Monthly Archives: August 2008

Lightwood drive and backups

Please could you spend a few minutes to ensure you have labelled your bo4smgf lightwood folder(s) (old and current) with your name and the species/project you are working on. Also there are several random files that are not in folders – ostracods and zebrafish mainly – please claim these if they are yours.

Every folder name and sub-folder name should be self expanatory so that anyone who is not familar with your work can understand what the contents are. I will then move all the folders of finished projects (those at least 2yrs old) to a new folder.

The lightwood drive (b04smgf and your own bo1… account) is backed up in numerous locations and very regularly by the university (so is the best place to use and to back up your work). Please do not rely solely on your hard-drives for backups.

All visitors should be using the bo4smgf lightwood drive and regularly backing-up and on completion of their lab visit must ensure that a final well-labelled copy of the completed work remains at the Facility. Visitor’s personnel accounts are deleted soon after folk leave and have limited access so should not be used for file or data storage by visitors.

Thanks

Debs

Job Adverts

Two post-doctoral and two technician positions in the Division of Biology at Imperial College London, Silwood Park Campus. 1) NERC Post-doctoral Research Associate on ecological and evolutionary responses to changing environments in a laboratory assemblage of bacterial species. Requires experience of microbial laboratory techniques and ecology and/or evolution. Full details at: http://www3.imperial.ac.uk/employment/research/ns2008140jt           (closing date 28 Aug ’08) 2) BBSRC Post-doctoral Research Associate on the evolutionary characterisation of bacterial diversity from DNA sequence data. Requires experience of computer programming and evolutionary theory and/or bioinformatics. Full details at: http://www3.imperial.ac.uk/employment/research/ns2008139jt             (closing date 1 Sep ’08) 3) NERC-funded technician implementing laboratory evolution experiments and assays on a laboratory bacterial community. Must have experience of bacterial culturing and lab techniques. Full details at:  http://www3.imperial.ac.uk/employment/technical/ns2008142jt       (3 years. Closing date 28 Aug ’08) 4) BBSRC funded technician conducting molecular laboratory work on bacteria and bdelloid rotifers. Must have experience of molecular lab techniques, e.g. DNA extraction, PCR, sequencing. Full details to appear soon at http://www3.imperial.ac.uk/employment/technical         (2 years initially. Closing date 1 Sep ’08) Informal enquiries to Dr Tim Barraclough, t.barraclough@imperial.ac.uk. Application details can be found by following the respective links above. 

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Dr Timothy G. Barraclough,

Reader in Evolutionary Biology

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Division of Biology,

Imperial College London,

Silwood Park Campus,

Ascot, Berkshire, SL5 7PY, UK

E-mail: t.barraclough@imperial.ac.uk

Telephone: +44 (0)207 594 2247

Fax: +44 (0)207 594 2339

Web-page: www.imperial.ac.uk/people/t.barraclough

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** MSc course in Ecology, Evolution and Conservation **

www3.imperial.ac.uk/naturalsciences/courses/pg/ls/ecology

DNA and RNA sequencing SOLID Platform – 22nd Sept

Senior Lecturer Francesco di Giovine (Molecular Medicine, Medical School) is organising a seminar by ABI on the SOLID platform to identify the potential users from within the University and NHS.  There will be technical people from ABI and perhaps one user from the only SOLID platform installed in the UK at the moment.

The seminar will be held:

Lecture Theatre 3, F  Floor , Medical School
Monday 22nd Sept,  about 10:30 – 12:30

Francesco’s contact details:

Francesco S. di Giovine  MD,PhD
Senior Lecturer in Molecular Medicine
Director, Genomic Core Facility
University of Sheffield Medical School,
Beech Hill Road
Sheffield
S10 JF

lab coat

hey folks, i’m back from field work. could whoever borrowed my lab coat please return it, preferably with all pens still in it and my 1000 pesata label too.

jamie

Frontiers in Zoology/ Use of blocking primers in prey DNA

1. Frontiers in Zoology

This may be a journal worth considering for some papers. This is one of the BMC journals and claims an unofficial impact factor of 3.24 (cf BMC Genetics at 1.58, but the Frontiers factor will be based on a small sample). It used to be cheaper to publish in than the other BMC journals but not anymore. As with other BMC journals, they will publish some papers for free and you can ask about this before submission.

2. The following paper is technically clever in using blocking primers to inhibit the amplification of “host” DNA. They analyse diet in krill using universal primers for 28S RNA that they claim will amplify in all eukaryotes. The blocking primers are designed from the krill sequence – the only sequence that they detect when they don’t use the blocking primer. The method, and blocking primers more generally, may have multiple applications.

http://www.frontiersinzoology.com/content/5/1/12/abstract

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

Hege Vestheim and Simon N. Jarman

Frontiers in Zoology 2008, 5:12doi:10.1186/1742-9994-5-12
Published:     20 July 2008
Abstract (provisional)

Background

Identification of DNA sequence diversity is a powerful means for assessing the species present in environmental samples. The most common molecular strategies for estimating taxonomic composition depend upon PCR with universal primers that amplify an orthologous DNA region from a range of species. The diversity of sequences within a sample that can be detected by universal primers is often compromised by high concentrations of some DNA templates. If the DNA within the sample contains a small number of sequences in relatively high concentrations, then less concentrated sequences are often not amplified because the PCR favours the dominant DNA types. This is a particular problem in molecular diet studies, where predator DNA is often present in great excess of food-derived DNA.
Results

We have developed a strategy where a universal PCR simultaneously amplifies DNA from food items present in DNA purified from stomach samples, while the predator’s own DNA is blocked from amplification by the addition of a modified predator-specific blocking primer. Three different types of modified primers were tested out; one annealing inhibiting primer overlapping with the 3′ end of one of the universal primers, another annealing inhibiting primer also having an internal modification of five dI molecules making it a dual priming oligo, and a third elongation arrest primer located between the two universal primers. All blocking primers were modified with a C3 spacer. In artificial PCR mixtures, annealing inhibiting primers proved to be the most efficient ones and this method reduced predator amplicons to undetectable levels even when predator template was present in 1000 fold excess of the prey template. The prey template then showed strong PCR amplification where none was detectable without the addition of blocking primer. Our method was applied to identifying the winter food of one of the most abundant animals in the world, the Antarctic krill, Euphausia superba. Dietary item DNA was PCR amplified from a range of species in krill stomachs for which we had no prior sequence knowledge.
Conclusions

We present a simple, robust and cheap method that is easily adaptable to many situations where a rare DNA template is to be PCR amplified in the presence of a higher concentration template with identical PCR primer binding sites.

BBQ CHANGE OF PLAN

Hi everyone,

Given that the weather forecast for tomorrow is looking pretty appalling, I have decided to abandon the BBQ idea and organise a curry for Jamie’s birthday instead.  I have booked a table at Jaflong in Crookes for 8pm on Saturday, but actually have no idea how many people are going to come, so please can let me know if you want to come asap (partners, housemates etc are welcome too).  It would be great to see lots of you there! So please get in touch: a.llewellyn@shef.ac.uk, 07717202715 or find me in B54b to let me know if you can make it. Cheers!

Amy

Revival of Mol Ecol Lab Meetings


The Molecular Ecology lab meetings have been revived and will take place on the first Tuesday of each month, at 10.30am in B52. The first meeting will therefore be on Tuesday 2nd September.

Two members of the lab will each present a 10-15min talk. Please email me (h.dugdale@sheffield.ac.uk) to volunteer to give a talk – this is a great opportunity to let the lab know about your current or previous research! Members presenting their talks will be asked to bake a cake for the meeting.

I will also collate any lab news, so please email me before the meeting if you have any recent papers accepted, successful grant applications etc. that you’d like the lab to know about.

TAB Group Meeting – Friday 8th Aug B52, 10am

Hi all,

the next TAB group meeting is tomorrow in B52 from 10am.

(This excludes visitors to the MGF – your meeting will be next week.)

Milk Kitty

Hi there,

in case you don’t already know, there’s a Milk kitty for the B1 locker.  You can join at the bargain price of £1 per month and save yourself the hassle of going to the shops.  The milk bottle (plastic, half fat) is kept in the locker fridge, with a white K on the lid.  We don’t have access to glass bottles any more, so please don’t help yourselves to those!

Let me know if you want to join!

Updating our people webpage

Hi all,

could you have a look on the “personnel” page of our website to check that  your details are correct? (and that you are included too!)  If not, send me an email on C.pagnier@shef.ac.uk

Thanks!

http://www.sheffield.ac.uk/molecol/personnel