Author Archives: Terry

Babysitter needed this evening

For just a few hours.  Is someone willing to volunteer? Small financial compensation. Should require no real effort (no babies as such!) Please email t.a.burke@

Terry

Fridge and TV available free

Very basic standard size fridge in working order available to anyone who wants it (not for lab use). If interested tell me IMMEDIATELY! Also a large old style (cathode ray) 26 inch Sony TV in perfect working order. Very heavy!

Terry

Terry’ group meeting today – postponed

Apologies, but I have to postpone today’s meeting. Will reorganise some time next week. Anything urgent please email/ see me.

Terry

Graduate seminars and other talks

If you are going to give a talk in the department, perhaps in the Graduate Seminar Series, at a specific group’s lab meeting or elsewhere in the department, including “practice runs” for conferences, then please do not be modest and do let everyone know via this blog.

Xmas Meal

I’ve added a comment to the earlier posting.

Congratulations to Clemens and Sophy

on their new positions! Well done. I’ll let them tell us all what they’re going to be doing?

Mouldy plants

Just to say thanks to all the volunteers who helped Maria Elena this week – it’s much appreciated!

Terry

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.

Spare household items

We have an oldish but (as far as I know) functional Electrolux vacuum cleaner going free if anyone wants it. Also an ironing board (if anyone actually uses one). Also a clothes drying rack that Kenta left behind that’s just about functional. And for anyone going the whole hog domestically we have lots of spare prams, stair gates etc…! Any takers?

House sitter wanted – August

From Virpi:

3-BEDROOM HOUSE AVAILABLE FOR AUGUST ALMOST FREE

I am going away for the whole of August and need someone to live in my house and
look after my plants and fish (not a big job but requires close to daily visits
from someone). I will take all my dogs with me! No rent needed as long as you
cover the gas, electricity etc bills. It is a 3-bedroom Victorian terraced with
a sunny garden in Hillsborough, 1 minute walk from the tramline (10 mins from
APS), close to shops, pubs and park, and coming with telly, internet and all
the furniture. Moving in already before August is possible.

cheers
virpi

Dr. Virpi Lummaa
Department of Animal and Plant Sciences
University of Sheffield
Western Bank, Sheffield S10 2TN
United Kingdom

tel. +44 (0)114 222 0051
fax. +44 (0)114 222 0002
email. v.lummaa@sheffield.ac.uk