25/01/12: IDT Launch gBlocks, a Revolutionary New Approach to Gene Synthesis & Alternative to Cloning
January 25, 2012 by Peter · Leave a Comment
I am sooo excited about this new product from IDT. By making genes more affordable, while significantly increasing the speed of delivery, IDT are making synthetic genes more accessible to labs than they have been before.
In short, gBlocks™ Gene Fragments are double-stranded, sequence-verified DNA blocks up to 500 bp in length that can be shipped in 3–4 working days. You define the sequence. Prices are great (EUR 89/DKK 662/ SEK 787), which makes them a realistic alternative to cloning. Users can simply order individual gBlocks, assemble them and drop them straight into their favourite vector.
Anyway, enough from me. If you want to learn some more, please visit the IDT website and try them out!
Update, 27th January:
There are several resources on isothermal assembly, which is one of the recommended methods by which gBlocks can be used to create larger gene fragments. Here is the protocol on the Megason Lab wiki page. The page also contains a link to the original Nature Methods paper, describing the technique.
I wonder if it is just a matter of time before a commercial kit comes out for this…
20/01/12: Upcoming Conference in Denmark: Integrative Network Biology 2012, 11-13 May 2012
January 20, 2012 by Peter · Leave a Comment
This conference in Denmark looks really interesting for anyone interested in Systems and Network Biology. The organizers have done a great job in getting together a good set of international speakers and it is not too expensive. Plus, May is one of the nicest months to visit Denmark. The conference venue is reasonably close to the nice beach at Snekkersten, if my memory is correct.
Check out the conference homepage here.
The only downside (for me at least) is that I won’t be able to make it!!
11/01/12: Core Center for “Next Generation Sequencing” to Open in Aarhus
January 11, 2012 by Peter · Leave a Comment
In Danish: http://www.auh.dk/presse/nyheder/visnyhed?visNyhed=104792
I know this lab reasonably well. They have lots of equipment in modern labs close to Skejby Hospital. Good luck to them.
21/12/11: Video of Palm PCR in Action is Now Available
December 21, 2011 by Peter · Leave a Comment
For those of you who are a little curious about the Palm PCR instrument, there is a video demonstration available (see below).
Only problem I have with this vid is that it is a bit long and the changes in speed don’t help. A 7 minute video should also have a bit of music/commentary too. I never thought I would miss “cheesy marketing voice-over man,” but I do!
Still, this video is great because it shows the Palm PCR instrument in operation and gives researchers an idea of how it could be used. It would be cooler if it was shown being used somewhere far away from a lab bench, but maybe that will come later.
06/10/11: Scientists, if you are organizing a conference: some tips on getting sponsorship money
October 6, 2011 by Peter · 2 Comments
This post is inspired by a conversation I had earlier this week with a researcher who is trying to get one of the companies I represent to sponsor his conference. If you are thinking of doing something similar, I hope you will find the post useful. The ideas are primarily aimed at someone in a university setting who is hosting a “typical” academic conference, but may well be useful in other circumstances.
Sponsorship from companies is really important for scientific conferences. It often pays for a big part of the costs for hiring the venue, the food, flying in big-name speakers, printing of the abstract book etc. It also helps keep the cost of registration down, so that as many people who are interested can actually attend. Therefore, I am convinced that sponsorship is a big factor in deciding whether a conference is successful or not.
Despite this, I have experienced that many researchers organising scientific conferences seem to treat sponsors – once they’ve got the money - the way they treat a used latex glove: hold with fingertips at arms length and discard quickly. The attitude can be summed up as: “We buy your products (or in some cases ” are thinking about buying”). Please sponsor us. Thank you. We can now spend the next 2 days ignoring your exhibit.”
To be honest, in the past, some companies have gone along with this and might well have contributed to this “easy money, no respect” attitude. I am definitely guilty, making dumb decisions and justifying them with such lame excuses as:
- “Professor Big Name is the organiser (well one of his post-docs in reality). He might finally buy from us if we suck up to him,”
- “Company X are there so we have to be there,”
- “it’s about raising awareness,”
- “I’ve never been to Prague.” (OK, this last one was never stated out loud)
Anyway, my message to you is this: by and large, those days are over. Believe it or not, companies actually want to get something for their money.
I’ll let you into a secret. Companies talk about ROI. It stands for Return On Investment. So, if a company spends $20K on attending a conference, but can only link the sale of one enzyme kit worth $75 back to the conference, that is a “lousy ROI.” Remember, in addition to sponsorship, a company will pay for its employees travel and hotel rooms, shipping of exhibit material, maybe flying in a specialist. All that can actually cost more than the actual sponsorship. Lousy ROI means no sponsorship for you, no more trips to Prague for company reps. Everybody loses out.
How can you, as organiser, ensure that your conference delegates are going to be good for a company’s ROI? Well, actually you can never guarantee that, but that’s OK, because there is something else you should know about ROI: it is actually quite difficult to measure – and many companies don’t measure it, even if they talk about it. You can use this fact to your advantage, because as conference organiser, your job is to think about doing stuff that increases ”potential ROI” and sell that potential to the likely sponsors. If you do a good job on organising with a thought to their ROI, it might well turn into ” real good ROI” for the companies involved. They will be happy and more likely to cough up for your next conference. Nice, eh?
All of the above preamble is to set the scene for a few ideas that you can use to encourage company sponsorship of your conference:
1. Do everything you can to encourage delegates to visit the company exhibits during the conference breaks. Look, we company people know a whole bunch of stuff that you scientists don’t. We know what’s new, what’s upcoming, we know which products are good, we can arrange samples, discounts, instrument demos, tell you which applications are hot and what other researchers are using. Plus, scientists are clever, right? So they are not going to fall for a dumb sales pitch, are they? Therefore, they have great reasons for talking to company representatives without any obligation to spend money.
To get your delegates visiting the exhibits, try these ideas:
- Good location. You have to get researchers in the same room as the exhibitors. That means coffee breaks, buffet lunch and poster sessions should be held in the same room as the exhibits. Obvious? Yes, but you’d be surprised how often this does not happen.
- Set up a prize competition that requires delegates to get information/stamps/whatever from each of the exhibitors. A quiz is a good idea.
- Remind delegates - every now and then - who is paying for a big chunk of the conference. Visiting the exhibits is simply a nice way of being polite and saying “thanks.”
- Make the breaks a decent length. 20 minutes minimum for coffee breaks.
- Allow perhaps one exhibitor to have a stand during the main conference dinner and pay for the privilege. If you put them in charge of the extra wine, their stand will be very popular and they will be very happy.
2. Give out the delegate list after the conference is over. Marketing departments like this (and they normally hold the purse strings for conference spending). You can choose to make this exclusive, a condition of “special, pricier sponsorship,” so that it does not go to all companies. More sponsorship cash for you.
3. Sponsored speaking sessions. Many companies will be happy to bring in a researcher to give a talk about their research that highlights a company technology (usually forming just a small part of the talk). The researcher will have something interesting for the delegates to hear and will not be “salesy” with respect to the technology. Companies appreciate the kudos this gives them and it gives a good chance for interested researchers to visit their exhibit and learn some more. For this reason, consider making these sessions just before breaks.
4. Assign seats at the conference dinner, mixing company people up with delegates. Actually, I think this is generally a good rule for academic-style conferences anyway. Get people out of their comfort zone and mix up PIs with postgrads and postdocs from different parts. After all, a conference should be a networking opportunity for everyone there. That will get the party started.
I believe that if you try out these ideas, in addition to the normal ideas (advertising in abstract, logo placement etc.), you’re sending out the message that you understand what sponsoring companies are after and are willing to work with them. Having an interesting conference program with some big-name speakers is not enough in itself to get companies to sponsor your conference. If you’re successful and get decent sponsorship, you might be able to hold your conference somewhere really nice. Like Prague. I never did get to go in the end.
What do you think? Any additional ideas would be appreciated too.
12/09/11: Recombinant protein expression in Bacillus subtilis
September 12, 2011 by Peter · Leave a Comment
Just received this news from BioSilta and think it will be of interest to quite a few. Further down is a link to detailed info, but here are the headlines:
17-fold increase in specific activity
When compared with LB, the EnPresso medium delivered a 17-fold increase in beta-galactosidase activity after 48 hours. The pH value remained stable between 7.0 and 7.5.
90-fold increase in volumetric yield
Compared to LB, the EnPresso medium delivered a volumetric yield of up to 90-fold.
Details of Materials and Methods, Results and Conclusions are available as a Poster:
Please click here to download: protein expression in Bacillus subtilis, http://www.biosilta.com/webyep-system/program/download.php?FILENAME=65-9-at-Poster_PDF.pdf&ORG_FILENAME=Bacillus.Protein.Society.2011.pdf
Enjoy! And if you would like a free trial of EnBase, please don’t hesitate to contact You Do Bio.
07/09/11: Alert: MIQE Seminars in Copenhagen and Aarhus, September 27th and 29th
September 7, 2011 by Peter · Leave a Comment
Just a short post to inform researchers in Denmark about the upcoming MIQE Events in Copenhagen and Aarhus.
I am very lucky in being able to get Raza Ahmed from Agilent’s genomics team over for a few days. Raza has tons of experience in qPCR, having worked for Stratagene before they became part of Agilent. Raza has agreed to give an introduction to MIQE (read more on the Events page) that should serve to educate and inform researchers about the guidelines. There will be plenty of time to ask Raza about qPCR subjects not related to MIQE as well.
Please come along, say “hej”, listen and learn and enjoy a coffee.
27/06/11: Change of Address for You Do Bio
June 27, 2011 by Peter · Leave a Comment
As of June 10th, I have moved from Frederiksberg to the even greener pastures (and bigger garden) of Rødovre. Except for being rather difficult to pronounce (a Polish researcher I know said it was possibly the worst place to live as a foreigner in Denmark, because no native Dane would understand where you lived) – I am loving living inRødovre. I also get to cycle over 14 Km per day (if working from the city), so I should get healthier too! Anyway, for the record, You Do Bio’s new address is:
Hendriksholms Boulevard 59
2610 Rødovre
Denmark
14/04/11: Bioreagents – a Choosers Guide
April 14, 2011 by Peter · 1 Comment
Agilent are running a special Easter promotion that gives 25% or more discount on “Bioreagents” if ordered before April 31st, 2011. This is a short post aimed at researchers who might be interested in trying these reagents out by taking advantage of the offer. I have highlighted some tried-and-tested products in ten key application areas.
1. Application: High Fidelity PCR
When you really cannot afford errors.
Go for: PfuUltra II Fusion HS DNA Polymerase.
Here’s why: PfuUltra II is the highest fidelity enzyme out there and is available in a hotstart format. Capable of targeting up to 19kb.
OR
Go for: Herculase II
Here’s why: Herculase II has outstanding performance for GC-rich templates – even with targets that contain as high as 85% GC content. Also has short extension times (15s) and can work with targets up to 12kb.
2. Application: Routine PCR
When you are looking for an economical price.
Go for: Paq5000 DNA Polymerase
Here’s why: Paq5000 has better sensitivity than Taq and can amplify much longer target sequences (up to 6kb). Also available as a hotstart mastermix, very competitively priced.
3. Application: Real-Time PCR (qPCR)
When you are looking to improve your results or need to run assays in the fastest possible time.
Go for: Brilliant III, Brilliant III, Brilliant III (just to be sure you got the message)
Here’s why: Brilliant III uses a new and unique Taq mutant that is almost certain to give you higher sensitivity and specificity than your current reagent.
4. Application: Reverse Transcription
When you are looking for high cDNA yield across a range of temperatures with low input RNA.
Go for: AffinityScript
Here’s why: AffinityScript has great performance across all temperatures from 37-55 °C. Excellent for low input RNA.
5. Application: RNA Isolation/Purification
When you are looking for pure, high-quality RNA from your samples, even down to single cells.
Go for: Absolutely RNA Kits.
Here’s why: Get high yields of intact, full-length DNA-free RNA. Flexible sizing to fit your requirements: Mini-, micro- and nano-prep kits. The last one of these has a 10µl elution volume and can isolate RNA from a single cell.
6. Application: Cloning
When you are looking for easy, reliable and affordable topoisomerase-based cloning.
Go for: StrataClonePCR Cloning Kits
Here’s why: Contains PfuUltra II DNA Polymerase for high accuracy and an easy, reliable protocol.
7. Application: Transformation of Competent Cells
When you are cloning large or difficult-to-clone DNA.
Go for: XL10 Gold Ultra-competent Cells
Here’s why: XL10 Gold cells were created specifically for transformation of large DNA molecules at high efficiency. Get 20-30 fold higher transformation than general cloning hosts.
8. Application: Transfection
When you want the same performance as the market leading product, but with significant cost savings.
Go for: GeneJammer Transfection Reagents
Here’s why: high transfection efficiencies with minimal cytotoxicity and you will probably save money
9. Application: Protein Expression in Mammalian Cells
When you are looking for affordable, fast and easy topoisomerase-based PCR cloning and expression.
Go for: Strataclone Mammalian Expression Vector Systems
Here’s why: uses a rapid protocol, with higher-fidelity enzymes than commonly found elsewhere.
10. Application: Site-Directed Mutagenesis
When you need tools to help you analyze protein functions, but don’t want to waste time on the molecular biology.
Go for: QuikChange Lightning Kits
Here’s why: QuikChange Lightning provides an accelerated protocol in a kit that is capable of handing short and long templates, all while maintaining the high accuracy, reliability and efficiency.
13/04/11: On organizing company seminars to scientists
April 13, 2011 by Peter · Leave a Comment
This is a busy time of year for those of us involved in the business side of the Life Sciences. Conference season is in full swing, customers are deep into their research projects (new Ph.D.s have been at it for a few months already) and things need to get done before Summer brings things to a halt.
Anyway, one of the tasks I recently undertook was to organize the Danish part of Agilent’s Nordic genomics roadshow. As usual, if you’re not focused on making these events a success you will end up with a last minute panic. Which is exactly what happened.
It’s easy enough to know what to do: arrange some rooms, make sure there is food, invite people. However, bringing it all together involves a lot of running around at the last minute. And I really don’t like raising a sweat in my nice, clean “customer-facing” clothes just before I meet those customers. However, unless I get organized (I mean really organized), it will be the same next time.
Arranging Venues
Getting a room at DTU was easy – thanks to Laurent, head of the core lab there who took care of that. Århus was a bit more difficult. Due to some rules at Århus University, there are not exactly open arms for vendors who are not official suppliers to turn up and give presentations. Such restrictions are a pain for both small companies and many researchers interested in their products (maybe I will write about that in another post one day). However, my contact there, Jørgen, did a great job in fighting our corner and was able to secure the rooms. OK, that was the rooms sorted!
Food
Arranging food at DTU was remarkably easy. I just went to the canteen, spoke to the man in charge and arranged the whole thing in a few minutes, with a follow-up by email. They deilvered it on time and it was good. With Århus, the location for the seminar was next to the Maths Canteen. I had sent them an email explaining what I wanted (which is what they told me to do, on the phone), but when I turned up it seems that they had not got the message! Ooops, However, to their great credit after I spoke to one of the managers there they managed to get sandwiches, fruit and drinks (hot and cold) for 25 people delivered in just 20 minutes!! Damn fine job – thanks guys.
Getting Customers to the Event
Now we come to the most important bit. That is the issue of getting people to come to these events. Since Agilent are supplying five speakers, travelling from all over Europe, this has to be worth it. I don’t want them to talk to an empty lecture theatre.
So the mission is to get a room full of interested researchers! The standard way that companies try to do this is to send an email “blast.” It’s cheap, you can do it from your computer and get the satisfaction of sending an email to thousands of people at once. That makes you feel like you really accomplished something! Great – except that it is almost useless as a way of getting people’s interest. In fact, I’ve no faith in email blasts, or maybe we’re not doing them well enough. In any case, with 6 days to the event in Copenhagen, we have 17 registrants. However, 4 of them are not going to show (you know, because you spoke to them and one is on maternity leave) and 2 are from another company, so they don’t count. Given that 2-3 will forget on the day, we are below the “magic 10″ at which you don’t feel the whole thing has been a waste of time. Also, to be honest, Agilent probably wouldn’t want to run a similar event in the future if there was a low turnout.
At this point, panic sets in and you do what should have been done anyway: invite people personally. So, I printed up some A5 flyers and went to the University of Århus – Institute for Human Genetics and Molecular Biology – and just knocked on doors. On Monday, I did the same at KU’s Biologisk Insitut. One of the great things about Danish Universities is that you can still just walk in, knock on someone’s door and have a chat. Nine times out of ten, I get a friendly reception. Guess what? Most people are interested. No, they never knew there was such an interesting event close by (even those that you know got the email blast and the reminder, which proves my point). Both those actions, plus sending a lot of personal emails, got the number of registrants into double figures.
The biggest lesson I learned from this is to start inviting people, personally, at least a month before such an event. Otherwise, calendars are full and you never really get the time to invite all the people you would like. And yes, I did know that before I started.
12/04/11: Agilent Easter Promotions on Bioanalyzer and Bioreagents!
April 12, 2011 by Peter · 1 Comment
Enjoy Easter with Agilent’s special promotions!
Spring is coming (yes, even though this is Denmark – I just looked out of the window and it is definitely there, hiding around the corner). To celebrate, Agilent are offering two special promotions:
20% off the Bioanalyzer and one free kit
25% off or more on your Bioreagents order
To benefit from these great offers, contact Agilent before April 30th, 2011 and mention promotion code S_EASTER11 when you place your order.
To simplify your choices when it comes to Bioreagents, I have written a short post on tried and tested Agilent products in ten application areas here.
05/04/11: New SureSelect Custom Kits Capture up to 34 Mb
April 5, 2011 by Peter · Leave a Comment
It’s been in the pipeline for a bit, but Agilent can now announce the launch of newSureSelect XT Custom Kits – now supporting large custom captures up to 34 MB.
You can download a PDF file explaining more about these new SureSelect XT Custom Kits here, or by clicking on the image below: SureSelectXT Custom Flyer April 4 2011.
With this new SureSelect XT Custom product line extension, Agilent Genomics has increased the maximum SureSelect XT Custom capture by 5-fold. Now researchers can obtain NGS target enrichment kits for captures ranging from <200 kb up to 34 Mb. This greatly expands the research applications possible by genomic enrichment, especially by facilitating large custom captures for NGS studies in non-human species.
Danish researchers, please contact Peter at You Do Bio to learn more.
26/01/11: Microarrays and Sequencing Support Each Other
January 26, 2011 by Peter · Leave a Comment
Link to an interesting article from GEN: http://www.genengnews.com/gen-articles/microarrays-sequencing-assume-supporting-roles/3472/. Both technologies have their roles to play, depending on your study.
20/01/11: Protocols for SureSelect RNA Capture Now Available
January 20, 2011 by Peter · Leave a Comment
The protocols for RNA capture have been posted even though this product is not yet available to order. Here’s some links:
G7580-90000, SureSelect RNA
http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=68662
G7580-90010, SureSelect RNA Multiplexed
http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=70221
G7580-90001, SureSelect SOLiD
http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=68663
G7580-90010, SureSelect SOLiD Multiplexed
http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=68665
29/10/10: Exhibiting at Symposium of the Danish Microbiological Society, 9th November 2010
October 29, 2010 by Peter · Leave a Comment
You Do Bio will be exhibiting at the 2010 Symposium of The Danish Microbiological Society. The symposium will be held between 0900-2100 at the University of Copenhagen Faculty of Life Sciences, Thorvaldsensvej 40, 1870 Frederiksberg C. 
Visit the DMS Homepage to learn more about the meeting, registration etc.
If you are planning on attending the symposium, or just happen to work at KU-Life, I look forward to meeting you.
Of particular interest to microbiologists will be the presentation of EnBase products from BioSilta. I will have technical information about these exciting products and limited supply of free samples.
03/09/10: I made it as an advertising model, thanks to DSB
September 3, 2010 by Peter · Leave a Comment
A customer pointed out that they saw me on the internet the other day. Very easy these days of course, with social networking sites, but no – I’ve made it to an ad on the DSB website and if you’re interested, check it out here.
25/08/10: Here at Epigenetics & Stem Cells Conference
August 25, 2010 by Peter · Leave a Comment
I am exhibiting at the Epigenetics/Stem Cell conference at the Biologisk Institut in Copenhagen until Friday lunch. Come along and say hello (and maybe learn something too).
Conference link is here.
29/07/10: Now, 7 Publications involving Agilent’s SureSelect Sequence Capture Technology
July 29, 2010 by Peter · Leave a Comment
2010 list of SureSelect publications:
- Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing. Lalonde E et al. Hum Mutat. 2010 31, p918-23.
- Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene. Sun et al. Am J Hum Genet. (2010) 9, p146-153.
- Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Walsh et al. PNAS (2010) online release
- Whole Exome Sequencing and Homozygosity Mapping Identify Mutation in the Cell Polarity Protein GPSM2 as the Cause of Nonsyndromic Hearing Loss DFNB82. Walsh et al. Am J Hum Genet. (2010) online release
- De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Hoischen A et al. Nat Genet. (2010) 42, p483-5.
- Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. Johnston JJ et al. Am J Hum Genet. (2010) 14, p743-8
- F6 mutations in T-cell acute lymphoblastic leukemia. Van Vlierberghe P, et al. Nat Genet. (2010) 42, p338-42
07/06/10: Methods Paper on Rapid Quantification of DNA Libraries for NGS Sequencing
June 7, 2010 by Peter · Leave a Comment
Agilent has developed a very nice qPCR-based method for quantifying NGS libraries. This application gives researchers a useful and fast tool for their NGS workflows. At the Science Direct website, you can find a paper describing the technique and other benefits of using it. For example, the authors “find that qPCR quantification may allow improvements to current NGS workflows, including reducing the amount of library DNA required, increasing the accuracy in quantifying amplifiable DNA, and avoiding amplification bias by reducing or eliminating the need to amplify DNA before sequencing.”
The relevant product page on the Agilent Genomics website can be found here.
19/05/10: BGI expands into Denmark
May 20, 2010 by Peter · Leave a Comment
BGI will create a $10 million European headquarters in Copenhagen, where it plans to eventually hire up to 150 scientists and support employees.
BGI will recruit between 20 and 50 people during the first year of the Copenhagen HQ — to be called BGI Europe — then establish a sequencing platform allowing for the hiring of between 50 and 100 people. The project will be China’s largest investment in Denmark.
Read the news in Danish here: http://www.dr.dk/Nyheder/Penge/2010/05/17/152105.htm
