Monthly Archives: July 2009

new postdoc in the dept looking for accommodation

Carmen Dorca Fornell  is a new Postdoctoral Researcher who will be working with Andrew Fleming and Paul Quick. She is looking for a place to live in Sheffield for her and her partner, and was wondering if anyone here in the department could help.

If you think you can help please contact Carmen direct on carmendorca@hotmail.com

Lab news:

Congratulations to Arnaud Bataille, who’s recently published some of his work
studying mosquitoes in Galapagos has had a lot of publicity.

A. Bataille, A. A. Cunningham, V. Cedeño, L. Patiño, A. Constantinou, L.D.
Kramer and S.J. Goodman. 2009. Natural colonization and adaptation of a
mosquito species in Galápagos and its implications for disease threats to
endemic wildlife. Proceedings of the National Academy of Sciences, published
online 2 June 2009.

Arnauds work has been highlighted on NERCs website Planet Earth, ZSL Institute
of Zoology website and the Independent.ie

http://planetearth.nerc.ac.uk/news/story.aspx?id=438

Congratulations are also due to Mathias Craul and Akos Klein who successfully
defended their theses in June:

Klein A. (2009) PhD Thesis (Eötvös Loránd University, Hungary) The possible
effects of extreme winters on the barn owl (Tyto alba Scop., 1769) population
in Hungary: survival, physiology and population genetics.

Craul M. (2009) PhD Thesis (University of Cardiff / Leibniz Universitaet
Hanover, Germany) Molecular phylogenetics and conservation genetics of sportive lemurs (Lepilemur edwardsi) in northwestern Madagascar.

David Martin-Galvez, Akos and Michelle Simeoni all had their primer notes
published online and Jim Groombridge and Richard Phillips also published
Facility-supported work this month.

see
http://www.shef.ac.uk/nbaf-s/publications.html

PhD studentship in evolutionary ecology and conservation at University of Otago, New Zealand.

with our very own Shinichi…more details, here: phd-studentship.doc

tuesday ucas visit

hey folks

just to repeat what Susie emailed you about, but its TUESDAY for me.

Firstly – I am doing UCAS demos on TUESDAY 7/7/09 from 2 til 2.45pm, and I really
need to use Alain and Dan’s benches over this time. If this is a real
problem please let me know asap. Apparently a lot of people are coming, so please be patient if visitors are blocking the door to the cold room/tip box cupboard/drying oven – just wait until they are gone!

Secondly – Because of the size of the groups, I need to borrow a laptop
to run my presentation from. Does anyone know of any spare or can
someone lend me theirs from 1.50 to 2.50pm?? Please!

Thanks!

Jamie

Running GeneMapper on Macs!!!

Jess has sussed out a way of running GeneMapper on Macs (something many of us thought impossible)…Mihaly has just successfully installed it on his

Jess said 

“I use windows emulation software on my MAC. Since all the platforms run on INTEL chips you can run mac, linux, and windows all on one machine. I use a program called VMware Fusion. There are others – Bootcamp and Parrallels – but I like this VMware the most because you don’t need to reboot your computer to open windows.  Once Windows OS is installed you can install any windows program, including genemapper. I have Windows XP discs, I am not sure how well VISTA works on VMware. ”

Mihaly said
“I set up XP on my Mac, and it seems to work fine.
At the moment I run Fusion on the free version, but I will buy a licence. To set it up is and run Xp is easy, I chose shared files option, since mirror option doubles the files on the computer. RAM is recommended to be 1 G at least, this you can adjust afterwards as well. It is also recommended to set the CD drive (D:) for the virtual machine, this way you can install Genemapper.”

Message from Conservation Genetics journal

Dear All,

just an update on how things are progressing with Conservation Genetics in our 10th year.  As you may have seen, we’ve now separated the technical papers into their own new journal: Conservation Genetics Resources.
The main objectives of the new journal are to:

  • Focus on the problems and species which are of concern to conservation biologists and managers
  • Provide a forum for exchanging resources which support research in conservation genetics (including primer notes, but with a broader remit than that)
  • Provide a forum for reporting on the practical incorporation of genetic data into the development of management practice and conservation policy

You can find more detail on the new journal’s website:
http://www.springer.com/life+sci/ecology/journal/12686

This move allows Conservation Genetics to focus more exclusively on full studies and applications, though we’ll retain Short Communication and Review paper formats.  Our impact is steadily improving (IF=2.4 for 2008), and we expect that our change in focus will help increase that further, as was the experience at
Molecular Ecology.  A new feature that we’re introducing this year is the inclusion of special issues, with a target of including one of these every 1-2 years.  The first will be published early in 2010, based around the final meeting of the EU ConGen program with an excellent set of invited authors.
Overall the journal is progressing very well, and we look forward to year 11!
Thanks to all of you for your input and support over the years.

Best, Rus

…RNA treated DNA preps and the Nanodrop

This is from the Nanodrop people..”After RNase treatment I would purify the DNA by passing through a column. The free nucleotides themselves will pass through the column (e.g by Qiagen or Sigma), leaving only intact DNA bound, which can then be eluted. I cannot find a definitive answer in the literature, but I would expect the degraded RNA to still absorb at 260nm, therefore I would recommend the additional purification step.”

I don’t know fully if digested RNA fragments are co-precipitated with DNA and hence a column/gel cutting is the only way of separating these 260nm absorbing fragments from the DNA. Anyone got any evidence? 

 Also- in general be careful with preps from columns- there is definitely something ‘weird’ with absorbance profiles samples from the silica plate method (and possibly from other columns). If in doubt use the ‘safer’ quant. method (presuming that Hoeschst dye binds only to DNA).

Anyway…I hope you get the picture!!

DNA quantity and quality

…there seems to be confusion as to how to best *estimate* the concentration and quality of DNA. I summarise which method you should use when! It is really difficult to get an *absolute* measurement but you *must* use the most appropriate method to get the best estimate. 

Agarose gel (stained SYBRSafe or rarely ethidium Bromide)- quantity and physical quality of DNA (using known lambda DNA standards held in the lab stock). RNA will fluoresce. Use on DNA from all tissue types.

Nanodrop (no dye- it is a spectrophotometer)- quantity and purity (salts etc. and proteins) for both DNA and RNA solutions. Both absorb maximally at 260nm so you cannot tell how much of each in a mixed sample. Use when you know there is no RNA in the DNA solution or vice versa (as a guide bird blood is usually OK- tissue samples are not- if you don’t know run on an agarose gel 1st).

Fluorometer-(Hoechst33258)-  asesses the quantity of DNA only (binds to AT- calf thymus DNA standard which we use has an AT of 58% which should reflect your organism- if it doesn’t you will need to do an adjustment calculation- it is good for most plant and animal DNA). Take care when quantifying DNA with difft. conformation from the standard (SS DNA, plasmids).

 hope that helps!

Accomodation wanted

A new visitor, Jen Smith, is looking for a room in Sheffield from the end of July to the end of September. I can pass the contact details on, if anybody might be able to help.

Alain