Monthly Archives: August 2008

Great Yorkshire Run

Hi everyone,

I’m taking part in the 10km Great Yorkshire Run on Sunday 7th September to raise money for Amnesty International.  I have never ran 10km before, so this will be a real challenge for me.  I would be extremely grateful to anyone willing to sponser me!

Thanks very much!


multiplex- programme to screen oligos/combinations

Hi folks- have a look at this link for a free programme for testing whether you markers are good together (and whether they produce primer dimer and hairpins). Anyone embarking on multiplex or having problems currently should have a look at this. It is obvious that some markers just do not seem to work in multiplex and you may be able to screen these oligos/combinations out before you start (e.g. Carl Vangestel found that the program highlighted that the pigtail on one of his markers was the problem- by replacing it with non-pigtailed he managed to get it to work nicely). Alex Ball (+ others?) is using this so if you need a quick instruction ask him. 

 (AutoDimer: a screening tool for primer-dimer and hairpin structures.  Biotechniques. 2004 Aug;37(2):226-31)

Black-and-white animal party

Hi all,I’m getting older, so let’s have some fun! I’m having a house and (hopefully) garden party at my place on 28th August (59 Mona Road, Crookes). Fancy dress required – I know it is quite a challenge but there are lots of black and white animals out there.
It’s Thursday, but well, you can be a bit sleepy one Friday at work ;)I’ll be awaiting you from 6pm.Looking forward to seeing you!DorotaPS. I may reveal that I’ll be a sheep 😉

Accomodation for Kenta

Kenta needs Accomodation for three nights
from the 1st Sept. Email him direct on

Real-time PCR machine (Rotor-Gene 6000)

Please have a look at the Real-time PCR machine that it is possible Roger may jointly purchase. Amy and I have seen a demo of it and the software and are pretty impressed (it also comes in a choice of colours outback red or bondi blue- which I think is really nice as most PCR machines do look a bit boring). …..Anyway…. the samples rotate in an oven and the well-to-well temp. variation is apparently 0.01degree whereas this can be 0.5degree on a normal 96-well block. It will also do HRM analysis and also allow multiplex reactions (2 colours c£24K and 5 colours c£30K).

 The only downside I can see is that it is not 96-well compatible (so would have to weigh up whether the loading could be done manually or via a robot c£19K). This may be a pain if you want to run 100’s of samples.

The link is below for those interested in having a  say (Julie Scholes is probably going to get one and the question would be whether we chip in and share it).

TAB Group meeting – not until Friday 5th September

Dear all,

the next TAB Group meeting (MGF visitors included) will be on Friday 5th September, with a new start time of 12 to 1.30pm, but still in B52.  This is not to be confused with the monthly Molecular Ecology Lab (MEL) meeting organised by Hannah and held on Tuesday 2nd September.  Any question, you can always ask me!

By the way, the cakes last meeting were great 😉

BLAST E-values

Hi everyone,

I have a BLAST related question:

When you get a really good match the E value is reported as 0.0, presumably because it is actually so low it is below a threshold level that will be reported.  It seems a bit confusing to report E values as 0.0 though so I was wondering if anyone knows what the cut-off is?



Real-Time PCR Training Workshop 21st Oct

Dear Researcher,

May I cordially invite you and your colleagues to our Real-Time PCR Training Workshop hosted in a local attraction near you (Millenium Galleries, Sheffield, 21st October 2008). Places are limited, so please book early to avoid disappointment.

Applied Biosystems present: Real-Time PCR Training Workshop

Who should attend?
Any PCR users who have an interest in starting to use real-time PCR or current new users who want further training on Gene Expression Applications:Absolute and Relative Quantitation, Theory, Analysis, and Optimisation.


Principles of and workflows using real-time PCR
Applications for quantitative and qualitative analysis
Absolute and relative quantification
Sample preparation: choice of the correct extraction/purification method
Assay design: from sequence to primer and probe
Software Set-up and Analysis
Experimental optimisation and validation


At the end of the course you will be familiar with the theory and practice of realtime PCR and you will learn the most cost-effective way to set-up, run and analyse your gene expression experiments. Find out about new real time PCR developments and have time to discuss your own real-time PCR experiments with Application Support Specialists. View a Live StepOne Real-Time PCR instrument demonstration that will be used throughout sections of the course.

The trainer:

The Applied Biosystems Training-Team consists of highly qualified members who have extensive experience in professional support for real-time PCR. The number of participants is restricted to 30 per venue.

Fees (All prices exclude VAT):

There is a small course fee, but all delegates will recieve money-off certificates for common QPCR consumables and QPCR systems; completely covering the cost:

UK: £125 per person (for registrations received by August 29th 2008)
£150 per person (for registrations received after August 29th 2008)


Detailed course material as well as a lunch and beverages are included in the fees. The registration starts at 9:00 am and the course ends at 4:45 pm.You will receive full venue details with the confirmation of registration.

Other local Real-Time PCR Training Workshop Venues are:

Museum of Science and Technology, Manchester, 9th October 2008.
Millenium Galleries, Sheffield, 21st October 2008

The Applied Biosystems team is looking forward to welcoming you!

Click here to register:

APS journal club

The APS journal club takes place every third Thursday and the next one is on 21st Aug, 4pm, APS tea-room. Everyone is very welcome, and we particularly encourage PhD students to come along, so please join us for beer-enthused discussion of the merits of double-blind peer review. Free beer is provided!

The paper we will be discussing is: Budden, A.E., et al., Double-blind review favours increased representation of female authors. TREE, 2008. 23, 4–6.

Mol Ecol Group Meetings: Clarification

The Mol Ecol Group Meetings are intended for all visitors to the facility and everyone working with Jon, Roger and Terry (nb: this is different to the meetings posted on the blog that Terry/Celine organise on Fridays).


The Mol Ecol Group Meetings will take place on the first Tuesday of each month. The idea is that Andy Krupa will update everyone on lab news and I will update everyone on publications/grants by members of the group. Then two people (visitors to the facility or students/staff of Roger, Terry and Jon) will present a 10–15 min talk on their previous or current work.


First Mol Ecol Group Meeting: Tuesday 2nd September, 10:30-11:30, B52

Raj and Dunja will practice talks that they are presenting at BES meeting & Genetics Society Meeting in Bath, respectively


Please email me with any publication/grant/etc news that you want the group to know about at the meeting! Also, if you would like to practice a talk at future meetings then please let me know.