we typically buy.

Bananas hold a world record: they are the world’s largest herbaceous plant, with many being 5 m or 15 feet tall. They are not trees since they do not have a trunk or produce wood – the stem (‘pseudo-stem’) is actually mostly made up of leaf bases, like a grass. After flowering and producing the fruit, which takes 9 to 12 months, the stem is cut back, and another side-sucker allowed to grow to produce the next generation. After 2 to 8 crops, the plants are replaced typically with new, disease free plants. We do occasionally see banana plants, and their close relatives Canna, as ornamentals, but the leaves have other uses as plates for food or as building materials. Wild bananas have seeds, but most of the cultivated types are sterile.

A wild diploid banana with large seeds surrounded by only a little pulp. Most cultivated bananas are triploid and sterile.A wild diploid banana with large seeds surrounded by only a little pulp. Most cultivated bananas are triploid and sterile.

A wild diploid banana with large seeds surrounded by only a little pulp. Most cultivated bananas are triploid and sterile. without seeds (although unusually, the fruits still develop in the absence of the seeds).

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AoB Blog maintenant en français / and now in French AoB Blog

AoBBlog is delighted to welcome two guest authors who are carrying out project work with Annals of Botany Editor Dr Karine Alix. Aurélien and Antoine introduce themselves below, and will be making posts in both English and French over the next months. While most words can be translated between the languages, I am always interested and pleased when one finds a word for which there is a valuable and well defined meaning in another language but no equivalent in English. “Animateur” is a brilliant French word, with connotations including leading activities, moderating, and organizing or putting forward ideas for discussion. I’m happy to introduce our new ‘animateurs’.

Antoine Le Gal

Antoine Le GalI am currently a student at AgroParisTech, the French Graduate Institute in Science and Engineering, in the second year of the engineering course (equivalent to Master degree). After having completed a course about Management and Environmental Engineering, I chose to carry out an engineering project called Introduction to the biology research from April to May 2013 supervised by Dr Karine Alix, Lecturer at AgroParisTech. Within this framework we chose, with Aurélien, to write several articles covering various topics for the blog of Annals of Botany.

Fascinated by evolutionary biology and its ability to shed light on the other fields of biology, I chose AgroParisTech for the courses provided in this field. I would like to better understand the link between evolutionary biology and our history through the study of our heritage of biodiversity management and agricultural practices. However, I still hesitate to turn towards courses of management and strategy for life and environmental businesses. I hope that my various trainings which will occur from April 2013 until August 2014 will help me to make my decision.

I invested a lot in the community life of AgroParisTech. First, I was official for relationships between companies and the leading student association during my first year. Currently, I am member of the Junior Enterprise of AgroParisTech; in this organization, students have to accomplish missions assigned by companies. During these activities, I have discovered my personal taste for innovation, entrepreneurship and especially for sharing, all values that I hope to show during the time I will spend in animating the blog of Annals of Botany.

Je suis actuellement étudiant à AgroParisTech, la Grande Ecole d’Ingénieurs Française des Sciences du Vivant, en seconde année du cursus ingénieur (équivalent au niveau Master 1). Après avoir suivi cette année un parcours de Gestion et d’Ingénierie de l’Environnement, j’ai choisi de mener durant les mois d’avril et mai 2013 un projet d’ingénieur d’initiation à la recherche en biologie, encadré par Dr Karine Alix, maître de conférences à AgroParisTech. Dans ce cadre, avec Aurélien, nous avons choisi d’apporter notre contribution au blog AoBBlog de la revue scientifique Annals of Botany.

Passionné par la biologie de l’évolution et le regard qu’elle apporte sur les autres branches de la biologie, j’ai choisi AgroParisTech pour la formation à la recherche proposée dans ce domaine. J’aimerais pouvoir développer le lien entre la biologie de l’évolution et notre Histoire à travers l’étude de notre patrimoine de pratiques de gestion de la biodiversité ou encore agronomiques. J’hésite cependant encore à m’orienter vers des enseignements de gestion et de stratégie pour la performance dans les entreprises du vivant. J’espère que mes différents stages qui se dérouleront d’avril 2013 à août 2014 m’aideront à prendre ma décision.

Je m’investis beaucoup dans la vie associative de l’école : j’ai été responsable des relations aux entreprises de la principale association étudiante de l’école pendant ma première année et je suis actuellement membre de la Junior-Entreprise de l’école, une association qui a pour but de faire réaliser des missions confiées aux étudiants par des entreprises proches de nos secteurs d’activités. Dans ces activités j’ai découvert mon goût pour l’innovation, l’entrepreneuriat et surtout un goût affirmé pour le partage, autant de valeurs que j’espère pouvoir transmettre durant mon passage au blog d’ Annals of Botany.

Aurélien Azam

Aurélien AzamA student in my second year at the master’s degree institute in science and engineering AgroParisTech, I’m working nowadays in a project named ‘Initiation to the Research in Biology’, supervised by Dr Karine Alix, Lecturer at my school. This project consists in writing popular science articles about plants biology for AoB Blog (in relation with the journal Annals of Botany). I have already an agricultural two-year technical degree specialized in laboratory analysis, thus I chose this project because it permits me to meet my taste for advanced genetic research. So, it matches my professional project. Indeed I want to be a Lecturer in genetics and that since my training period of two-year technical degree. This project permits me to really dive in scientific investigation on various subjects I will select with Antoine Legal, my colleague on this project. Even though I do not know if I want to be specialized in animal, plant or human genetics, making bibliographic searches on plants biology gives me the opportunity to satisfy my curiosity, being passionate by sciences, but also to perfect my writing during the redaction of these articles. My concern will be to share with you my passion for sciences through articles on topics that are important for me.

Étudiant en deuxième année à l’école d’ingénieur AgroParisTech, je suis actuellement en projet d’initiation à la recherche en biologie, encadré par Dr Karine Alix, maître de conférence à mon école. Ce projet consiste à rédiger des articles de vulgarisation scientifique dans le domaine de la biologie végétale pour AoB Blog (en relation avec la revue Annals Of Botany). Possédant un BTS Agricole spécialisé en analyses de laboratoire, j’ai choisi ce projet qui me permet de répondre à mon goût pour les avancées de la recherche en génétique. Il correspond ainsi à mon projet professionnel. En effet, je désire devenir enseignant-chercheur en génétique, et ce, depuis mon stage professionnel de première année de BTS. Ce projet me permet donc de me plonger véritablement dans l’investigation scientifique sur des sujets variés que j’aurai choisis avec Antoine Le Gal, mon collègue sur ce projet. Même si je ne sais pas encore si je souhaite me spécialiser dans la génétique animale, végétale ou humaine, faire des recherches bibliographiques en biologie végétale me donne l’occasion de satisfaire ma curiosité, étant un passionné des sciences, mais aussi de parfaire mon écriture lors de la rédaction de ces articles. Mon souci sera donc de vous faire partager ma passion des sciences au travers d’articles sur des sujets qui me tiennent à cœur.

DNA tests, horse meat, Richard III and BBC Radio Leicester Drive Time

DNA and Farm Animals

DNA and Farm Animals

DNA testing is an important part of our life now – as we have seen with proving that a skeleton in Leicester comes from the body of the last Plantagenet King Richard III, and not a mediaeval Monk, or with the implications of finding horse meat in a lot of beef products. I’ve just done an interview with Ben Jackson on BBC Radio Leicester about tracking the provenance of our food. Here are my notes and some comments about the things discussed at the live interview by Ben Jackson. It will be available for the next week at http://www.bbc.co.uk/programmes/p013nxz2 starting after the news and traffic roundup at about 17.15, 2hr15min from the start.

There is a very welcome move towards traceability of our food from farm to fork – that’s what why there are ever more complex codes stamped on every food item you buy. But the traceability relies on a paper trail, and where there is money to be made by passing off something cheaper as something more expensive, somebody is going to try to falsify the documents – fraudulent labelling of inferior products. So that is where testing comes in: a retailer, or in the horsemeat case it seems even the manufacturers, can check that some parts of the paper trail are correct. For those reading this blog outside the UK and Ireland, at the end of last year and published in January, a high proportion of horsemeat was found in beefburgers (that’s English for hamburgers internationally) on sale in Ireland, by the Food Standards Agency of Ireland, and the same manufacturing plants were supplying similar product to many UK shops. Not surprisingly, nobody had really tested beef products for horse, horsemeat almost never being eaten in the UK. But now the test are being done, even after the originally suspect products were pulled from the shelf, both contamination of beef with pork, and outright fraud of selling horse as beef in processed foods, has come to light in many products still on sale. Now the UK Food Standards Agency has started testing on a larger scale, the latest news this week is a ‘beef’ lasagne where over 60% of the meat is horse. (I’m afraid the true cynics amongst us are surprised that there was indeed meat in such products; personally I would prefer a more botanical dish!)

The Radio Leicester interview was played in with the Prime Minister talking at a press conference this morning, “It’s important to say there’s no reason to believe any frozen food currently on sale is unsafe or a danger to health. It’s not about food safety – it’s about proper food labelling and about confidence in retailers”. “Economical with the truth”, in the UK at least, has become a polite expression, as used in Parliament, for accusing someone of telling an outright lie. So I’m not quite sure how I say that our Prime Minister was being economical with the truth, but in the most literal sense.  There are exceptionally rigorous rules about every aspect of treatment of our food animals from birth, through death and onwards to processing for food. Most people are entirely unaware of the huge recording, licensing and monitoring overheads that are there for keeping farm animals: for some species, the paperwork needed for moving them in a van from one field to another is the longest part of the task, while every drug is recorded, their diet strictly defined, and both welfare and health monitored and recorded. (As a friend said to me when his wife had to wait 10 weeks for a hospital appointment, he’d be in jail if his lame cow had to wait two weeks to see the vet.) While these rules are onerous, the Prime Minister should know that they are in place for two reasons: food safety and animal welfare. If the paper trail in the supply chain is so compromised that there is no proper record even of the species in our food, it is almost certain that the safety of the food is in jeopardy, and will not meet anything like the standards of farming or of processing that we have come to expect.

Fortunately, it seems people aren’t poisoned or allergic to horsemeat, but most horses are treated at some point in their life and have a residue of an anti-inflammatory painkiller, ‘bute’, or phenylbutazone which is not safe enough for human use. Perhaps the worst recent food contamination in the last decade was addition of melamine powder, from a plastic which includes nitrogen in its molecules, to milk powder. Tests at that time could not separate melamine from protein, and about 300,000 children in China were given milk with melamine to make it look like high-protein milk.

DNA is a remarkably stable molecule, and is present in all the foods we eat that is made up of cells. Each cell has hundreds of millions of four DNA letters (A, T, C and G) in a particular sequence, and in that sequence of four letters (bases) in the DNA, there are characteristic signatures of whichever animal or plant made the cells. There are several ways to see which organism made the DNA depending what is required. Many tests will only tell you what is there when you test for that particular animal. That seems to be the case with the testing of processed food in Ireland and the UK until now: nobody was testing for horse. How far should you go in making tests? Rabbit, donkey … or  less palatable products: mink or dog; or rare but perhaps cheap meat: river buffalo, camel, elephant?

Now, most DNA tests will use a molecular method called PCR to amplify very characteristic pieces of DNA from a test sample. If they amplify, then that animal was used in the product – and you can see the product easily in the laboratory. But this test will only say whether what you are testing for is there: you need to do a different test for each species. The test will take typically 8 hours.

More specific, but much more expensive is reading the DNA letters to see which species if comes from. In this test, again specific pieces of DNA are amplified from the test sample (exactly the same as was done in Leicester with Richard III), and then they are sequenced, and the DNA code made up of the four letters is compared with reference samples. Anybody can see these reference DNA sequences over the internet – search at www.ebi.ac.uk for example. This will tell you all the animals that are present in a sample. I saw one supermarket company reported these tests will cost £400 or £500 per sample ($/€ 750): this is higher than my lab but what a well-documented result would cost (my raw costs without labour or paying for facilities would be £5 for DNA extraction, £5 for amplification, £10 for separation and purification, £50 for the cloning of the DNA and isolation, then say 20 sequence runs totalling £200 so a total of c. £300 per sample). Altogether, this will take something like a week: this is acceptable for frozen food although expensive in terms of storage and stock capital. For fresh food, a week waiting for a test would not be possible. Sequencing DNA will identify all the species present in the sample, but not the proportion present with any accuracy. For that, another quantitative PCR methods with specific primers is needed.

Other tests are also possible: each animal has characteristic proteins, and antibodies (made in other animals) can be used to test to origin of the proteins in meat. Formerly, hybridization with radioactive DNA probes was used: now my lab. does this to see how DNA is organized in a species, but not to examine the origin of the DNA.

DNA testing today needs the most minute sample: less than the weight of a pin is ample. This sensitivity might be valuable for identifying a crook from a drop of blood, or a King from a few fragments of bone marrow, but it brings another problem for food. A factory will typically be handling hundreds if not thousands of tons of food each week, so how do you obtain a ‘typical’ sample? A fragment of meat will originate from one animal – but will certainly not be an ‘average’ of the whole production of the factory. For sampling grain arriving from a truck off the combine, there are many elaborate but accurate bulk sampling approaches (pictured) but how can it be done with meat in a factory? Another problem is contamination: if samples are not carefully taken and stored, they can become mixed with other samples. Moreover, modern DNA tests are so sensitive that a stray hair in a sample, perhaps pulled from a pet, would easily be detected.

Over the last decades, food testing has been a growing industry: food safety has been driving the increase, but followed closely by identification of food composition, whether that is with respect to allergens, or misrepresentation of ingredients as with horse in beef lasagne or burgers. The testing of food – and feed – is mostly done by official feed and food control laboratories which in the UK are mostly designated by the Food Standards Agency. As far as I know, there are none in Leicestershire.

International trade has always been important for food – think of the spice routes of the middle ages. But now it is a global market – some products can’t be grown in the UK, in other cases, they are surplus in some countries. Kidney and liver not typically eaten in US, or ducks feet in the UK, but high value elsewhere (I once sat next to the UK duck-foot export expert on a flight to China!). But the scale of food transport is increasing – we want cheap food, but would rather have a less productive natural landscape around us, and want the same food year-round, so hence we are importing and transporting on an unprecedented scale. In the horsemeat case, the retailers pass the blame to the manufacturers, who pass it to their suppliers. What is notable to me is just how diverse and distant these suppliers, who seem to have had the tampered documentation, are from the producers. My laboratory in Leicester works closely with the researchers at Teagasc – The Irish Agriculture and Food Development Authority, on the genetics of grass crops, a multibillion euro industry used to feed animals. It is clear from my in-box and Twitter traffic the potential devastation of the Irish cattle industry, up to now a byword for quality and purity, by the malpractices revealed by the DNA tests.

My lab and the University of Leicester does not do ‘food testing’ on a commercial scale, but we develop the science that is underpinning the tests that are applied to food. This work is also important for understanding the genetic and evolutionary relationships between food species – both animals and plants. We want to characterize their nearest wild relatives, trace the genetic differences with modern species, and see how new breeds of varieties are developed which are disease resistant and productive. My research group works with both plants and animals. For example, for a number of years we worked with the relationships of all animals in the bovid group. This means we developed what could be used as DNA tests for different animals such as river buffalo (pw and user both ‘visitor'; a close relative of cows), or the many deer species.

I think these paragraphs covered most of the areas I wanted to discuss: the main point was to say DNA testing was now important to verifying the paper-trail showing the origin of our food. We should be worried about the level of deceit and fraud that has been revealed in the last two months; it looks as though it has not had a food safety impact but certainly testing must be increased so we can be sure we buy what we want to eat.

 

 

Snow in the botanic gardens

University of Leicester Botanic Garden in the Snow

University of Leicester Botanic Garden in the Snow

Since every newspaper in the UK is featuring pages of pictures of the snow, I thought I would add some from the Botanic Gardens of the University of Leicester. After unseasonably warm, spring-like weather, the bulbs were growing and birds singing last week. Now an unusual 15cm/6″ of snow has fallen in 24 hours, and is forecast to remain for several days. So for those nearby, it’s your chance to visit the gardens; for others, here are some pictures largely without words.

The Botanic Gardens are about 2 miles/3km from the Leicester city centre and main University site, and occupy about 6ha/16acres. The were founded by bringing together the gardens of four large houses, now student residences and conference centres. The mission of the Gardens is to explore, conserve and explain the world of plants with a diverse collection underpinned by and underpinning botanical research. There are National Collections of Skimmia, Aubrieta, hardy Fuchsia and (one I’m personally less proud of …) Lawson’s Cypress.

Catkins

Catkins

Sculpture next to the pond

Sculpture next to the pond

Not trees ... but ice in the ornamental pond

Not trees … but ice in the ornamental pond

DSC07526

Some new visitors: I hope they were counted correctly

Some new visitors: I hope they were counted correctly

Formal gardens in snow

Formal gardens in snow

Poly the Bioline molecular biology bear with friend pet makes a trip out of the lab freezer

Poly the Bioline molecular biology bear, with friend Pet, makes a trip out of the lab freezer

The Knoll, one of the four houses in the gardens

The Knoll, one of the four houses in the gardens

The Knoll house in the Botanic Gardens

The Knoll house in the Botanic Gardens

Snow weighing down branches

Snow weighing down branches

culptures in the botanic gardens - is it Pan?

Sculptures in the botanic gardens – is it Pan?

My bananas in the lit research greenhouse - keeping a bit warmer

My bananas in the lit research greenhouse – keeping a bit warmer

Snow face

Snow face

Building an igloo

Building an igloo

A restful bench awaiting spring

A restful bench awaiting spring

Snow and branches

Snow and branches

Proteaceae, Banksia, Macadamia nuts and the Annals of Botany Cover

Leucospermum flowers in the family Proteaceae on the cover of Annals of Botany

Leucospermum flowers in the family Proteaceae on the cover of Annals of Botany

Our videoblog discusses plants in the family Proteaceae, a well-known Southern hemisphere family with many beautiful and well-known representatives in Africa and Australia. The striking red flowers of the genus Leucospermum, from South Africa feature on the cover of the Annals of Botany for this year. Banksia is a well-known Australian genus, the bottle brush flowers, with attractive flowers and remarkable cone-like fruits. Protea, the type genus for the family, is from South Africa; the name of both genus and family is apposite, being named after the Greek God Proteus who was very variable in his form. Interestingly, there are no important food crops originating from Australia, despite its large area and range of climatic zones, and the now world-wide importance of Eucalyptus as a tree for construction timbers and paper-making fibre. In the family Proteaceae, Macadamia is the most internationally-significant food plant of any Australian native species; it’s very fat-rich nuts (75%) are widely available and much appreciated.

 

 

The videoblog is on YouTube:

Suggestions needed for the ten best of everything: plants for botanists

Three plant species for my ten best of everything: wheat, pine and arabidopsis

Three plant species for my ten best of everything: wheat, pine and arabidopsis

Some time ago, I started on an AoBBlog post (or maybe posts) on ten plants that all botanists should know quite a lot about. Criteria for inclusion on my list include, at the least, importance in the environment, importance to people as food or culturally, scientific interest, global nature, and evolutionary position. Together, the species (genera? even families?) chosen should illustrate a wide range of botany and complement each other. So, here I give my current list of starters; the order is computer-sorted random.

Wheat (or rice)

Arabidopsis

Drosera (or Pinguicula)

A legume – but which one? Acacia? Arachis? Trifolium? Pisum? Glycine?

Physcomitrella (or Sphagnum or another non-vascular plant)

Wollemi pine (Ponderosa pine?)

Rose

Banana

Lycopodium

Oak

I’m deliberately not including reasons for my choices here – they will be included in the final posts – but suggestions of what I have missed would be welcome – along with those species that should not make the cut and should be replaced. I suppose I could stretch to a dozen species if needs be.

Comments below please!

Carving in Perugia: the cultural importance of three families of my top ten species

Carving in Perugia: the cultural importance of three families of my top ten species

Gentamicin and special-purpose antibiotics

Gentamicin antibiotic: a 30S prokaryotic ribosome  inhibitor (wiki)

Gentamicin antibiotic: a 30S prokaryotic ribosome inhibitor (wiki)

Gentamicin is an unusual antiobiotic with two properties that make it particularly useful in plant cell culture: it is autoclavable so is added to media before autoclaving/sterilization, and it is active against mycoplasmas as well as gram positive and gram negative bacteria. Over the last week, I too have been getting it. I discovered this way other unusual properties: while nearly any other drug is metabolized in the body, gentamicin is excreted unchanged. There is also much more than the usual fuss in prescribing it: careful does correlation of ‘lean body weight’ against dose (7mg/kg up to 640mg max daily) , and blood testing after the first dose to check the excretion rate: it will bind to many molecules so travels slowly out of the system. It is given intravenously, diluted in c. 100ml of 0.9% saline, as it is not absorbed orally, so is a drug restricted to hospitals.

It is isolated from the gram-positive aerobic and mycelial soil bacterium Micromonospora purpureand was discovered in 1963. Despite both the name of the antibiotic and species from which gentamicin is isolated, it is a white powder or clear solution. Why is it spelt ‘-micin’ rather than the ‘-mycin’ of products from other mycelial bacteria and fungi? It seems that aminoglycoside antibiotics from this genus end with -micin, to distinguish them from those from those isolated from Streptomyces with different taxonomic affinities (e.g. neomycin and streptomycin).
Gentamicin shares some properties with another antibiotic widely used in plant research, kanamycin: both are aminoglycosides and work partly by interaction with the 30S subunit of prokaryotic ribosomes, inhibiting prokaryotic protein synthesis. However, the two antibiotics act independently, and there are resistance genes which confer resistance only to gentamicin. The 30S inhibition means these are two of the antibiotics active against mycoplasmas (http://www.sigmaaldrich.com/life-science/core-bioreagents/learning-center/antibiotic-selection.html). Interestingly, Micromonospora seems to gain resistance to its own antibiotic through methylation of 16S ribosomal RNA (rRNA) in the 30s ribosomes. Although resistance among other bacteria is rare, this methylation has recently appeared as a mechanism of resistance against aminoglycosides among gram-negative pathogens; given the therapeutic use still, perhaps gentamicin resistance is not the ideal selectable marker to use in plasmids.

Taylor Lockwood, mushrooms and the holey veil: DVD video review

The holey veil mushroom (Dictyophora indusiata /Phallus indusiatus) by Taylor Lockwood

The holey veil mushroom (Dictyophora indusiata /Phallus indusiatus) by Taylor Lockwood

We bought a television two years ago. Sadly, despite the 723 channels available, my worst suspicions about quality have been confirmed: there is almost nothing I want to watch, especially now that I have seen everything there is from Attenborough, “How it’s made” and “Mythbusters”. If only programmes like Taylor Lockwood’s “In search of the holey veil” were regularly shown, I would have been more than happy with the light entertainment provided!

The 55 minute film tells us about his 3-month expedition looking for Dictyophora or Phallus indusiatus, the long net stinkhorn or veiled lady mushroom, across India, Nepal, China, and Thailand. I liked the way this search for the particularly impressive species gives a storyline which carries the narrative nicely, making it more than either a travelogue or documentary. On the way, we gain insight into life, people and travel in these remote locations, as well as impressive range of pictures of the fungi Taylor encounters. Large and small species are covered, sometimes with a (very) little about their biology and ecology. Approximate localities are given and, for most of the pictures, the species are named (although it would have been nice to have either captions selectable on the disk or a listing, and there were a couple of cases where I would have liked to see a hand for scale!).

There is a trailer on YouTube; I suggest starting at 45 seconds, which shows a locality and them some of the range of the mushrooms. The still photography is particularly impressive, and is cut with video footage flowing into high-resolution still pictures that do justice to the beauty of the fungi. The first half of the trailer is more doubtful, with the Indiana Jones style perhaps somewhat off-putting, although actually, it is at its most excessive in the first few minutes of the film.

Taylor Lockwood also has an outstanding library of mushroom photographs at www.fungiphoto.com and related material at www.mushroompro.com, along with other videos including some on mushroom identification. In “In search of the holey veil”, his passion for mushrooms and photography comes over and is transmitted to carry an entertaining and very watchable video.

Taylor Lockwood's DVD "In search of the holey veil"

Taylor Lockwood’s DVD “In search of the holey veil”

Price $14.95 (+P&P: c. $2.39 US or $5.64 EU/AustralAsia). Available from www.mushroom.pro