international online community for dna barcoding professionals
I am from Pakistan, and worling on Taxonomy of Elateridae (Coleoptera) from Pakistan, i am intrested to do barcoding of Pakistani elaterids, could anyone help me.
is it possible online training ? or i send specimens to someone?
Thanks to allow me to join.
Muhammad Atique Akhter
Dear Dr. Schindel,
I'm now in the network. Please let me know how I can equip myself with DNA barcoding techniques as I have to supervise a number of B. Sc., M. Sc. and Ph. D. Biotech students working under me and my colleagues in barcoding projects of Nepalese medicinal plants and prospective microbes (fungi and bacteria). Thanking you.
with best regards
Sangita Shrestha, PhD
Dear Dr Sangita,
We are into barcoding of agriculturally important insect species in Punjab. Default genes for DNA barcoding of plants are 'matK' and 'rbcL', for bacteria it is '16s ribosomal DNA', for fungi it is ITS spacer region situated between the 18S (SSU) and 28S (LSU) genes in the nrDNA repeat. You can find sequences from internet/ BOLD site.
Most appropriate and economical for you will be following steps.
1. DNA isolation from different organisms.
2. Get the primers synthesized by custom facilities.
3. Standardize PCR amlification conditions and purification of PCR product of desired size.
Most scientists go for Direct sequencing of PCR product (unpurified). However I have found following problem
i. The secondary bands in PCR product interfere with sequencing to give either no results or poor results.
ii. even in the best case of sequencing results on the first 20-25 bases are lost.
I prefer PCR cloning of PCR products in a PCR cloning vector in which cloning site is bordered by M13 sequencing primers. This takes care of sequence data that is lost during sequencing on first bases. The sequence is always the best.
3. Submit bacterial clones in stabs direct to the custom sequencing facilities (many are available in India, But best is Xcelris, Ahmedabad). This will save you from reisolating and purifying recombinant plasmids for sequencing.
I am sure you are a molecular biologist and will be able to understand and adapt to my suggestions. All the best.
Dr V K Gupta, PhD
Department of Entomology
That sounds like a great project...how is it going? I'd love to hear more! I did avian ecology and reproductive ecology research with high school students in MO, and that was so rewarding! What species have you all worked with to date? I'm about to start sequencing my shellfish species here in NC. Are your high school students actually doing the sequencing? Or are they working with other researchers at local universities? I'm just interested in connecting with people who are/have been barcoding marine species, especially bivalves. If you know of anyone with experience with those species, I'd love a referral/introduction.