Inquiry Exercise - Introduction to Bioinformatics

Challenge
  
Diagnose and treat Cancer  by using Bioinformatics 

 It is the year 2014 and in this real world Bioinformatics exercise, you will play the role of a Molecular Pathologist. Your job is to analyze cancer at the genomic (DNA) level and to suggest molecular therapies.  The human genome ( 3 billion nucleotides of DNA sequence) was first sequenced in 2000 and cost about 3 billion dollars. At present, the cost of sequencing the human genome has decreased to $20,000. It is now economical to sequence the genome of human cancer cells to find out what has gone wrong and predict therapies that may work. In this introductory exercise, a preliminary analysis has been performed to identify sequences in a lung tumor that are different from the normal human sequence.  Your job is to determine whether these changes could cause cancer and where possible, suggest molecular therapies.


Click here to download   introductory exercise

Inquiry Exercise 12

Challenge :

Generate  an example of  cell specific gene expression.

Inquiry Exercise 8

Challenge:

Demonstrate  the catalytic conversion of Starch into Glucose    

Inquiry Exercise 5

Challenge:

Provide convincing  evidence that molecules move.

Prep of LB plates and LB media

LB media is the universal  growth media  in Molecular Biology. Although  LB  is often thought to  stand for  Luria Broth , in fact it was an abbreviation for lysogeny broth and LB should perhaps be more  correctly referred to as Luria Bertrani broth.  There are many variations,  but here  is our favorite  recipe:  

LB Agar plates
Dissolve  7.5 g of  Bacto Agar ( Difco ) and 12.5 g of   LB medium  ( MP Biochemicals)  in  water, Q to 500mL in a "Wheaton"  1 liter glass bottle.  Check that pH is 7, if not titrate with NaOH. Autoclave at 121 for 15 minutes and store at RT.  To pour plates, melt on hotplate and dispense.  If adding antibiotic , cool to 45 degrees centigrade, add the antibiotic and pour.

LB Media
Dissolve  12.5 g of   LB medium  ( MP Biochemicals)  in water, Q to 500mL in a "Wheaton"  1 liter glass bottle.  Check that pH is 7 , if not  titrate with NaOH.  Autoclave at 121 for 15 minutes and store at RT. 

The Biotech Revolution

The future of Biotechnology is here now !

Bridging the Gap Between Undergraduate Education and Research

An interesting  student  article on  Science Education.

"Undergraduate science education is changing.  Fading are the days of large introductory lectures, where faceless students are merely consumers of certain knowledge to be later regurgitated on an exam. That model of teaching might get the information across, but it fails to engage students.  Where the infamous ‘weed-out’ courses do succeed, however, is in depleting the science talent pool: only 40% of students intending to major in a STEM discipline actually graduate with that major. "

Kaiser - Looking at genomes before conception

The Kaiser Permanente Center in Portland has  been awarded an NIH grant to  sequence the genomes of couples before they have children.
“Most of the time, couples don’t find out that they carry these mutations until after the mother is already pregnant, or until after the child is born,” said Katrina Goddard, a genetic epidemiologist, principal investigator on the project and researcher with Kaiser’s Center for Health Research "

Paper Clips - Listen for 5 minutes and learn a biological concept !

The journal Cell produces a series of conversations with scientists  called paper clips. These audio segments are ideal to listen to when you are sitting on the bus, waiting for lectures to start  or  in the lab and waiting while  the gel is running. Here is the archive

Interns are the new best friend of the lean biotech startup !

Interesting article on the key role of interns in Biotech startups.

Loss of Function of the Melanocortin 2 Receptor Accessory Protein 2 Is Associated with Mammalian Obesity

Studies in mice indicated that loss of function of the Melanocortin 2 Receptor Accessory Protein 2 increased obesity. The investigators then looked at human subjects and found that mutations in this gene were associated with human  obesity. 

3D print your favorite protein !

It is often difficult to appreciate the nuances of protein structure by viewing a spinning image on a monitor. Being able to look at a solid model,  often reveals major insights.  In this blog article , a simple step by step  protocol is presented that enables students  to create a 3D model of their favorite protein. All you need is a 3D printer !

Inquiry Exercise 1

Student challenge:

What  is the  quantitative relationship between the volume and weight of water ?

Learning to do Science - Inquiry Exercises ?

Although there has been significant discussion in the education  community about  the need for   "doing science to learn science", most curricula  employ Inquiry laboratory exercises that are still simply "cook book "exercises in which the student cannot assume ownership.  Typically,  the hypothesis is already presented and the student  simply gets to choose a variable  in the experiment .  In the Capital  Biotechnology program,  we have been devising  novel Inquiry exercises that require  almost complete  independence  to achieve the objective. The exercises take the form of simple challenges. They are more difficult to run than  standard laboratory  exercises , since the students are likely to move in  unanticipated directions . Thus,  the instructor notes  are quite complex. In the following posts , we will describe our Inquiry Exercises , invite instructors to use them in their own courses,  and provide feedback .

Gene Signature Predicts Reponse to Aspirin

Many people take low doses of aspirin with the hope that  it may decrease the risk of heart attack  or stroke . It has been well known that only some people respond to this preventative therapy.  In this article in the NIH director's blog, Dr Francis Collins reviews new gene expression  data that may help to  identify the  people who will benefit from aspirin therapy.

Synthetic Biology Start Ups - The new Apples and Googles ?

Some interesting reflections on the new synthetic biology Start Ups. But....don't drop out ...take our Basic  Techniques in Biotechnology  course and learn to clone DNA !

Sentence Adverbs - To use or not to use ? Is that the(a) question?

Much of scientific writing  contains  stock phrases that  are universally recognized. A  bioinformatician ( with maybe too much time on his hands)  has analysed the use of the  "sentence adverb" in scientific papers.   Interestingly,  adding more to the  lexicon ?

An Organic Perfume ?

Steven Lergos is the first student to be enrolled in the new Basic Techniques in Biotechnology course at Capital. Steve is a typical non-traditional student in that he is coming to Capital to learn new job skills that will enable him to pursue a new career. Steve is an entrepreneur at heart and has become interested in the biomanufacturing of organic perfumes. Chemical synthesis of perfume is toxic to the environment and also does not efficiently produce the isomer with the desired aromatherapeutic effect. In his first bioengineering project,  he will be using the iGEM plasmid repository to generate and express a tagged form of jasmonic acid carboxyl methyltransferase. This is the enzyme that converts jasmonic acid to the highly desirable   methyl jasmonate or Jasmine. The tagged version of the enzyme  will enable it’s affinity purification and the production of a catalytic nano gel that will carry out the organic synthesis. 

Roche looking to buy Alexion for $23 billion ?

Rumors are flying that Roch intends to buy Alexion  and this would be one of the biggest Biotech deals this year.