Dry Ice vs. Liquid Nitrogen

Liquid Nitrogen Ice Cream - Short Version

Liquid Nitrogen Experiments: The Carnation

Liquid Nitrogen vs. Liquid Oxygen: Fire

Liquid Nitrogen Demonstration

Cooking with Liquid Nitrogen - Ferran Adria and Harold McGee

A men for Science Education after receiveng his Nobel Prize

Carl Wieman, is a Nobel Laureate in Physics. He gave in the last years a series of lectures about the scientific assesment of teaching science.

On of these lectures about how to teach science given at Harvard can be seen here.

The conclusions are refreshing: there is a way of teaching science outside the laboratories too.

One of the tools he is suggesting is modelling of real experiments. He developedd and made freely available a set of basic experiments.

You can have a look to these and use them at the website of the Colorado University here.

In his lectures he is refering to a book abour expertieze end experts, The Cambridge Handbook of Expertise and Expert Performance. Seems to be a relevant book int this topic:

I moved!!!

Dear colleagues,

I moved from wordpress to Blogger using this excellent tool:

http://www.ampercent.com/wordpress-to-blogger-migration/4882/

Best,

Balint.

Sizes in Biology

Dear colleagues,

An excellent tool is available to get a feeling about molecular sizes in Biology.

The tool is available here and was developped by "Learn Genetics" program from the University of Utah.

You can have a short movie on it below, but please check the original one from here!!!








You can also have a deep immersion in the issue here:

Designing a gene or "Gene design"

On this tutorial you can see an easy way to design oligos for gene synthesis, or in other words Gene design.

The description is based on the Instructional Videos from the iGEM website!

Gene design in less than 10 minutes!

Good luck!!!




Some usefull tools:

1. Gene design web page
2. Tools at DNA20
3. Tools at DNA Works
4. A Revese-Complement Tool
5. Gene designer a comprehensive tool to artificial gene design from DNA20 described here.


If you would like to read about the application of design principles in Drug Discovery you should read this book:
 

IDEA Generation and Brain storming

One of the first step in generating a project is to generate ideas. One of the best known technique for idea generation is  Brainstorming.

Below you can see excerpts from the very well writen and detailed description of the Wikipedia:

Basic rules:

There are four basic rules in brainstorming. These are intended to reduce social inhibitions among group members, stimulate idea generation, and increase overall creativity of the group.

1. Focus on quantity.


2. Withhold criticism. In brainstorming, criticism of ideas generated should be put 'on hold'. By suspending judgment, participants will feel free to generate unusual ideas.


3. Welcome unusual ideas. They can be generated by looking from new perspectives and suspending assumptions. These new ways of thinking may provide better solutions.


4. Combine and improve ideas: Good ideas may be combined to form a single better good idea, as suggested by the slogan "1+1=3". It is believed to stimulate the building of ideas by a process of association.

 

Method

 

Set the problem

Before a brainstorming session, it is critical to define the problem.

Create a background memo

The background memo is the invitation and informational letter for the participants, containing the session name, problem, time, date, and place. The problem is described in the form of a question, and some example ideas are given. The memo is sent to the participants well in advance, so that they can think about the problem beforehand.

Select participants

1. The facilitator

2. Participants:

• a. core members


• b. guests from outside the project, with affinity to the problem.

3. One idea collector who records the suggested ideas.

 

Create a list of lead questions

The facilitator should stimulate creativity by suggesting a lead question to answer, such as Can we combine these ideas? or How about looking from another perspective?. It is best to prepare a list of such leads before the session begins.

Another alternative method that could be used even on-line is the one described as:

"Group passing technique

Each person in a circular group writes down one idea, and then passes the piece of paper to the next person in a clockwise direction, who adds some thoughts. This continues until everybody gets his or her original piece of paper back. By this time, it is likely that the group will have extensively elaborated on each idea.

The group may also create an "Idea Book" and post a distribution list or routing slip to the front of the book. On the first page is a description of the problem. The first person to receive the book lists his or her ideas and then routes the book to the next person on the distribution list. The second person can log new ideas or add to the ideas of the previous person. This continues until the distribution list is exhausted. A follow-up "read out" meeting is then held to discuss the ideas logged in the book. This technique takes longer, but it allows individuals time to think deeply about the problem."

I think an iGEM group could create these tools for the group on the google group page which the members can access at the group site.

Another very good web site in the topic is JBP.

Have fun!

What is a COMMITMENT?

Dear Collegues,

 

Please find below some words of Yehuda Berg about what a Commitment means.

 

"...a commitment is ongoing. It needs to be made and remade every day.

If you decide to run a marathon, you aren’t just choosing to show up on the day of the event.

You’re choosing a path, and that means conditioning every day. If you skip a week of training, you might not make it to the marathon.

Being committed to a spiritual path means sometimes we’ll be alone. We might feel like a black sheep. Other times, people might want us to fail. Or at least when we succeed, their insecurities will be awakened and they won’t be happy about our success.

And one thing’s for sure: we will be tested. Not on our decision, but on our commitment."

Starting a project, any project, needs a commitment.

A succesfull  iGEM teem needs a written commitment as described in the paper of  Wayne Materi.  We commit ourselfs to work hard, teach/learn lots and have fun.

Worth thinking about Yehuda's thoughts in general.

 

Best,

 Balint.

Prezi - a new tool for making better prezentations

One of the most interesting development in the field of prezentation tools is Prezi.



Beside using it for presentations, you can use it for Mind Mapping too, like here:



And here you can see some tricks for masters:



You can use it for free, and if you are using it for educational purposes, there is an edu version for it, with lot of cool features.

So, why not using a better tool for the same job?

iGEM Hungary

Dear Colleagues,

You might have heard about iGEM, the International Genetically Engineered Machine competition (iGEM). I personally became interested in this competition after Malcolm Campbell gave a lecture for us in December 2009. You can see his lectures including the one he gave at the University of Debrecen ( through video connection ) here.  The group coordinated by Malcolm has an excellent Synthetic Bio summary here.

Synthetic Biology is about changing the design of biological entities (like vectors or small systems) into a more predictable, engineer type design.

 

So we registered with a team Debrecen Hungary. I hope I can keep you updated with the developments.

The best short video about what synthetic biology is can be seen below.

QPCR oligo design

Designing QPCR oligos might seem complicated but there are some rules and softwares that can make it easy. In our lab, majority of data points we generate are probably measured by QPCR, so I think  it is worth to review an algorithm for desiging QPCR assays.

So, today I will describe the way I design QPCR oligos. You can have a basic intro in PCR here.
More than a year ago I switched to the UPL system, the library of probes designed by Exiqon and now marketed by Roche. The concept is quite clear, the LNA modified oligonucleotides bind much stronger to the DNA template than the average oligonucleotides. By this we can decrease the lengths of them by keeping the Tm unchanged. The UPL library consists of 165 individual oligonucleotides that are in general nine basepair long and together cover the entire genome in respect of the coverage needed to design a QPCR oligo set for any gene. You can read more about the LNA nucleotides here and here. A good website where you can calculate the Tm of the LNA oligos here: http://lna-tm.com/. The UPL system is described here.

The system allows the design of an oligo set for any DNA sequence in the UPL Design Centre. You can access the Design Centre directly here.

[caption id="attachment_581" align="aligncenter" width="468" caption="UPL Assay Design Center"][/caption]

Before we design an assay let us first look for the transcripts of a specific gene. It is very important to use annotated data, since in the annotated genomic data we have informations about possible SNP variations. This might be important, since the oligos and especially the probe should bind to an SNP free free region, because an SNP might disturb the binding of the probe to the template.

To make this data available we should use not the sequence but the transcript ID from the Ensembl.

[caption id="attachment_586" align="aligncenter" width="468" caption="Ensembl"][/caption]

At Ensembl select your species of interest, e.g. mouse and write the name of your gene of interest in the search box:



If you write into the box a gene of interest (e.g. COUP-TF2) we will see the results as it is shown here:



Here I have to click on the link of the gene and I will find the following screen: The most important info we are looking for is in the table on the top of the page:



The two transcripts of the gene are:
ENSMUST00000089565
ENSMUST00000032768.

We will use these ID-s in the UPL Assay Design Centre. First select as organism the "Mouse", and write into the box the two Ensembl transcript ID-s selected by commas. If you follow the steps the results will be like this:

Below this data you can see two links as it follows:To design an assay that would measure all transcripts select: "common assays".

The results will be given in a downloadable pdf report. Save this file and name is by the name of the gene you used as input.

The results in the pdf file look like this:



You can see that the amplicon is 95 bp long, there is no SNP in the binding regions of the primers and probes and the probe is closer to one of the primers. There is an SNP in the gene that was avoided by the program. You can have an SNP even in the amplicon, unless is not in the binding site of the primers or the probe.

Before I order the oligos, I usually test them with e-PCR on the UCSC Genome Browser.

[caption id="attachment_608" align="aligncenter" width="468" caption="UCSC Genome Browser"][/caption]

Select the PCR view and paste the oligos into the given locations. Select the genome, the assembly and the target as "UCSC Genes"(If you used a genomic sequence for design use the target: "genome assembly").

If you have a hit, click on the link provided and the results will be represented in the genome as seen here:



The oligos are intron spanning and in the right location. Order the oligos in an HPLC pufied form in the lowest available scale for the first try. Be aware that according to the experience of several groups, and my own experience too,  only 2/3 of the UPL assays work without further optimization. This means, if you want to be sure from the first you better try two, three different assays for the same gene. The UPL Design Centre will generate several primer-probe sets and you can retrive these results too. Since the UPL library is given and one or two of the three ordered assays will work, it this worth trying three from the beginning!

In general the rules for a good QPCR assay:

1. The amplicon should be as short as possible (60-70 bp is ideal, but should be shorter than 100bp).

2. The Tm of the oligos should be around 60C, while the Tm of the probe 10C higher.

3. The distance between the the oligo and the probe should be as small as possible for a better exonuclease activity of the Taq polymerase.

4. The GC content of the two oligos should be as close as possible.

5. The number of GC bases in the last five nucleotides on the 3' ends of the two primers should be identical (if possible).

6. Select for oligo sets with week internal bonds (less than four H bonds in the same conformation).

7. Avoid primer dimers that could produce artefacts due to the 3' elongation of one of the primers.  The same for internal conformations.  See below:

8. Verify the oligos with e-PCR on the UCSC Genome Browser. The test should give one single hit!

9. If possible use annotated sequences to avoid the SNP effect.

10. If you are looking for genes (cDNA measurement) use exons that are common for all transcripts variants (or use the "batch assay-common assays" in the UPL Assay Design Centre)

Good luck!