'Old News' from the Molecular Cytogenetics Research Group

Genomics, Molecular Cytogenetics, Chromosomes
Cell and Systems Biology and Genome Organization

Pat Heslop-Harrison and Trude Schwarzacher, Department of Biology,
University of Leicester, LE1 7RH UK

E-mail: PHH4(a)le.ac.uk and TS32(a)le.ac.uk
Phone: +44/0 116 252 5079 or 3381; FAX: +44/0 116 252 2791

   
Previous News Items - removed from homepage 17 April 2012

We have made two YouTube Videos for University Practical Classes in the BS1003 Cell and Developmental Biology. The related part of the course booklet is here. The first video shows sterile tissue cultures of tobacco leaves and carrot roots.

The second shows control of pigment production by phytochrome involving reception of red and far red light

6th September 2011: Talk at Plant Genome Evolution, Amsterdam (6Mb PDF) Follow on Twitter with #PGE11 or Pathh1

1st September 2011: Talk at International Chromosome Conference Manchester ICC18
See also www.AoBBlog.com for my thoughts on the meeting, and storify.com/pathh1 for other updates, as well as following pathh1 and #ibc18 on Twitter

 BBC One ShowYes, we have no bananas ... Bananas & Pat Heslop-Harrison in greenhouse, University of LeicesterThe One Show, banana diseases, biodiversity and our research projects - May 2011

A discussion and more pictures related to the interview of Pat Heslop-Harrison by Jay Rayner is posted on www.AoBBlog.com. This site also encourages comments and questions about the article. Pictures of banana diseases and the banana genome are shown in a recent lecture here - sorry for the large PDF download.

This website, www.molcyt.com, gives technical information about our research projects, including links to the primary publications which are used by other scientists, plant breeders and policy makers, as well as by students studying these areas.

Science Signalling Network Reduction CoverAn algorithm to reduce complexity but maintain dynamic properties of networks

All biological systems involve complex networks with genes and regulatory interactions. In this manuscript with the lab of Kwang-Hyun Cho, KAIST, Korea, we develop an algorithm that systematically removes redundant verticies and nodes from a complete network, leaving a simplified "kernel" that is functionally and dynamically equivalent to the original complex network. The full paper is at 10.1126/scisignal.2001390. The paper was chosen for an Editor's Summary here and the concept is illustrated on the cover of the issue.

J.-R. Kim, J. Kim, Y.-K. Kwon, H.-Y. Lee, P. Heslop-Harrison, K.-H. Cho, Reduction of Complex Signaling Networks to a Representative Kernel. Sci. Signal. 4, ra35 (2011).

 

Pat Heslop-Harrison presented a talk "Adventures, Bananas, Cytogenetics, Diversity and Evolution" to the Association of Clinical Cytogeneticists ACC Spring Meeting in Durham in April 2011. (Sorry, thats a link to a large PDF - it will take up to 5 min to download). The title sounds rather contrived but actually jumped out from a (deadly!) bullet point list of the main points when I was outling the talk. It was quite a challenge - a very welcome one - to talk to this expert audience and excite them about the range of our work and its implications. In March, Pat Heslop-Harrison has made presentations on molecular cytogenetics at the European Cytogeneticists Association training course and at a graduate level course in Leicester. A version of the slides from these courses are linked here: in both cases, I left in several blocks of slides which enabled me to alter the focus depending on discussions. 

Plant and Animal Genome Conference, San Diego 2011 - Pat Heslop-Harrison made two presentations

Lecture title: Musa Banana Repetitive DNA

Repetitive DNA evolution in Musa/Banana

Lecture title: Genomic divergence outside genesGenomic divergence outside genes

 

Banana LecturePat Heslop-Harrison presented a lecture at the Society of Biology Regional Annual General Meeting in November 2010 on "Bananas, genetics and appropriate biotechnology" The PDF of the text slides is linked here.

ECA course in Nimes 2010 - Plant Molecular Cytogenetics slides here (11MB large PDF - wait for download).

A paper on "Biology and Engineering: Coming Together in Systems Biology" was presented in Korea (link on title opens 8MB PDF of my talk). Video-on-demand VOD of my talk is at http://www.eimbl.org/club.intro.seminar.list.screen?p_cate=35

A paper on Genomics, Economics and Bananas was presented at the OECD meeting on Tropical Fruits in (indirect link).

Feedback loops and oscillationsNetworks, Noise and Nodes

Xuerong Mao organized and exciting workshop on The Stochastic Modelling of Biological Networks in September 2010 at the University of Strathclyde. Pat Heslop-Harrison's lecture overviewed current systems biology work in collaborations with Jongrae Kim (University of Glasgow), Declan Bates (University of Exeter) and Kwang-Hyun Cho (KAIST, Korea). The PDF of the lecture (with a few deletions, as well as the extra slides skipped when I ran out of time) is here.

Key points included the critical nature of noise in inducing and maintaining oscillations that are important to control, the costs of control and feedback loops to a cell, and the synchronization of oscillations.

 

Crocus Saffron Flower with StigmaThe EU Project Crocusbank was highlighted at the University of Leicester Botanic Gardens Crocus Days.

Focus on the crocus - Leicester's internationally acclaimed genetics research involved in European project into saffron production.

Details are presented in our news story - Focus on the Crocus

Photographs of posters and gardens are here:

Richard Gornall (Centre_ and  Pat Heslop-Harrison (Right) Discussing Crocus Origins With David Watkin (left, Chair of the Friends of the Botanic Garden)
Crocus flowering under Japanese maple in the Botanic Gardens Crocus flowering in the Botanic Gardens, University of Leicester
Crocus vernus flowering in Italy

Saffron flowers

SEB Presidents Commentary on Communications May 2010

Biomass Gene Locations (QTLs) Identified in Ryegrass April 2010

 
 

Synchronization of Oscillations

Synchronization of oscillations by coupling PP oscillatorsNew work published in February 2010 shows that weak coupling between cellular oscillators can lead to rapid synchronization. With such a strong effect, there is often no need for cellular processes to be connected to any centralized or controlling clock.

See the work with colleagues from Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST) in Journal of Cell Science

Kim J-R, Shin D, Jung SH, Heslop-Harrison P, Cho K-H. 2010. A design principle underlying the synchronization of oscillations in cellular systems. Journal of Cell Science doi: 10.1242/jcs.060061 (password for this link only)

A movie film shows the induction of synchronization by the interactions.

Lecture to the BSBI June 2010

DNA extraction

Pat Heslop-Harrison talked about DNA and Chromosomal Evolution to the Botanical Society of the British Isles at their Annual General Meeting.

The lecture slides are linked here (4.5MB PDF).

DNA extraction was as follows:
25 ml "Smoothie" drink (mashed banana or kiwi works as well but takes a bit longer)
12 ml water
5 ml hair shampoo (technically, one that contains a non-ionic detergent like SLS/SDS - sodium lauryl sulfate or sodium dodecyl sulfate - EDTA, and sodium citrate)
2 large pinches of salt
Stir together (try to avoid foaming) and leave 5 min

Pour into a coffee filter and allow to drip through for 15 min

Add 25 ml ice cold alcohol/ethanol - UK standard 40% vodka will not work well; I used Irish Poteen at 60%; strong rum is also suitable; or rubbing alcohol)

Wait 2 to 10 min, and the DNA will precipitate out as white, sticky, fibrous strands. (If you want to purify further, you can pour off the alcohol/water/protein/salt/detergent liquid, rinse the DNA with more alcohol, and redissolve the DNA in water, then reprecipitate).

The shampoo gently disolves the cell membranes and proteins, leaving the DNA intact, the EDTA stabilises the DNA from enzyme attack, and the salt-sodium citrate is a weak buffer. DNA is soluble in salt solutions but not in dilute ethanol, unlike most other cellular components which are insoluble (filtered out) or remain dissolved.

Pat Heslop-Harrison and sequenced plant species

We are all involved with the dissemination of the science we
do. But in the connected world, what is meant by dissemination? Think about where you find out about experimental biology– your own areas of interest, and the subject in its much broader context. Key sources of information about what is happening – the breakthroughs, the details and the controversies – will come from a
wide range of sources. While
information overload is infinitely
preferable to information deficit, how do you filter the amount of information which could reach each one of us?

Full SEB Bulletin March 2010 here.

QTL for Biomass on Lolium Chromosome 3 Anhalt et al. 2009Olli Anhalt, who completed her PhD working with Susanne Barth at TEAGASC, Ireland, and in Leicester, has identified a major QTL for fresh and dry weight which explains around 30% of the phenotypic
variance in a large field experiment involving 360 F2 plants. The discovery of loci with such huge genetic effects is very important for understanding how to increase yield of grasses and biomass crops more generally. The full results are in: Anhalt UCM, Heslop-Harrison JS, Piepho HP, Byrne S, Barth S. 2009. Quantitative trait loci mapping for biomass yield traits in a Lolium inbred line derived F2 population. Euphytica 170: 99-107. doi: 10.1007/s10681-009-9957-9

(first link needs password, second needs subscription)

 

DNA Satellite Evolution

Guto Kuhn reports for the first time interspersion between non-homologous satellite DNA repeats in Drosophila. The article features on the Heredity website for May 2009

Extended DNA fibres from Drosophila nuclei showing junctions between non-homologous satDNA sequencesMolecular analysis of satellite DNA junctions revealed that they have evolved by multiple events of illegitimate recombination with subsequent rounds of unequal crossing-over expanding the copy number of some junctions.

This work also revealed satDNA monomers organized as higher-order repeats – a rarely reported feature in the Drosophila genus. (Link here our other work on Drosophila satellite DNA.)

See full paper at: Kuhn GCS, Teo CH, Schwarzacher T, Heslop-Harrison JS. 2009. Evolutionary dynamics and sites of illegitimate re-combination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species. Heredity 102: 453-464. doi: 10.1038/hdy.2009.9.
Colour plate linked here.

Title for talk on Chromosomes and Evolution26th Conference on the Theme of Genetics and Breeding: University of Sao Paulo, Piracicaba, Brazil, October 2009

In an exciting meeting focussing on Darwin, evolution and cytogenetics, Pat Heslop-Harrison presented a talk on "What the chromosomes say about evolution", (link to PDF click here - quite large file) starting with quotations from Darwin and then showing how experimental work with crop species shows chromosome evolution in action. This information is used for crop improvement.

European Cytogeneticists Association - 7th European Cytogenetics Conference, Stockholm, 4-7 July 2009

Title page of Charles Darwin The Variation of Animals and Plants under DomesticationPat Heslop-Harrison presented a plenary lecture on Darwin, Domestication and Plants. A PDF of the presentation is linked to the title. The article by Charles Darwin's son, Francis, published in 1899 entitled The Botanical Work of Darwin in Annals of Botany is a relevant reference. The webresource with the full text of all of Charles Darwin's writings at http://darwin-online.org.uk/ is extremely valuable.

 

From the cover: Feb. 2009 Times Higher Education on our joint letter about saving research from red tape

Times Higher Education Cover Blue Skies Appeal

Link to letter in THE. Associated Editorial is important with comments from readers. Many blogs, eg here, now discuss this article.

LATEST PAPER MAY 2009

Guto Kuhn reports for the first time interspersion between non-homologous satellite DNA repeats in Drosophila. The article features on the Heredity website for May 2009

Extended DNA fibres from Drosophila nuclei showing junctions between non-homologous satDNA sequencesMolecular analysis of satellite DNA junctions revealed that they have evolved by multiple events of illegitimate recombination with subsequent rounds of unequal crossing-over expanding the copy number of some junctions.

This work also revealed satDNA monomers organized as higher-order repeats – a rarely reported feature in the Drosophila genus. (Link here our other work on Drosophila satellite DNA.)

See full paper at: Kuhn GCS, Teo CH, Schwarzacher T, Heslop-Harrison JS. 2009. Evolutionary dynamics and sites of illegitimate re-combination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species. Heredity 102: 453-464. doi: 10.1038/hdy.2009.9.
Colour plate linked here.

Annals of Botany Cover with Roses

Annals of Botany

PLANT - POLLINATOR SPECIAL ISSUE - Click for link to Annals of Botany ContentSnapshots

2009: The Chief Editor of Annals of Botany is based in the Molecular Cytogenetics Group. The background cover picture for 2009 shows Rosa canina from Barnack Hills and Holes National Nature Reserve.

 

A talk on Banana: Past Present and Future was presented to the Warwickshire Womens Institute.

ECA course in Nimes 2009 - Plant Molecular Cytogenetics slides here (11MB large PDF - wait for download).

A paper on "Biology and Engineering: Coming Together in Systems Biology" was presented in Korea (link on title opens 8MB PDF of my talk). Video-on-demand VOD of my talk is at http://www.eimbl.org/club.intro.seminar.list.screen?p_cate=35

A paper on Genomics, Economics and Bananas was presented at the OECD meeting on Tropical Fruits in November 2008 (indirect link).

Related websites: www.SBLab.org for our Systems Biology work.
www.BioAstral.com for our spin-out company involved in hyperspectal quantitative imaging.
www.CrocusBank.org for information about a new EU project on Saffon Crocus and its relatives

Link to PubMed database and paper downloads (click on 'page' icon next to title).

 
   

 

 


     

 

www.molcyt.com - index.htm